7Y3M | pdb_00007y3m

Structure of SALL4 ZFC1 bound with 16 bp AT-rich dsDNA

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth I]	zf-C2H2_1	e7y3mI2	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-C2H2_1	ECOD (1.6)
L [auth I]	zf-H2C2_5	e7y3mI1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-H2C2_5	ECOD (1.6)
I [auth J]	zf-C2H2_1	e7y3mJ1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-C2H2_1	ECOD (1.6)
I [auth J]	zf-H2C2_5	e7y3mJ2	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-H2C2_5	ECOD (1.6)
H [auth F]	zf-C2H2_1	e7y3mF1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-C2H2_1	ECOD (1.6)
H [auth F]	zf-H2C2_5	e7y3mF2	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-H2C2_5	ECOD (1.6)
G [auth A]	zf-C2H2_1	e7y3mA1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-C2H2_1	ECOD (1.6)
G [auth A]	zf-H2C2_5	e7y3mA2	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-H2C2_5	ECOD (1.6)
F [auth C]	zf-C2H2_1	e7y3mC1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-C2H2_1	ECOD (1.6)
F [auth C]	zf-H2C2_5	e7y3mC2	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-H2C2_5	ECOD (1.6)
E [auth B]	zf-C2H2_1	e7y3mB2	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-C2H2_1	ECOD (1.6)
E [auth B]	zf-H2C2_5	e7y3mB1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: zf-H2C2_5	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], L [auth I]	PF00096	Zinc finger, C2H2 type (zf-C2H2)	Zinc finger, C2H2 type	The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, an ...	The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], L [auth I]	Sal-like protein 4	DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure heart development animal organ development ventricular septum development circulatory system development cardiac septum development cardiac chamber development cardiac ventricle development somatic stem cell population maintenance maintenance of cell number stem cell population maintenance regulation of cellular process 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 regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process 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 positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process limb development appendage development embryonic limb morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis inner cell mass cell proliferation cell population proliferation developmental growth growth in utero embryonic development blastocyst growth blastocyst development	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle intracellular membrane-bounded organelle cytoplasm nucleus membrane-enclosed lumen intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle intracellular membrane-bounded organelle cytoplasm nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex
B [auth H], D [auth E], K [auth L]	DNA (16-mer)	-	-	-
A [auth G], C [auth D], J [auth K]	DNA (16-mer)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], L [auth I]	IPR013087	Zinc finger C2H2-type	Domain
E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], L [auth I]	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], L [auth I]	IPR051565	Sal C2H2-type zinc-finger	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], E [auth B], F [auth C], G [auth A], H [auth F], I [auth J], L [auth I]	Pharos: Q9UJQ4	Duane-radial ray syndrome IVIC syndrome Duane retraction syndrome Craniofacial Abnormalities osteosarcoma breast carcinoma coloboma intellectual disability lung adenocarcinoma ovarian cancer atypical teratoid rhabdoid tumor cancer esophageal squamous cell carcinoma polydactyly ventricular septal defect Duane-radial ray syndrome IVIC syndrome Duane retraction syndrome Craniofacial Abnormalities osteosarcoma breast carcinoma coloboma intellectual disability lung adenocarcinoma ovarian cancer atypical teratoid rhabdoid tumor cancer esophageal squamous cell carcinoma polydactyly ventricular septal defect breast cancer choanal atresia Holt-Oram syndrome

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.