OSCR

Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches
  1. [1] § Methods › Single-particle cryo-EM image processing ↔ mask3D_cyl.py, lines 9–39 · score 0.63 · outer diameter, inner diameter, cyl, helical, mrc, command
  2. [2] § Methods › Single-particle cryo-EM image processing ↔ MTSeamSym.py, lines 97–186 · score 0.58 · neighboring, seam, max, outer, inner, rotation

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

Python · 107 lines · 3.2 KB · no license · 1 match

  1. #!/usr/bin/env python
  3. import optparse
  4. import os,sys
  5. from EMAN2 import *
  6. import math
  9. #===============
  10. def setupParserOptions():
  11. parser = optparse.OptionParser()
  13. parser.set_usage("""%prog -f helical.mrc --DO --DI --DZ --boxsize --apix
  14. to apply a soft mask to both ends of a 3D helical volume (z direction),
  15. together with a soft inner and outer mask (x-y plane)""")
  16. parser.add_option("-f", dest="mrc", type="string", metavar="FILE",
  17. help="3D helical.mrc file to be masked. If not specified, will only output mask3D.mrc")
  18. parser.add_option("--DO", dest="DO", type="int", metavar="INT",
  19. help="outer diameter in x-y plane, in angstrom")
  20. parser.add_option("--DI", dest="DI", type="int", metavar="INT", default=0,
  21. help="inner diameter in x-y plane, in angstrom, default=0")
  22. parser.add_option("--DZ", dest="DZ", type="float", metavar="FLOAT",
  23. help="diameter in z direction, if >1, in angstrom; if <1, in percentage")
  24. parser.add_option("--boxsize", dest="boxsize", type="int", metavar="INT",
  25. help="boxsize")
  26. parser.add_option("--apix", dest="apix", type="float", metavar="FLOAT",
  27. help="apix")
  29. options,args = parser.parse_args()
  30. if len(args) > 0:
  31. parser.error("Unknown commandline options: " +str(args))
  32. if len(sys.argv) < 2:
  33. parser.print_help()
  34. parser.error("no options defined")
  35. params = {}
  36. for i in parser.option_list:
  37. if isinstance(i.dest, str):
  38. params[i.dest] = getattr(options, i.dest)
  39. return params
  41. # Generate 2D slices to be inserted into mask3D volume
  42. def createMask2D(params):
  43. from itertools import product
  44. apix = params['apix']
  45. RO = float(params['DO'])/apix/2
  46. RI = float(params['DI'])/apix/2
  47. if params['boxsize']:
  48. nx = int(params['boxsize'])
  49. else:
  50. vol = EMData(params['mrc'])
  51. nx = vol.get_xsize()
  52. falloff_r = 6 # use steeper falloff
  53. mask2D = EMData(nx,nx)
  54. mask2D.to_one()
  55. for x,y in product(range(nx),range(nx)):
  56. dx = abs(x-nx/2)
  57. dy = abs(y-nx/2)
  58. r2 = dx**2+dy**2
  59. if r2 > RO*RO:
  60. wt1 = 0.5*(1 + math.cos(math.pi*min(1,(math.sqrt(r2)-RO)/falloff_r)))
  61. mask2D.set(x,y,wt1)
  62. elif r2 < RI*RI:
  63. wt2 = 0.5*(1 + math.cos(math.pi*min(1,(RI-math.sqrt(r2))/falloff_r)))
  64. mask2D.set(x,y,wt2)
  65. #mask2D.write_image('mask.mrc')
  66. return mask2D
  68. def createMask3D(params,mask2D):
  69. apix = params['apix']
  70. RO = float(params['DO'])/apix/2
  71. RI = float(params['DI'])/apix/2
  72. nx = mask2D.get_xsize()
  73. if params['DZ'] > 1.0:
  74. RZ = float(params['DZ'])/apix/2
  75. else:
  76. RZ = (nx/2*params['DZ'])
  77. mask3D = EMData(nx,nx,nx)
  78. falloff_z = 6.0
  79. # now apply soft mask
  80. for z in range(nx):
  81. img = EMData(nx,nx)
  82. img = mask2D.copy()
  83. # here "img = mask2D" won't work !!
  84. dz = abs(z-nx/2)
  85. if dz > RZ:
  86. wt3 = 0.5*(1 + math.cos(math.pi*min(1,(dz-RZ)/falloff_z)))
  87. img.mult(wt3)
  88. #img.write_image("test_%d.mrc"%z)
  89. mask3D.insert_clip(img,(0,0,z))
  91. name = 'mask3D_%d-%dx%d_apix%.2f.mrc'%(params['DO'],params['DI'],math.ceil(RZ*apix*2),apix)
  92. mask3D.write_image(name)
  93. return mask3D,name
  98. #===============
  99. if __name__ == "__main__":
  100. params = setupParserOptions()
  101. mask2D = createMask2D(params)
  102. mask3D,name = createMask3D(params,mask2D)
  103. if params['mrc']:
  104. vol = EMData(params['mrc'])
  105. vol.mult(mask3D)
  106. vol.write_image('%s_mask.mrc'%(params["mrc"][:-4]))
  107. #os.system("bhead -origin 0,0,0 -recalculate -sampling %.3f %s %s"%(params['apix'],name,name))

