5OWO

Human cytoplasmic Dynein N-Terminus dimerization domain at 1.8 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb5OWO/pdb

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

Deposited: 2017-09-01 Released: 2018-07-11
Deposition Author(s): Urnavicius, L., Lau, C.K., Elshenawy, M.M., Morales-Rios, E., Motz, C., Yildiz, A., Carter, A.P.
Funding Organization(s): Wellcome Trust, Medical Research Council (United Kingdom), National Institutes of Health, National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.229
R-Value Work: 0.196
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Cryo-EM shows how dynactin recruits two dyneins for faster movement.

Urnavicius, L., Lau, C.K., Elshenawy, M.M., Morales-Rios, E., Motz, C., Yildiz, A., Carter, A.P.

(2018) Nature 554: 202-206

PubMed: 29420470 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nature25462
Primary Citation of Related Structures:
5OWO, 6F1T, 6F1U, 6F1V, 6F1Y, 6F1Z, 6F38, 6F3A

PubMed Abstract:
Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased towards recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two dyneins. We find that the shift towards a double dynein complex increases both the force and speed of the microtubule motor. Our 3.5 Å resolution cryo-electron microscopy reconstruction of a dynein tail-dynactin-BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side-by-side. Our work provides a structural basis for understanding how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein-dynactin transport machine.

Organizational Affiliation

Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Francis Crick Avenue, Cambridge CB2 0QH, UK.

Macromolecule Content

Total Structure Weight: 90.19 kDa
Atom Count: 5,380
Modelled Residue Count: 637
Deposited Residue Count: 804
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic dynein 1 heavy chain 1	A, B, C, D	201	Homo sapiens	Mutation(s): 0 Gene Names: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325
UniProt & NIH Common Fund Data Resources
Find proteins for Q14204 (Homo sapiens) Explore Q14204 Go to UniProtKB: Q14204
PHAROS: Q14204 GTEx: ENSG00000197102
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14204
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain LA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	CA [auth C] DA [auth C] E [auth A] F [auth A] G [auth A] CA [auth C], DA [auth C], E [auth A], F [auth A], G [auth A], LA [auth D], Q [auth B], R [auth B], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain PA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D]	P [auth A], PA [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain PA [auth D] Interactions & Density Focus chain P [auth A] Focus chain PA [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain QA [auth D] MOL2 format, chain QA [auth D] mmCIF format, chain QA [auth D]	QA [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain QA [auth D] Interactions & Density Focus chain QA [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] EA [auth C] FA [auth C] GA [auth C] H [auth A] AA [auth B], EA [auth C], FA [auth C], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.229
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.242	α = 90
b = 175.56	β = 90
c = 50.444	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-07-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	WT100387
Medical Research Council (United Kingdom)	United Kingdom	MC_UP_A025_1011
National Institutes of Health	United States	GM094522
National Science Foundation (NSF, United States)	United States	MCB-1055017
National Science Foundation (NSF, United States)	United States	MCB- 1617028

Revision History (Full details and data files)

Version 1.0: 2018-07-11
Type: Initial release
Version 1.1: 2018-08-22
Changes: Data collection
Version 1.2: 2019-10-16
Changes: Data collection
Version 1.3: 2022-03-30
Changes: Author supporting evidence, Database references, Derived calculations
Version 1.4: 2024-10-16
Changes: Data collection, Structure summary