9GNQ

Microtubule-associated Kif5B IAK tail mutant bound to ADP

PDB DOI: https://doi.org/10.2210/pdb9GNQ/pdb
EM Map EMD-51477: EMDB EMDataResource

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

Deposited: 2024-09-03 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: 2.90 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: 147.16 kDa
Atom Count: 9,309
Modelled Residue Count: 1,166
Deposited Residue Count: 1,304
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 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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	B [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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-1 heavy chain	C [auth K]	408	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

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 E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	TAXOL C₄₇ H₅₁ N O₁₄ RCINICONZNJXQF-MZXODVADSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
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]
GDP Query on GDP 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]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain H [auth K] MOL2 format, chain H [auth K] mmCIF format, chain H [auth K]	H [auth K]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth K] Interactions & Density Focus chain H [auth K]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 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