mask3D_cyl.py at commit 159aa8b, no license · at the source

Overview

Authors: Elena A. Zehr1, Shufeng Sun1, Stephanie L. Sarbanes1, Antonina Roll-Mecak1,2
ORCID iDs: Antonina Roll-Mecak
  1. Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke,Bethesda, MD USA
  2. Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute,Bethesda, MD USA
Institutions: National Institute of Neurological Disorders and Stroke (United States); National Heart, Lung, and Blood Institute (United States)
Journal: Nature structural & molecular biology, volume 33, issue 4, pages 631-640
Dates: received 2 July 2025; accepted 4 March 2026; published online 8 April 2026; in print 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41594-026-01787-7 · PMID 41951886 · PMCID PMC13095656 · OpenAlex W7151889715
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: histology / microscopy (modality), human (organism), cellular / molecular (subfield)
Methods: Connectivity
Keywords: Cryoelectron microscopy, Microtubules
MeSH: Axons*, Guanosine Diphosphate*, Guanosine Triphosphate*, Microtubules*, Cryoelectron Microscopy, Humans, Induced Pluripotent Stem Cells, Neurogenesis, Neurons, Tubulin (* major topic)
Topic: Microtubule and mitosis dynamics (Cell Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Citations: cited by 8 papers (Europe PMC); 89 references in the paper

Abstract

Microtubules scaffold cells, supporting signaling and cargo transport. They assemble from GTP–tubulin, which hydrolyzes to GDP–tubulin during polymerization. GTP–microtubule lattices are stable; GDP lattices depolymerize rapidly. In vitro, hydrolysis triggers lattice compaction. Lattice spacing regulates motors and microtubule-associated proteins; however, the conformation of tubulin in microtubules in cells is unknown. Here, we present the atomic-resolution cryo-electron microscopy structure of human microtubules in situ, in the axons of human cortical neurons derived from induced pluripotent stem cells (iPS cells). Our 2.7-Å-resolution reconstruction delineates bound water molecules and reveals that axonal microtubules adopt an expanded GTP-like lattice, despite being GDP bound. Using cryo-electron tomography and power spectrum analysis, we find that, unlike in axons, microtubules in undifferentiated iPS cells are compacted. Therefore, lattice expansion is part of neuronal differentiation. Our work provides molecular insights into neurogenesis and has implications for understanding microtubule stability and effector recruitment in neurons.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

rui--zhang/Microtubule

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 159aa8b8a8a62a6684ccc8a88cefb457bd2fbadf, 13 June 2025
Languages: Python (25)
Size: 32 files, 25 scripts
Software Heritage: not archived
Found in: the text, “Single-particle cryo-EM image processing”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (15 files), Matplotlib (4 files)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
26 files
At the source: github.com/rui--zhang/Microtubule

RollmecakLab/Layer-Line-Analysis

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: e24db88aa95bd28849f30bcc67bc30f2a8979a5a, 19 April 2026
Languages: Python (3)
Size: 9 files, 3 scripts
Software Heritage: not archived
Found in: the text, “Tomography image processing and layer-line analy”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (2 files), Matplotlib (1 file), Pillow (1 file), scikit-learn (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
4 files
At the source: github.com/RollmecakLab/Layer-Line-Analysis

bioinformatics.ccr.cancer.gov/btep/classes

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: the link answers
Software Heritage: not checked
Found in: the text, “Tomography image processing and layer-line analy”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 29 September 2026: the link answers (HTTP 200)
  • 29 September 2026: the link answers (HTTP 200)
At the source: bioinformatics.ccr.cancer.gov/btep/classes/chirp-chatbot-for-intramural-research-program

Code availability

Scripts used for power spectrum analysis are feely available on GitHub (https://github.com/RollmecakLab/Layer-Line-Analysis).

Reproduced under the paper's license (CC BY), from the paper cited above.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 28 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data availability

Cryo-EM maps and atomic models were deposited to the EM Data Bank and PDB under accession numbers EMD-70956 (http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-70956) and 9OX7 (https://doi.org/10.2210/pdb9OX7/pdb), respectively, with accompanying raw half-maps. Tomograms were deposited to the EM Public Image Archive under the following accession codes: tomograms of axons, EMPIAR-13239 (https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/13239/); tomograms of iPS cells, EMPIAR-13240 (https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/13240/); tomograms of in vitro assembled GDP-bound porcine brain microtubules, EMPIAR-13241 (https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/13241/) and EMPIAR-13242 (https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/13242/); tomograms of in vitro assembled GMPCPP-bound porcine microtubules, EMPIAR-13243 (https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/13243/) and EMPIAR-13244 (https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/13244/). Data and materials can be obtained from the corresponding authors upon request. Source data are provided with this paper.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 2 keywords, 10 MeSH terms, 89 references.

