8RHH | pdb_00008rhh

Microtubule-associated kinesin-1 tail complex bound to AMPPNP, two-headed state

PDB DOI: https://doi.org/10.2210/pdb8RHH/pdb
EM Map EMD-19176: EMDB EMDataResource

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

Deposited: 2023-12-15 Released: 2024-11-20
Deposition Author(s): Atherton, J., Chegkazi, M.S., Steiner, R.A.
Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Microtubule association induces a Mg-free apo-like ADP pre-release conformation in kinesin-1 that is unaffected by its autoinhibitory tail

Atherton, J., Chegkazi, M.S., Peirano, E., Pozzer, L.S., Foran, T., Steiner, R.A.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.11.11.622991

Macromolecule Content

Total Structure Weight: 542.44 kDa
Atom Count: 12,261
Modelled Residue Count: 1,533
Deposited Residue Count: 4,748
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	A [auth B]	445	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554 Go to UniProtKB: P02554
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02554
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-1 heavy chain	B [auth K], C [auth L], E [auth T], F [auth t]	963	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33176
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	D [auth A]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TA1 Query on TA1 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	TAXOL C₄₇ H₅₁ N O₁₄ RCINICONZNJXQF-MZXODVADSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain I [auth K] SDF format, chain L MOL2 format, chain I [auth K] MOL2 format, chain L mmCIF format, chain I [auth K] mmCIF format, chain L	I [auth K], L	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain I [auth K] Focus chain L Interactions & Density Focus chain I [auth K] Focus chain L
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth K] SDF format, chain K [auth L] SDF format, chain N [auth A] MOL2 format, chain J [auth K] MOL2 format, chain K [auth L] MOL2 format, chain N [auth A] mmCIF format, chain J [auth K] mmCIF format, chain K [auth L] mmCIF format, chain N [auth A]	J [auth K], K [auth L], N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth K] Focus chain K [auth L] Focus chain N [auth A] Interactions & Density Focus chain J [auth K] Focus chain K [auth L] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-20

Deposition Author(s):

Atherton, J.

Chegkazi, M.S.

Steiner, R.A.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	206175/Z/17/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V006568/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/S000828/1