6OMB | pdb_00006omb

Cdc48 Hexamer (Subunits A to E) with substrate bound to the central pore

PDB DOI: https://doi.org/10.2210/pdb6OMB/pdb
EM Map EMD-20124: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Mutation(s): No

Deposited: 2019-04-18 Released: 2019-07-17
Deposition Author(s): Cooney, I., Han, H., Stewart, M., Carson, R.H., Hansen, D., Price, J.C., Hill, C.P., Shen, P.S.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the Cdc48 segregase in the act of unfolding an authentic substrate.

Cooney, I., Han, H., Stewart, M.G., Carson, R.H., Hansen, D.T., Iwasa, J.H., Price, J.C., Hill, C.P., Shen, P.S.

(2019) Science 365: 502-505

PubMed: 31249134 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.aax0486
Primary Citation Related Structures:
6OMB, 6OPC

PubMed Abstract:
The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite extensive studies, the mechanism of Cdc48 has remained obscure, and its reported structures are inconsistent with models of substrate translocation proposed for other AAA+ ATPases (adenosine triphosphatases). Here, we report a 3.7-angstrom-resolution structure of Cdc48 in complex with an adaptor protein and a native substrate. Cdc48 engages substrate by adopting a helical configuration of substrate-binding residues that extends through the central pore of both of the ATPase rings. These findings indicate a unified hand-over-hand mechanism of protein translocation by Cdc48 and other AAA+ ATPases.

Organizational Affiliation

Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT 84112, USA.

Macromolecule Content

Total Structure Weight: 467.42 kDa
Atom Count: 21,815
Modeled Residue Count: 2,797
Deposited Residue Count: 4,197
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 48	A, B, C, D, E	835	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.6.4.6
UniProt
Find proteins for P25694 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25694 Go to UniProtKB: P25694
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25694
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Substrate of Cdc48	F [auth G]	22	Saccharomyces cerevisiae S288C	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain V [auth C] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth E] SDF format, chain EA [auth E] SDF format, chain BA [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain V [auth C] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain V [auth C] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain BA [auth D]	BA [auth D] EA [auth E] FA [auth E] G [auth A] J [auth A] BA [auth D], EA [auth E], FA [auth E], G [auth A], J [auth A], M [auth B], O [auth B], S [auth C], V [auth C], Y [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth C] Focus chain Y [auth D]
BEF Query on BEF Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain T [auth C] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] SDF format, chain CA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain T [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain T [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain CA [auth D]	CA [auth D] H [auth A] K [auth A] P [auth B] R [auth C] CA [auth D], H [auth A], K [auth A], P [auth B], R [auth C], T [auth C], W [auth C], Z [auth D]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain CA [auth D] Focus chain H [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth D] Focus chain H [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth C] Focus chain W [auth C] Focus chain Z [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain U [auth C] SDF format, chain Q [auth B] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain I [auth A] SDF format, chain DA [auth D] SDF format, chain AA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] DA [auth D] I [auth A] L [auth A] N [auth B] AA [auth D], DA [auth D], I [auth A], L [auth A], N [auth B], Q [auth B], U [auth C], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain DA [auth D] Focus chain I [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth D] Focus chain I [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	P50GM082545

Revision History (Full details and data files)

Version 1.0: 2019-07-17
Type: Initial release
Version 1.1: 2019-08-14
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Author supporting evidence, Other
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations