9YRC | pdb_00009yrc

p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP

PDB DOI: https://doi.org/10.2210/pdb9YRC/pdb
EM Map EMD-73365: EMDB EMDataResource

Classification: TRANSLOCASE
Organism(s): Homo sapiens, Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-10-16 Released: 2026-03-25
Deposition Author(s): Li, H., Rapoport, T.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.97 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The deubiquitinating enzyme Otu1 releases substrates from the conserved initiation complex of the Cdc48/p97 ATPase for proteasomal degradation.

Li, H., Guan, H., Rapoport, T.A.

(2026) Sci Rep 16

PubMed: 41795027 Search on PubMed
DOI: https://doi.org/10.1038/s41598-026-42811-6
Primary Citation Related Structures:
9YRC

Organizational Affiliation

Department of Cell Biology, Harvard Medical School, Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA, 02115, USA. Hao_Li@hms.harvard.edu.

Macromolecule Content

Total Structure Weight: 653.27 kDa
Atom Count: 28,118
Modeled Residue Count: 3,568
Deposited Residue Count: 5,827
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transitional endoplasmic reticulum ATPase	A, B, C, D, E A, B, C, D, E, F	806	Homo sapiens	Mutation(s): 0 Gene Names: VCP, HEL-220, HEL-S-70 EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens) Explore P55072 Go to UniProtKB: P55072
PHAROS: P55072 GTEx: ENSG00000165280
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55072
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear protein localization protein 4 homolog	G	608	Homo sapiens	Mutation(s): 0 Gene Names: NPLOC4, KIAA1499, NPL4
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAT6 (Homo sapiens) Explore Q8TAT6 Go to UniProtKB: Q8TAT6
PHAROS: Q8TAT6 GTEx: ENSG00000182446
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TAT6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin recognition factor in ER-associated degradation protein 1	H	307	Homo sapiens	Mutation(s): 0 Gene Names: UFD1, UFD1L
UniProt & NIH Common Fund Data Resources
Find proteins for Q92890 (Homo sapiens) Explore Q92890 Go to UniProtKB: Q92890
PHAROS: Q92890 GTEx: ENSG00000070010
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92890
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	I	76	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RPL40A, UBI1, YIL148W
UniProt
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CH08 Go to UniProtKB: P0CH08
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CH08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain T [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain T [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain T [auth F]	J [auth A] K [auth A] L [auth B] M [auth B] N [auth C] J [auth A], K [auth A], L [auth B], M [auth B], N [auth C], O [auth C], P [auth D], T [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain T [auth F] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain T [auth F]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E]	Q [auth D], R [auth E], S [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Interactions & Density Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E]