Annotations: 6QNX

Structure of the SA2/SCC1/CTCF complex

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21581	Stromalin conservative domain (SCD)	Stromalin conservative domain	-	Repeat
A	PF24571	Cohesin subunit SCC3/SA, HEAT-repeats domain (HEAT_SCC3-SA)	Cohesin subunit SCC3/SA, HEAT-repeats domain	-	Repeat
A	PF08514	STAG domain (STAG)	STAG domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Transcriptional repressor CTCF	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 DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific 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 DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription factor binding transcription coregulator binding protein binding chromatin binding chromatin insulator sequence binding chromatin DNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process localization protein localization to chromosome, centromeric region protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization cell cycle chromosome segregation cell cycle process developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation chromatin looping regulation of cellular component organization regulation of cell cycle process chromosome organization sister chromatid cohesion regulation of chromosome organization regulation of organelle organization centromeric sister chromatid cohesion organelle organization regulation of centromeric sister chromatid cohesion regulation of sister chromatid cohesion regulation of cell cycle negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation cardiac muscle cell development cellular developmental process cell development muscle cell differentiation striated muscle tissue development muscle structure development striated muscle cell development muscle cell development cell differentiation cardiac cell development muscle tissue development system development heart development cardiac muscle tissue development animal organ development cardiac muscle cell differentiation tissue development cardiocyte differentiation circulatory system development striated muscle cell differentiation positive regulation of DNA-templated transcription positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II sexual reproduction reproductive process cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation epigenetic programming of gene expression multicellular organismal reproductive process genomic imprinting germ cell development negative regulation of transcription by RNA polymerase II mitochondrion organization positive regulation of transcription by RNA polymerase II	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen chromosome condensed chromosome chromosome, centromeric region chromosomal region nucleoplasm male germ cell nucleus germ cell nucleus
B	64-kDa C-terminal product	RNA binding binding lncRNA binding nucleic acid binding chromatin binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription factor binding protein binding RNA binding binding lncRNA binding nucleic acid binding chromatin binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription factor binding protein binding DNA-binding transcription factor binding	cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process replication-born double-strand break repair via sister chromatid exchange cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process replication-born double-strand break repair via sister chromatid exchange cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation tumor necrosis factor superfamily cytokine production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process regulation of metabolic process homologous recombination sexual reproduction reproductive process meiotic cell cycle process cellular component organization meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process meiotic cell cycle organelle fission reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process cell division regulation of cell cycle phase transition G2/M transition of mitotic cell cycle negative regulation of cell cycle cell cycle phase transition mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle negative regulation of cell cycle phase transition regulation of cell cycle cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process regulation of cell cycle G2/M phase transition negative regulation of cell cycle process regulation of mitotic cell cycle phase transition mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition chromosome segregation localization protein localization to chromatin protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization apoptotic process cell death programmed cell death interleukin-1 production regulation of interleukin-1 beta production negative regulation of interleukin-1 beta production negative regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production chromosome organization sister chromatid cohesion positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process positive regulation of cell cycle process positive regulation of cellular process regulation of chromosome organization positive regulation of sister chromatid cohesion regulation of organelle organization positive regulation of cell cycle positive regulation of chromosome organization regulation of sister chromatid cohesion mitotic sister chromatid cohesion establishment of mitotic sister chromatid cohesion establishment of sister chromatid cohesion neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process regulation of neuron apoptotic process chromatin looping chromatin organization interleukin-10 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of interleukin-10 production positive regulation of interleukin-10 production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus establishment of meiotic sister chromatid cohesion meiotic sister chromatid cohesion regulation of glial cell apoptotic process negative regulation of glial cell apoptotic process glial cell apoptotic process RNA metabolic process regulation of primary 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 nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription regulation of mitotic nuclear division negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization mitotic sister chromatid separation negative regulation of sister chromatid segregation negative regulation of cellular component organization sister chromatid segregation regulation of mitotic sister chromatid segregation regulation of chromosome separation negative regulation of mitotic nuclear division regulation of chromosome segregation regulation of mitotic sister chromatid separation regulation of metaphase/anaphase transition of cell cycle regulation of mitotic metaphase/anaphase transition