5ECJ | pdb_00005ecj

Crystal structure of monobody Mb(S4) bound to Prdm14 in complex with Mtgr1

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)
B [auth F]	d5ecjf_	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth E]	d5ecje_	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	automated matches	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	SCOP2 Family	TAFH domain-like	8061472	4001422	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TAFH domain-like	8061473	3001535	SCOP2 (2022-06-29)
C [auth B]	SCOP2B Superfamily	TAFH domain-like	8061473	3001535	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	GST_N_3	e5ecjA1	A: a/b three-layered sandwiches	X: Carbon-nitrogen hydrolase-like	H: HTH	T: winged helix domain	F: GST_N_3	ECOD (v294.1)
C [auth B]	UPAR_LY6	e5ecjB1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: Snake toxin-like	T: Snake toxin-like	F: UPAR_LY6	ECOD (v294.1)
B [auth F]		e5ecjF1	A: a/b three-layered sandwiches	X: CBS-domain	H: Porins	T: Invertebrate chitin-binding proteins	F:	ECOD (v294.1)
D [auth E]		e5ecjE1	A: a/b three-layered sandwiches	X: CBS-domain	H: Porins	T: Invertebrate chitin-binding proteins	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (utative)
A	1.20.120.1110	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	TAFH/NHR1 domain	CATH (utative)
C [auth B]	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (utative)
C [auth B]	1.20.120.1110	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	TAFH/NHR1 domain	CATH (utative)
B [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF07531	NHR1 homology to TAF (TAFH)	NHR1 homology to TAF	-	Family
A, C [auth B]	PF21549	PR domain zinc finger protein 2, PR domain (PRDM2_PR)	PR domain zinc finger protein 2, PR domain	This domain is found in PR domain zinc protein 2 from humans (PRDM2) and similar proteins from animals. PRDM2 is a histone methyltransferase that functions as a DNA-binding transcription factor. It contains a PR (PRDI-BF1 and RIZ1 homology) domain, w ...	This domain is found in PR domain zinc protein 2 from humans (PRDM2) and similar proteins from animals. PRDM2 is a histone methyltransferase that functions as a DNA-binding transcription factor. It contains a PR (PRDI-BF1 and RIZ1 homology) domain, which is a distinct SET domain, that is responsible for its catalytic activity (this entry). This domain displays a typical SET fold consisting mainly of short beta-strands and intervening loops including a pseudo-knot at the C terminus [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	PR domain zinc finger protein 14,Protein CBFA2T2	DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity enzyme regulator activity methyltransferase regulator activity molecular function regulator activity RNA binding binding nucleic acid binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity enzyme regulator activity methyltransferase regulator activity molecular function regulator activity RNA binding binding nucleic acid binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity chromatin binding chromatin DNA binding histone methyltransferase binding protein binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding transcription corepressor activity transcription coregulator activity	developmental process cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment response to fibroblast growth factor cellular response to stimulus cellular response to growth factor stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of biological process developmental process cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment response to fibroblast growth factor cellular response to stimulus cellular response to growth factor stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of biological process regulation of signal transduction negative regulation of cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway negative regulation of fibroblast growth factor receptor signaling pathway regulation of biological process regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of signal transduction regulation of response to stimulus fibroblast growth factor receptor signaling pathway regulation of cell communication response to growth factor cellular response to fibroblast growth factor stimulus regulation of fibroblast growth factor receptor signaling pathway multicellular organismal process multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells cellular process involved in reproduction in multicellular organism cellular component biogenesis cellular component assembly chromatin organization anatomical structure development epigenetic programming of gene expression sex-chromosome dosage compensation negative regulation of metabolic process heterochromatin organization genomic imprinting regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process dosage compensation by inactivation of X chromosome regulation of macromolecule biosynthetic process metabolic process negative regulation of gene expression, epigenetic germ cell development macromolecule metabolic process regulation of metabolic process sexual reproduction reproductive process cell development developmental process involved in reproduction gamete generation cellular component organization inactivation of paternal X chromosome by genomic imprinting chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression multicellular organismal reproductive process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of biosynthetic process fertilization germ-line stem cell population maintenance maintenance of cell number stem cell population maintenance methylation regulation of developmental process positive regulation of biological process regulation of stem cell population maintenance positive regulation of developmental process positive regulation of stem cell population maintenance positive regulation of multicellular organismal process regulation of multicellular organismal process multicellular organism development multi-multicellular organism process female pregnancy embryo implantation multi-organism reproductive process positive regulation of locomotion regulation of cell motility regulation of reproductive process regulation of cilium-dependent cell motility positive regulation of flagellated sperm motility cilium or flagellum-dependent cell motility regulation of flagellated sperm motility cilium-dependent cell motility positive regulation of cell motility positive regulation of cilium movement cell motility locomotion positive regulation of cellular process positive regulation of reproductive process sperm motility positive regulation of cilium-dependent cell motility regulation of microtubule-based process regulation of microtubule-based movement cilium movement involved in cell motility regulation of cilium movement regulation of locomotion flagellated sperm motility microtubule-based movement microtubule-based process cilium movement regulation of cilium movement involved in cell motility anatomical structure morphogenesis cell morphogenesis chordate embryonic development embryo development inner cell mass cell differentiation in utero embryonic development blastocyst formation embryo development ending in birth or egg hatching anatomical structure formation involved in morphogenesis inner cell mass cell fate commitment blastocyst development RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cell projection organization neuron projection development neurogenesis neuron differentiation positive regulation of neuron projection development positive regulation of cell projection organization system development plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization epithelium development digestive system development intestinal epithelial cell differentiation tube development tissue development digestive tract development epithelial cell differentiation columnar/cuboidal epithelial cell differentiation negative regulation of cell projection organization negative regulation of cellular component organization negative regulation of neuron projection development Notch signaling pathway negative regulation of Notch signaling pathway regulation of Notch signaling pathway	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen
B [auth F], D [auth E]	Monobody Mb(S4)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR046341	SET domain superfamily	Homologous Superfamily
A, C [auth B]	IPR050331	Zinc finger PRDM4/PRDM1/PRDM14-like	Family
A, C [auth B]	IPR013087	Zinc finger C2H2-type	Domain
A, C [auth B]	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A, C [auth B]	IPR001214	SET domain	Domain
A, C [auth B]	IPR044408	PRDM14, PR/SET domain	Domain
A, C [auth B]	IPR002893	Zinc finger, MYND-type	Domain
A, C [auth B]	IPR003894	TAFH/NHR1	Domain
A, C [auth B]	IPR013289	CBFA2T family	Family
A, C [auth B]	IPR014896	NHR2-like	Domain
A, C [auth B]	IPR013291	Myeloid transforming gene-related protein-1 (MTGR1)	Family
A, C [auth B]	IPR037249	TAFH/NHR1 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.