3QML | pdb_00003qml

The structural analysis of Sil1-Bip complex reveals the mechanism for Sil1 to function as a novel nucleotide exchange factor

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3qmla1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3qmlb1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	SIL1-like	8046144	4004904	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	ARM repeat-like	8092966	3000116	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	ARM repeat-like	8092966	3000116	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	Carb_anhydrase	e3qmlA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Carb_anhydrase	ECOD (v294.1)
B		e3qmlB3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F:	ECOD (v294.1)
D	Carb_anhydrase	e3qmlD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Carb_anhydrase	ECOD (v294.1)
C		e3qmlC1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.30.30	Alpha Beta	2-Layer Sandwich	Defensin A-like		CATH (4.3.0)
A	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
B	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.30.30	Alpha Beta	2-Layer Sandwich	Defensin A-like		CATH (4.3.0)
B	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
D	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)
C	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00012	Hsp70 protein (HSP70)	Hsp70 protein	-	Family
C, D	PF16782	Nucleotide exchange factor SIL1 (SIL1)	Nucleotide exchange factor SIL1	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	78 kDa glucose-regulated protein homolog	protein binding binding heat shock protein binding ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding protein binding binding heat shock protein binding ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding unfolded protein binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity macromolecule transmembrane transporter activity active transmembrane transporter activity protein transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity protein-transporting ATPase activity transmembrane protein transporter activity transporter activity transmembrane transporter activity	protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus catabolic process response to stimulus protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress response to endoplasmic reticulum stress response to topologically incorrect protein response to unfolded protein sexual reproduction reproductive process conjugation with cellular fusion organelle fusion cellular component organization organelle organization nucleus organization karyogamy karyogamy involved in conjugation with cellular fusion cellular component organization or biogenesis detection of stimulus detection of unfolded protein detection of chemical stimulus localization protein localization to organelle macromolecule localization intracellular protein localization protein localization to endoplasmic reticulum fungal-type cell wall beta-glucan metabolic process fungal-type cell wall polysaccharide biosynthetic process glucan biosynthetic process cell wall beta-glucan metabolic process cell wall organization or biogenesis fungal-type cell wall beta-glucan biosynthetic process cellular component biogenesis beta-glucan biosynthetic process polysaccharide metabolic process glucan metabolic process cell wall polysaccharide metabolic process carbohydrate metabolic process beta-glucan metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process cell wall beta-glucan biosynthetic process cell wall biogenesis fungal-type cell wall organization or biogenesis cell wall macromolecule biosynthetic process cell wall polysaccharide biosynthetic process fungal-type cell wall biogenesis fungal-type cell wall polysaccharide metabolic process cell wall macromolecule metabolic process establishment of protein localization cellular localization transport protein targeting protein transmembrane transport establishment of localization in cell post-translational protein targeting to membrane, translocation establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport post-translational protein targeting to endoplasmic reticulum membrane localization within membrane establishment of localization protein targeting to membrane transmembrane transport establishment of protein localization to organelle protein transport intracellular protein transport protein targeting to ER SRP-dependent cotranslational protein targeting to membrane cotranslational protein targeting to membrane SRP-dependent cotranslational protein targeting to membrane, translocation regulation of biological process cellular response to topologically incorrect protein regulation of cellular process signaling biological regulation endoplasmic reticulum unfolded protein response cellular response to unfolded protein intracellular signal transduction cell communication signal transduction	cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum luminal surveillance complex cytoplasm endoplasmic reticulum protein-containing complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane endoplasmic reticulum chaperone complex nucleus
C, D	Nucleotide exchange factor SIL1	enzyme regulator activity nucleoside-triphosphatase regulator activity molecular function regulator activity adenyl-nucleotide exchange factor activity ATPase regulator activity	establishment of protein localization cellular localization transport protein targeting localization SRP-dependent cotranslational protein targeting to membrane protein transmembrane transport establishment of localization in cell cotranslational protein targeting to membrane intracellular protein localization establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport establishment of protein localization cellular localization transport protein targeting localization SRP-dependent cotranslational protein targeting to membrane protein transmembrane transport establishment of localization in cell cotranslational protein targeting to membrane intracellular protein localization establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport localization within membrane establishment of localization protein targeting to membrane transmembrane transport establishment of protein localization to organelle protein transport macromolecule localization SRP-dependent cotranslational protein targeting to membrane, translocation cellular process intracellular protein transport protein targeting to ER	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018181	Heat shock protein 70, conserved site	Conserved Site
A, B	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B	IPR042050	Endoplasmic reticulum chaperone BIP, nucleotide-binding domain	Domain
A, B	IPR029048	Heat shock protein 70kD, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR029047	Heat shock protein 70kD, peptide-binding domain superfamily	Homologous Superfamily
A, B	IPR013126	Heat shock protein 70 family	Family
C, D	IPR031884	Nucleotide exchange factor Sil1, fungi	Family
C, D	IPR011989	Armadillo-like helical	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.