9YZU | pdb_00009yzu

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence ATGAGTCATA and loaded with mutated Bzip region of GCN4 transcription factor

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002855	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002854	3000034	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth F], E [auth D], F [auth E]	PF07716	Basic region leucine zipper (bZIP_2)	Basic region leucine zipper	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth F], E [auth D], F [auth E]	General control transcription factor GCN4	TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding transcription regulator activity DNA-binding transcription factor activity mediator complex binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding	response to nutrient levels response to stimulus response to stress response to amino acid starvation response to starvation cellular response to stimulus cellular response to nutrient levels cellular process positive regulation of cellular response to amino acid starvation regulation of response to nutrient levels regulation of cellular process positive regulation of biological process regulation of cellular response to stress cellular response to amino acid starvation response to nutrient levels response to stimulus response to stress response to amino acid starvation response to starvation cellular response to stimulus cellular response to nutrient levels cellular process positive regulation of cellular response to amino acid starvation regulation of response to nutrient levels regulation of cellular process positive regulation of biological process regulation of cellular response to stress cellular response to amino acid starvation positive regulation of response to stimulus cellular response to stress regulation of response to stress positive regulation of cellular process regulation of biological process biological regulation cellular response to starvation regulation of response to stimulus regulation of cellular response to amino acid starvation positive regulation of response to nutrient levels transcription preinitiation complex assembly positive regulation of macromolecule biosynthetic process regulation of primary metabolic process cellular component biogenesis nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process cellular component assembly transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II primary metabolic process positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression biosynthetic process RNA polymerase II preinitiation complex assembly metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulation of RNA polymerase II transcription preinitiation complex assembly positive regulation of cellular component organization regulation of cellular component organization positive regulation of DNA-templated transcription RNA metabolic process cellular component organization protein-DNA complex organization RNA biosynthetic process nucleic acid biosynthetic process positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly positive regulation of biosynthetic process protein-containing complex assembly cellular component organization or biogenesis regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of RNA polymerase II transcription preinitiation complex assembly protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of transcription initiation by RNA polymerase II protein-DNA complex assembly regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression regulation of cellular component biogenesis macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II localization protein localization to organelle macromolecule localization protein localization to nuclear periphery protein localization to nucleus intracellular protein localization amino acid biosynthetic process amino acid metabolic process signaling signal transduction intracellular signal transduction cell communication negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of ribosomal protein gene transcription by RNA polymerase II negative regulation of ribosomal protein gene transcription by RNA polymerase II	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle
C	Replication initiation protein	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding	cellular process plasmid maintenance nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	-
B	DNA (31-MER)	-	-	-
A	DNA (31-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth F], E [auth D], F [auth E]	IPR004827	Basic-leucine zipper domain	Domain
D [auth F], E [auth D], F [auth E]	IPR050946	AP-1 Transcription Factor bZIP	Family
D [auth F], E [auth D], F [auth E]	IPR046347	Basic-leucine zipper domain superfamily	Homologous Superfamily
C	IPR000525	Initiator Rep protein, WH1 domain	Domain
C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C	IPR036390	Winged helix DNA-binding domain superfamily	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.