Cite

This paper

Zehr, E. A., Sun, S., Sarbanes, S. L., & Roll-Mecak, A. (2026). Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state. Nature structural & molecular biology, 33(4), 631-640. https://doi.org/10.1038/s41594-026-01787-7

BibTeX

@article{zehr2026microtubules,
author = {Zehr, Elena A. and Sun, Shufeng and Sarbanes, Stephanie L. and Roll-Mecak, Antonina},
title = {{Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state}},
journal = {Nature structural \& molecular biology},
year = {2026},
month = apr,
volume = {33},
number = {4},
pages = {631--640},
publisher = {Nature Portfolio},
issn = {1545-9993},
doi = {10.1038/s41594-026-01787-7},
url = {https://doi.org/10.1038/s41594-026-01787-7},
pmid = {41951886},
pmcid = {PMC13095656}
}

RIS

TY - JOUR
AU - Zehr, Elena A.
AU - Sun, Shufeng
AU - Sarbanes, Stephanie L.
AU - Roll-Mecak, Antonina
TI - Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state
T2 - Nature structural & molecular biology
J2 - Nat Struct Mol Biol
PY - 2026
DA - 2026/04/08
VL - 33
IS - 4
SP - 631
EP - 640
SN - 1545-9993
PB - Nature Portfolio
DO - 10.1038/s41594-026-01787-7
UR - https://doi.org/10.1038/s41594-026-01787-7
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s41594-026-01787-7",
"type": "article-journal",
"title": "Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state",
"container-title": "Nature structural & molecular biology",
"author": [
{
"family": "Zehr",
"given": "Elena A."
},
{
"family": "Sun",
"given": "Shufeng"
},
{
"family": "Sarbanes",
"given": "Stephanie L."
},
{
"family": "Roll-Mecak",
"given": "Antonina"
}
],
"container-title-short": "Nat Struct Mol Biol",
"volume": "33",
"issue": "4",
"page": "631-640",
"DOI": "10.1038/s41594-026-01787-7",
"PMID": "41951886",
"PMCID": "PMC13095656",
"ISSN": "1545-9993",
"publisher": "Nature Portfolio",
"URL": "https://doi.org/10.1038/s41594-026-01787-7",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
8
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1038/s41467-026-75564-x
Cooperative mechanism of neurotransmitter recognition and transport by the human vesicular polyamine transporter.
Journal: Nature communications
In common: ebi.ac.uk/pdbe/entry, histology / microscopy, cellular / molecular, 5 references
[2] doi:10.1038/s41594-026-01866-9 [code]
Structural and mechanistic insights into gating and allosteric modulation of GluN1-GluN3A NMDA receptors.
Journal: Nature structural & molecular biology
In common: Matplotlib, NumPy, ebi.ac.uk/pdbe/entry, histology / microscopy, cellular / molecular, 3 references
[3] doi:10.1038/s41467-026-76831-7
Structural origins of species-specific differences in TRPV2 activation.
Journal: Nature communications
In common: ebi.ac.uk/pdbe/entry, histology / microscopy, cellular / molecular, 4 references
[4] doi:10.1038/s41594-026-01845-0
Conformational plasticity of human acid-sensing ion channel 1a.
Journal: Nature structural & molecular biology
In common: ebi.ac.uk/pdbe/entry, histology / microscopy, cellular / molecular, 3 references
[5] doi:10.7554/elife.110011 [code]
Tau hyperphosphorylation impairs cooperative binding to microtubules and perturbs organelle trafficking in neurons.
Journal: eLife
In common: cellular / molecular, 5 references
[6] doi:10.1371/journal.pbio.3003777
Structure of the human P2X3 receptor reveals the basis for subtype-selective inhibition by sivopixant.
Journal: PLoS biology
In common: ebi.ac.uk/pdbe/entry, histology / microscopy, cellular / molecular, 3 references
[7] doi:10.1038/s41467-026-75444-4 [code]
Structural insights enable drug discovery for the neuronal NBCn2 carbonate transporter.
Journal: Nature communications
In common: Matplotlib, NumPy, ebi.ac.uk/pdbe/entry, histology / microscopy, cellular / molecular, 2 references
[8] doi:10.1038/s41467-026-75806-y [code]
Cryo-EM insights into isoform-specific properties of the IP&lt;sub&gt;3&lt;/sub&gt;R2 channel.
Journal: Nature communications
In common: Matplotlib, NumPy, ebi.ac.uk/pdbe/entry, histology / microscopy, cellular / molecular, 2 references
[9] doi:10.1038/s41467-026-70575-0
Structure of a pH-sensitive pentameric ligand-gated ion channel from the Sarcoptes scabies mite.
Journal: Nature communications
In common: ebi.ac.uk/pdbe/entry, histology / microscopy, cellular / molecular, 3 references
[10] doi:10.1038/s41467-026-75877-x
Structure of NHE6 and its lipid-mediated interactions regulating endosomal pH.
Journal: Nature communications
In common: ebi.ac.uk/pdbe/entry, histology / microscopy, cellular / molecular, 2 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.