9BP6 | pdb_00009bp6

Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP

PDB DOI: https://doi.org/10.2210/pdb9BP6/pdb
Entry: 9BP6 supersedes: 8V2I
EM Map EMD-44762: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2024-05-07 Released: 2024-06-12
Deposition Author(s): Zehr, E.A., Roll-Mecak, A.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM structures of human alpha1B/betaI+betaIVb microtubules shed light on isoform specific assembly

Zehr, E.A., Roll-Mecak, A.

(2023) bioRxiv

DOI: https://doi.org/10.1101/2023.12.01.569594

Macromolecule Content

Total Structure Weight: 202.03 kDa
Atom Count: 13,631
Modeled Residue Count: 1,732
Deposited Residue Count: 1,790
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C [auth I]	451	Homo sapiens	Mutation(s): 0 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P68363 (Homo sapiens) Explore P68363 Go to UniProtKB: P68363
PHAROS: P68363 GTEx: ENSG00000123416
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68363
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D [auth Q]	444	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P07437 (Homo sapiens) Explore P07437 Go to UniProtKB: P07437
PHAROS: P07437 GTEx: ENSG00000196230
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07437
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I MOL2 format, chain E [auth A] MOL2 format, chain I mmCIF format, chain E [auth A] mmCIF format, chain I	E [auth A], I	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain I Interactions & Density Focus chain E [auth A] Focus chain I
G2P (Subject of Investigation/LOI) Query on G2P Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth Q] MOL2 format, chain G [auth B] MOL2 format, chain K [auth Q] mmCIF format, chain G [auth B] mmCIF format, chain K [auth Q]	G [auth B], K [auth Q]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ GXTIEXDFEKYVGY-KQYNXXCUSA-N		Interactions Focus chain G [auth B] Focus chain K [auth Q] Interactions & Density Focus chain G [auth B] Focus chain K [auth Q]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth I] SDF format, chain L [auth Q] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth I] MOL2 format, chain L [auth Q] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth I] mmCIF format, chain L [auth Q]	F [auth A], H [auth B], J [auth I], L [auth Q]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth I] Focus chain L [auth Q] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth I] Focus chain L [auth Q]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
MODEL REFINEMENT	ISOLDE
RECONSTRUCTION	RELION	3.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-12

Deposition Author(s):

Zehr, E.A.

Roll-Mecak, A.

This entry supersedes: 8V2I

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS003164

Revision History (Full details and data files)

Version 1.0: 2024-06-12
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Structure summary
Version 1.2: 2025-06-11
Changes: Data collection, Database references