21ZV | pdb_000021zv

Cdc48-Ufd1-Npl4 complex processing Ub6 in the presence of ubx2

PDB DOI: https://doi.org/10.2210/pdb21ZV/pdb
EM Map EMD-68127: EMDB EMDataResource

Classification: PROTEIN BINDING
Organism(s): Saccharomyces cerevisiae S288C, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2026-01-05 Released: 2026-11-04
Deposition Author(s): Pan, M., Liu, L., Zheng, Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cdc48-Ufd1-Npl4 complex processing polyUbEOS in the presence of ubx2

Pan, M., Liu, L., Zheng, Q.

To be published.

Macromolecule Content

Total Structure Weight: 854.86 kDa
Atom Count: 22,567
Modeled Residue Count: 2,857
Deposited Residue Count: 7,674
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin fusion degradation protein 1	A [auth B]	361	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: UFD1, PIP3, YGR048W
UniProt
Find proteins for P53044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53044 Go to UniProtKB: P53044
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53044
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B [auth C], D [auth L], F [auth N], N [auth O]	76	Homo sapiens	Mutation(s): 0 Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens) Explore P62979 Go to UniProtKB: P62979
PHAROS: P62979 GTEx: ENSG00000143947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62979
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UBX domain-containing protein 2	C [auth D]	584	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: UBX2, SEL1, YML013W, YM9571.05
UniProt
Find proteins for Q04228 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04228 Go to UniProtKB: Q04228
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04228
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 48	E [auth A] G H [auth P] I [auth H] J [auth I] E [auth A], G, H [auth P], I [auth H], J [auth I], K [auth J], L [auth K]	835	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: CDC48, YDL126C 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

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear protein localization protein 4	M	580	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: NPL4, HRD4, YBR170C, YBR1231
UniProt
Find proteins for P33755 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33755 Go to UniProtKB: P33755
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33755
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 T [auth K] SDF format, chain S [auth J] SDF format, chain R [auth J] SDF format, chain Q [auth H] SDF format, chain P [auth G] SDF format, chain O [auth A] MOL2 format, chain T [auth K] MOL2 format, chain S [auth J] MOL2 format, chain R [auth J] MOL2 format, chain Q [auth H] MOL2 format, chain P [auth G] MOL2 format, chain O [auth A] mmCIF format, chain T [auth K] mmCIF format, chain S [auth J] mmCIF format, chain R [auth J] mmCIF format, chain Q [auth H] mmCIF format, chain P [auth G] mmCIF format, chain O [auth A]	O [auth A] P [auth G] Q [auth H] R [auth J] S [auth J] O [auth A], P [auth G], Q [auth H], R [auth J], S [auth J], T [auth K]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain O [auth A] Focus chain P [auth G] Focus chain Q [auth H] Focus chain R [auth J] Focus chain S [auth J] Focus chain T [auth K] Interactions & Density Focus chain O [auth A] Focus chain P [auth G] Focus chain Q [auth H] Focus chain R [auth J] Focus chain S [auth J] Focus chain T [auth K]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain V [auth M] SDF format, chain U [auth M] MOL2 format, chain V [auth M] MOL2 format, chain U [auth M] mmCIF format, chain V [auth M] mmCIF format, chain U [auth M]	U [auth M], V [auth M]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain U [auth M] Focus chain V [auth M] Interactions & Density Focus chain U [auth M] Focus chain V [auth M]