mitotic sister chromatid segregation negative regulation of mitotic metaphase/anaphase transition negative regulation of chromosome separation mitotic nuclear division negative regulation of chromosome segregation negative regulation of nuclear division negative regulation of organelle organization chromosome separation regulation of sister chromatid segregation negative regulation of mitotic sister chromatid separation regulation of nuclear division negative regulation of metaphase/anaphase transition of cell cycle nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle	midbody cellular anatomical structure membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear lumen nuclear matrix cytoskeleton midbody cellular anatomical structure membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear lumen nuclear matrix cytoskeleton spindle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane condensed nuclear chromosome nuclear chromosome chromosome condensed chromosome cytoplasm cytosol chromosome, centromeric region chromosomal region protein-containing complex mitotic cohesin complex cohesin complex nucleoplasm chromatin meiotic cohesin complex
A	Cohesin subunit SA-2	chromatin binding binding	cellular process cell division microtubule cytoskeleton organization membraneless organelle assembly mitotic cell cycle cellular component organization cellular component biogenesis cellular component assembly mitotic sister chromatid segregation cell cycle cellular component organization or biogenesis chromosome segregation microtubule cytoskeleton organization involved in mitosis spindle organization cellular process cell division microtubule cytoskeleton organization membraneless organelle assembly mitotic cell cycle cellular component organization cellular component biogenesis cellular component assembly mitotic sister chromatid segregation cell cycle cellular component organization or biogenesis chromosome segregation microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process mitotic nuclear division organelle assembly organelle fission chromosome organization sister chromatid segregation spindle assembly mitotic spindle organization mitotic spindle assembly organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation microtubule-based process cytoskeleton organization sister chromatid cohesion sexual reproduction reproductive process meiotic cell cycle mitotic sister chromatid cohesion establishment of mitotic sister chromatid cohesion establishment of sister chromatid cohesion	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membraneless organelle membrane chromosome cytoplasm cytosol fibrillar center chromosome, centromeric region chromosomal region protein-containing complex cohesin complex mitotic spindle spindle cytoskeleton mitotic spindle pole spindle pole microtubule cytoskeleton mitotic cohesin complex nucleoplasm chromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR050331	Zinc finger PRDM4/PRDM1/PRDM14-like	Family
C	IPR013087	Zinc finger C2H2-type	Domain
C	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
C	IPR056438	CTCF-like, C2H2 zinc finger	Domain
B	IPR023093	ScpA-like, C-terminal	Homologous Superfamily
B	IPR049589	NXP-1, middle HEAT-repeat binding domain	Domain
B	IPR039781	Rad21/Rec8-like protein	Family
B	IPR006910	Rad21/Rec8-like protein, N-terminal	Domain
B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B	IPR006909	Rad21/Rec8-like protein, C-terminal, eukaryotic	Domain
A	IPR039662	Cohesin subunit Scc3/SA	Family
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR056396	Cohesin subunit SCC3/SA, HEAT-repeats domain	Domain
A	IPR020839	Stromalin conservative domain	Domain
A	IPR013721	STAG	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	: P49711	intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome cancer Precursor T-Cell Lymphoblastic Leukemia-Lymphoma primary cutaneous T-cell non-Hodgkin lymphoma intellectual disability osteosarcoma schizophrenia granulomatous slack skin disease kidney Wilms tumor ovarian cancer microcephaly pancreatic intraductal papillary-mucinous neoplasm
B	: O60216	Cornelia de Lange syndrome myeloid leukemia Leukemia, Megakaryoblastic, of Down Syndrome Cornelia de Lange syndrome 4 chronic monocytic leukemia intellectual disability lung carcinoma malignant mesothelioma medulloblastoma oligodendroglioma acute myeloid leukemia breast cancer colorectal adenoma rheumatoid arthritis endometrium carcinoma in situ Cornelia de Lange syndrome myeloid leukemia Leukemia, Megakaryoblastic, of Down Syndrome Cornelia de Lange syndrome 4 chronic monocytic leukemia intellectual disability lung carcinoma malignant mesothelioma medulloblastoma oligodendroglioma acute myeloid leukemia breast cancer colorectal adenoma rheumatoid arthritis endometrium carcinoma in situ invasive ductal breast carcinoma lung adenocarcinoma Mungan syndrome osteosarcoma astrocytic tumor primitive neuroectodermal tumor colorectal cancer Roberts syndrome Cornelia de Lange syndrome 2 glioblastoma large cell medulloblastoma lung cancer malignant ependymoma plasma cell myeloma atypical teratoid rhabdoid tumor colorectal adenocarcinoma congenital anemia trichorhinophalangeal syndrome type II Cornelia de Lange syndrome 3 endometrial carcinoma
A	: Q8N3U4	urinary bladder cancer myeloid leukemia transitional cell carcinoma myelodysplastic syndrome chronic monocytic leukemia glioblastoma Leukemia, Megakaryoblastic, of Down Syndrome large cell medulloblastoma lymphoplasmacytic lymphoma malignant mesothelioma Alzheimer disease bladder benign neoplasm ovarian cancer pilocytic astrocytoma psoriasis urinary bladder cancer myeloid leukemia transitional cell carcinoma myelodysplastic syndrome chronic monocytic leukemia glioblastoma Leukemia, Megakaryoblastic, of Down Syndrome large cell medulloblastoma lymphoplasmacytic lymphoma malignant mesothelioma Alzheimer disease bladder benign neoplasm ovarian cancer pilocytic astrocytoma psoriasis Down syndrome holoprosencephaly leukemia malignant ependymoma medulloblastoma astrocytic tumor oligodendroglioma bladder carcinoma in situ pancreatic ductal adenocarcinoma congenital anemia plasma cell myeloma dermatomyositis rheumatoid arthritis Emery-Dreifuss muscular dystrophy urinary bladder carcinoma glioma juvenile dermatomyositis malignant glioma melanoma myopathy atypical teratoid rhabdoid tumor osteosarcoma breast cancer Pick disease cutaneous melanoma primitive neuroectodermal tumor diabetes mellitus Ewing sarcoma urinary bladder neoplasm

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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.

6QNX | pdb_00006qnx

Structure of the SA2/SCC1/CTCF complex

External Resource: Annotation

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation