6OJQ | pdb_00006ojq

Monomeric kinesin-1 motor domain in no-nucleotide state bound to GMPCPP-stabilized microtubule

PDB DOI: https://doi.org/10.2210/pdb6OJQ/pdb
EM Map EMD-20092: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Bos taurus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-04-12 Released: 2020-04-15
Deposition Author(s): Cha, H.K., Debs, G.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.67 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 6OJQ

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

Literature

Structural Intermediates of the Dimeric Kinesin Stepping Cycle Revealed by Cryo-EM

Cha, H.K., Debs, G., Liu, X., Liu, D., Sindelar, C.V.

To be published.

Macromolecule Content

Total Structure Weight: 133.03 kDa
Atom Count: 9,177
Modeled Residue Count: 1,164
Deposited Residue Count: 1,180
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	A [auth B]	426	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	B [auth A]	437	Bos taurus	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947 Go to UniProtKB: P81947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-1 heavy chain	C [auth K]	317	Homo sapiens	Mutation(s): 0 Gene Names: KIF5B, KNS, KNS1
UniProt & NIH Common Fund Data Resources
Find proteins for P33176 (Homo sapiens) Explore P33176 Go to UniProtKB: P33176
PHAROS: P33176 GTEx: ENSG00000170759
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33176
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 F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
G2P Query on G2P Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ GXTIEXDFEKYVGY-KQYNXXCUSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth A] MOL2 format, chain E [auth B] MOL2 format, chain G [auth A] mmCIF format, chain E [auth B] mmCIF format, chain G [auth A]	E [auth B], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain G [auth A] Interactions & Density Focus chain E [auth B] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.67 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01 GM 110530-01

Revision History (Full details and data files)

Version 1.0: 2020-04-15
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.