4AKG

Dynein Motor Domain - ATP complex

PDB DOI: https://doi.org/10.2210/pdb4AKG/pdb

Classification: MOTOR PROTEIN
Organism(s): Schistosoma japonicum, Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2012-02-22 Released: 2012-03-14
Deposition Author(s): Schmidt, H., Gleave, E.S., Carter, A.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.305
R-Value Work: 0.239
R-Value Observed: 0.242

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Insights Into Dynein Motor Domain Function from a 3.3 Angstrom Crystal Structure

Schmidt, H., Gleave, E.S., Carter, A.P.

(2012) Nat Struct Mol Biol 19: 492

PubMed: 22426545 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nsmb.2272
Primary Citation of Related Structures:
4AI6, 4AKG, 4AKH, 4AKI

PubMed Abstract:
Dyneins power the beating of cilia and flagella, transport various intracellular cargos and are necessary for mitosis. All dyneins have a ∼300-kDa motor domain consisting of a ring of six AAA+ domains. ATP hydrolysis in the AAA+ ring drives the cyclic relocation of a motile element, the linker domain, to generate the force necessary for movement. How the linker interacts with the ring during the ATP hydrolysis cycle is not known. Here we present a 3.3-Å crystal structure of the motor domain of Saccharomyces cerevisiae cytoplasmic dynein, crystallized in the absence of nucleotides. The linker is docked to a conserved site on AAA5, which is confirmed by mutagenesis as functionally necessary. Nucleotide soaking experiments show that the main ATP hydrolysis site in dynein (AAA1) is in a low-nucleotide affinity conformation and reveal the nucleotide interactions of the other three sites (AAA2, AAA3 and AAA4).

Organizational Affiliation

Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

Macromolecule Content

Total Structure Weight: 622.71 kDa
Atom Count: 41,634
Modelled Residue Count: 5,300
Deposited Residue Count: 5,390
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME, DYNEIN HEAVY CHAIN CYTOPLASMIC	A, B	2,695	Schistosoma japonicum, Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.5.1.18
UniProt
Find proteins for P08515 (Schistosoma japonicum) Explore P08515 Go to UniProtKB: P08515
Find proteins for P36022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36022 Go to UniProtKB: P36022
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P36022P08515
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B]	D [auth A], I [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	F [auth A], G [auth A], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B]	E [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.305
R-Value Work: 0.239
R-Value Observed: 0.242
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.326	α = 90
b = 117.918	β = 90.21
c = 202.762	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-14

Deposition Author(s):

Schmidt, H.

Gleave, E.S.

Carter, A.P.

Revision History (Full details and data files)

Version 1.0: 2012-03-14
Type: Initial release
Version 1.1: 2012-05-16
Changes: Other
Version 1.2: 2017-03-15
Changes: Source and taxonomy
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description