7DMZ | pdb_00007dmz

GMPCPP microtubule complex

PDB DOI: https://doi.org/10.2210/pdb7DMZ/pdb
EM Map EMD-30775: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Sus scrofa
Mutation(s): No

Deposited: 2020-12-08 Released: 2021-12-08
Deposition Author(s): Wang, Y.X.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7DMZ

This is version 1.1 of the entry. See complete history.

Literature

GMPCPP microtubule complex

Wang, Y.X.

To be published.

Macromolecule Content

Total Structure Weight: 305.55 kDa
Atom Count: 20,396
Modeled Residue Count: 2,562
Deposited Residue Count: 2,688
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A [auth D], B [auth A], C [auth B]	451	Sus scrofa	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	D [auth E], E [auth C], F	445	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554 Go to UniProtKB: P02554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02554
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAJ (Subject of Investigation/LOI) Query on TAJ Download:Ideal Coordinates CCD File SDF format, chain P [auth F] SDF format, chain N [auth C] SDF format, chain L [auth E] MOL2 format, chain P [auth F] MOL2 format, chain N [auth C] MOL2 format, chain L [auth E] mmCIF format, chain P [auth F] mmCIF format, chain N [auth C] mmCIF format, chain L [auth E]	L [auth E], N [auth C], P [auth F]	taccalonolide AJ C₃₄ H₄₆ O₁₄ LCGALHWJYVLUHN-KNRACXJJSA-N		Interactions Focus chain L [auth E] Focus chain N [auth C] Focus chain P [auth F] Interactions & Density Focus chain L [auth E] Focus chain N [auth C] Focus chain P [auth F]
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth D] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth D] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth D]	G [auth D], H [auth A], J [auth B]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth D] Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth D] Focus chain H [auth A] Focus chain J [auth B]
G2P Query on G2P Download:Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain O [auth C] SDF format, chain M [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth C] MOL2 format, chain M [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth C] mmCIF format, chain M [auth E]	M [auth E], O [auth C], Q [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ GXTIEXDFEKYVGY-KQYNXXCUSA-N		Interactions Focus chain M [auth E] Focus chain O [auth C] Focus chain Q [auth F] Interactions & Density Focus chain M [auth E] Focus chain O [auth C] Focus chain Q [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain I [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-12-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-12-08
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.