6X04 | pdb_00006x04

Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN5

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
L	d6x04l_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
J	d6x04j_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
H	d6x04h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
F	d6x04f_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
D	d6x04d_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
B	d6x04b_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	V-set_12	e6x04L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
J	V-set_12	e6x04J1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
H	V-set_12	e6x04H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
F	V-set_12	e6x04F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
D	V-set_12	e6x04D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
B	V-set_12	e6x04B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
K	Nucleoporin_N	e6x04K1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Nucleoporin_N	ECOD (1.6)
I	Nucleoporin_N	e6x04I1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Nucleoporin_N	ECOD (1.6)
G	Nucleoporin_N	e6x04G1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Nucleoporin_N	ECOD (1.6)
E	Nucleoporin_N	e6x04E1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Nucleoporin_N	ECOD (1.6)
C	Nucleoporin_N	e6x04C1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Nucleoporin_N	ECOD (1.6)
A	Nucleoporin_N	e6x04A1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Nucleoporin_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)
I	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)
E	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)
C	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D, F, H, J B, D, F, H, J, L	Heavy Chain	IGHV1	-	nucleoporin nup133	SAbDab (2025-11-07)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF08801	Nup133 N terminal like (Nucleoporin_N)	Nup133 N terminal like	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	VHH-SAN5	-	-	-
A, C, E, G, I A, C, E, G, I, K	Nucleoporin NUP133	structural molecule activity structural constituent of nuclear pore	nuclear pore localization cellular localization localization within membrane protein-containing complex localization cellular component organization localization nucleus organization organelle organization macromolecule localization cellular process cellular component organization or biogenesis telomere localization telomere tethering at nuclear periphery chromosome localization nuclear pore localization cellular localization localization within membrane protein-containing complex localization cellular component organization localization nucleus organization organelle organization macromolecule localization cellular process cellular component organization or biogenesis telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization RNA transport nitrogen compound transport nucleocytoplasmic transport transport nuclear transport nucleic acid transport intracellular transport tRNA export from nucleus establishment of localization RNA export from nucleus tRNA transport establishment of RNA localization establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport chromosome organization transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus regulation of cellular process negative regulation of biological process cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process establishment of protein localization protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport mRNA transport mRNA export from nucleus response to nitrogen compound mRNA export from nucleus in response to heat stress response to chemical poly(A)+ mRNA export from nucleus subtelomeric heterochromatin formation positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription double-strand break repair DNA metabolic process DNA damage response DNA repair post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process positive regulation of transcription by RNA polymerase II	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex nuclear pore outer ring intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex nuclear pore outer ring intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore nuclear membrane membrane organelle membrane cytoplasm cytosol membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR037624	Nuclear pore complex protein Nup133-like	Family
A, C, E, G, I A, C, E, G, I, K	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR014908	Nucleoporin, Nup133/Nup155-like, N-terminal	Domain

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.