9C13 | pdb_00009c13

XMAP215 TOG5 interaction with GMPCPP tubulin lattice

PDB DOI: https://doi.org/10.2210/pdb9C13/pdb
EM Map EMD-45100: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Bos taurus, Xenopus laevis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-05-28 Released: 2025-11-05
Deposition Author(s): McManus, C.T., Travis, S.M., Jeffrey, P.D., Zhang, R., Petry, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Starting Models: in silico, experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure and function of XMAP215s C terminal domains in microtubule nucleation

McManus, C.T., Travis, S.M., Jeffrey, P.D., Zhang, R., Petry, S.

To be published.

Macromolecule Content

Total Structure Weight: 264.3 kDa
Atom Count: 15,708
Modeled Residue Count: 1,978
Deposited Residue Count: 2,333
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	A [auth B], B [auth D]	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	C [auth A], D [auth C]	451	Bos taurus	Mutation(s): 0
UniProt
Find proteins for F2Z4C1 (Bos taurus) Explore F2Z4C1 Go to UniProtKB: F2Z4C1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F2Z4C1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoskeleton-associated protein 5-A,Cytoskeleton-associated protein 5-A,Green fluorescent protein	E	541	Xenopus laevis	Mutation(s): 0 Gene Names: ckap5-a, xmap215, GFP
UniProt
Find proteins for Q9PT63 (Xenopus laevis) Explore Q9PT63 Go to UniProtKB: Q9PT63
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9PT63
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 L [auth C] SDF format, chain J [auth A] MOL2 format, chain L [auth C] MOL2 format, chain J [auth A] mmCIF format, chain L [auth C] mmCIF format, chain J [auth A]	J [auth A], L [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain J [auth A] Focus chain L [auth C] Interactions & Density Focus chain J [auth A] Focus chain L [auth C]
G2P Query on G2P Download Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain F [auth B]	F [auth B], H [auth D]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ GXTIEXDFEKYVGY-KQYNXXCUSA-N		Interactions Focus chain F [auth B] Focus chain H [auth D] Interactions & Density Focus chain F [auth B] Focus chain H [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain K [auth A] SDF format, chain I [auth D] SDF format, chain G [auth B] MOL2 format, chain M [auth C] MOL2 format, chain K [auth A] MOL2 format, chain I [auth D] MOL2 format, chain G [auth B] mmCIF format, chain M [auth C] mmCIF format, chain K [auth A] mmCIF format, chain I [auth D] mmCIF format, chain G [auth B]	G [auth B], I [auth D], K [auth A], M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain I [auth D] Focus chain K [auth A] Focus chain M [auth C] Interactions & Density Focus chain G [auth B] Focus chain I [auth D] Focus chain K [auth A] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21-5207-000
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01 GM141100-01A1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32 GM142149-01A1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01 GM141100-01A1