3QCA

Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Domain Reveals The Conserved FcisP Touch-Turn Motif of UBX Domain Suffering Conformational Change

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3qcaa_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	UBX domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3qcab_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	UBX domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3qcac_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	UBX domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3qcad_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	UBX domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ubiquitin-like	8034467	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8034467	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8034467	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8034467	3000157	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	UBX	e3qcaA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: UBX	ECOD (1.6)
B	UBX	e3qcaB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: UBX	ECOD (1.6)
C	UBX	e3qcaC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: UBX	ECOD (1.6)
D	UBX	e3qcaD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: UBX	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00789	UBX domain (UBX)	UBX domain	This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	FAS-associated factor 1	protein binding binding protein domain specific binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding heat shock protein binding ubiquitin binding ubiquitin-like protein binding kinase binding enzyme binding protein kinase binding enzyme regulator activity protein binding binding protein domain specific binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding heat shock protein binding ubiquitin binding ubiquitin-like protein binding kinase binding enzyme binding protein kinase binding enzyme regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding	maintenance of protein location protein localization cellular localization regulation of cellular process cellular biosynthetic process negative regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process cytoplasmic sequestering of NF-kappaB negative regulation of NF-kappaB transcription factor activity nucleic acid biosynthetic process DNA-templated transcription localization maintenance of protein location protein localization cellular localization regulation of cellular process cellular biosynthetic process negative regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process cytoplasmic sequestering of NF-kappaB negative regulation of NF-kappaB transcription factor activity nucleic acid biosynthetic process DNA-templated transcription localization regulation of RNA metabolic process cellular macromolecule localization cytoplasmic sequestering of protein regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of molecular function biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process maintenance of location regulation of cellular biosynthetic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity macromolecule localization metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cytoplasmic sequestering of transcription factor cell adhesion regulation of cell adhesion cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress proteolysis protein metabolic process response to endoplasmic reticulum stress regulation of protein metabolic process regulation of catabolic process regulation of protein catabolic process positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of biological process regulation of cellular component biogenesis cellular component organization cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis positive regulation of cellular process apoptotic process cell death programmed cell death positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process positive regulation of nucleobase-containing compound metabolic process positive regulation of DNA replication DNA metabolic process positive regulation of metabolic process DNA replication positive regulation of DNA metabolic process positive regulation of macromolecule metabolic process regulation of DNA metabolic process regulation of DNA replication positive regulation of protein metabolic process positive regulation of protein catabolic process positive regulation of catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process positive regulation of cell communication extrinsic apoptotic signaling pathway via death domain receptors positive regulation of signal transduction signaling regulation of signal transduction extrinsic apoptotic signaling pathway cell communication positive regulation of apoptotic signaling pathway positive regulation of response to stimulus signal transduction regulation of signaling positive regulation of extrinsic apoptotic signaling pathway via death domain receptors cell surface receptor signaling pathway positive regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway via death domain receptors regulation of cell communication regulation of apoptotic signaling pathway positive regulation of signaling	membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane organelle envelope nuclear envelope nucleus cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen CD95 death-inducing signaling complex cell periphery plasma membrane protein complex plasma membrane death-inducing signaling complex ooplasm perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR044541	FAF1, UBA-like domain	Domain
A, B, C, D	IPR033043	FAS-associated factor 1-like, UBX domain	Domain
A, B, C, D	IPR049483	Fas-associated factor 1/2-like, UAS domain	Domain
A, B, C, D	IPR050730	UBX domain-containing protein	Family
A, B, C, D	IPR006577	UAS	Domain
A, B, C, D	IPR001012	UBX domain	Domain
A, B, C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9UNN5	androgenetic alopecia atypical teratoid rhabdoid tumor large cell medulloblastoma osteosarcoma type 2 diabetes mellitus atrial fibrillation cerebrovascular disorder maturity-onset diabetes of the young ovarian cancer attention deficit hyperactivity disorder, inattentive type glioblastoma medulloblastoma renal cell carcinoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.