6qnx

Structure of the SA2/SCC1/CTCF complex

Method: X-RAY DIFFRACTION D_max: 132.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cohesin subunit SA-2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 80–1060	Not recorded	64-kDa C-terminal product × 1 （O60216） Transcriptional repressor CTCF × 1 （P49711）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K	Resolution 2.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6QNX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4PJU crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1) Deposited 2014-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 80–1060（981 aa） Fragment：UNP residues 80-1060	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).	Resolution 3.05 Å R-free 0.238
4PJW crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1), with bound MES Deposited 2014-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 80–1060（981 aa） Fragment：UNP residues 80-1060	Non-standard monomer：Yes (specific site not provided by mmCIF)	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).	Resolution 2.85 Å R-free 0.225
4PK7 crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1) with bound MES, native proteins Deposited 2014-05-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 80–1060（981 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).	Resolution 2.95 Å R-free 0.251
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1231（1231 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K	Resolution 3.24 Å R-free 0.289
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–1231（1231 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K	Resolution 3.24 Å R-free 0.289
8K4D Structure of the SA2/Scc1/CENP_U complex Deposited 2023-07-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 81–1060（980 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.03 M CaCl2,0.03 M MgCl2, 0.1 M MOPS-HEPES, pH7.5, 10% PEG8000, 20% ethylene glycol	Resolution 3.52 Å R-free 0.269
9EP3 Structure of the SA2/SCC1/WAPL complex Deposited 2024-03-16	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 80–1060（981 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K	Resolution 3.08 Å R-free 0.268
9HMS Cryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2 Deposited 2024-12-09	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1231（1231 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9HMV Cryo-EM structure of SA2-SCC1 complex at 2.9 angstrom Deposited 2024-12-09	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1231（1231 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STAG2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–981； UniProt 80–1060

64-kDa C-terminal product

Homo sapiens

UniProt O60216

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 281–420	Not recorded	Cohesin subunit SA-2 × 1 （Q8N3U4） Transcriptional repressor CTCF × 1 （P49711）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K	Resolution 2.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6QNX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4PJU crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1) Deposited 2014-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 281–420（140 aa） Fragment：UNP residues 281-420	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).	Resolution 3.05 Å R-free 0.238
4PJW crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1), with bound MES Deposited 2014-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 281–420（140 aa） Fragment：UNP residues 281-420	Non-standard monomer：Yes (specific site not provided by mmCIF)	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).	Resolution 2.85 Å R-free 0.225
4PK7 crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1) with bound MES, native proteins Deposited 2014-05-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 281–420（140 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).	Resolution 2.95 Å R-free 0.251
6RRC Crystal structure of the N-terminal region of human cohesin subunit STAG1 in complex with RAD21 peptide Deposited 2019-05-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 321–345（25 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；277 K；2.1 M Ammonium Sulfate, 0.1 M MES pH 6.3	Resolution 2.37 Å R-free 0.248
6RRC Crystal structure of the N-terminal region of human cohesin subunit STAG1 in complex with RAD21 peptide Deposited 2019-05-17	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 321–345（25 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；277 K；2.1 M Ammonium Sulfate, 0.1 M MES pH 6.3	Resolution 2.37 Å R-free 0.248
6RRK Crystal structure of the central region of human cohesin subunit STAG1 in complex with RAD21 peptide Deposited 2019-05-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 356–395（40 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；16 % PEG 3350, 0.2 M DL-Mallic acid	Resolution 3.17 Å R-free 0.278
6RRK Crystal structure of the central region of human cohesin subunit STAG1 in complex with RAD21 peptide Deposited 2019-05-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 356–395（40 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；16 % PEG 3350, 0.2 M DL-Mallic acid	Resolution 3.17 Å R-free 0.278
6WG3 Cryo-EM structure of human Cohesin-NIPBL-DNA complex Deposited 2020-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain C 1–631（631 aa）	Mutation：R172A, D279A, R450A	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.30 Å
6WGE Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1 Deposited 2020-04-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 1–631（631 aa）	Mutation：R172A, D279A, R450A	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7W1M Cryo-EM structure of human cohesin-CTCF-DNA complex Deposited 2021-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain C 1–631（631 aa）	Mutation：R172A, D279A, R450A	ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 ZN ZINC ION × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–631（631 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K	Resolution 3.24 Å R-free 0.289
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–631（631 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K	Resolution 3.24 Å R-free 0.289
8K4D Structure of the SA2/Scc1/CENP_U complex Deposited 2023-07-18	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 281–420（140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.03 M CaCl2,0.03 M MgCl2, 0.1 M MOPS-HEPES, pH7.5, 10% PEG8000, 20% ethylene glycol	Resolution 3.52 Å R-free 0.269
8P0A Human Cohesin ATPase module Deposited 2023-05-10	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 558–629（72 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8.2 cryo-EM buffer pH 8.2 cryo-EM buffer pH 8.2 cryo-EM vitrification conditions Cryogen ETHANE cryo-EM vitrification conditions Cryogen ETHANE cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å
8PQ5 Human Cohesin ATPase module with an open DNA exit gate Deposited 2023-07-10	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 558–629（72 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8.2 cryo-EM buffer pH 8.2 cryo-EM buffer pH 8.2 cryo-EM vitrification conditions Cryogen ETHANE cryo-EM vitrification conditions Cryogen ETHANE cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
8RO6 Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Apo closed P-loop conformation Deposited 2024-01-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Hepes pH 7.0; 10% w/v PEG 6000	Resolution 2.20 Å R-free 0.244
8RO7 Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Open/closed P-loop conformation Deposited 2024-01-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Hepes pH 7.0; 10% w/v PEG 6000	Resolution 2.09 Å R-free 0.223
8RO8 Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Apo closed P-loop conformation Deposited 2024-01-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium malonate dibasic monohydrate; 0.1 M Bis-Tris propane pH 6.5; 20% w/v PEG 3350	Resolution 1.90 Å R-free 0.231
8RO9 Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Open/closed P-loop conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide; 0.1 M Bis-Tris propane pH 6.5; 20% w/v PEG 3350	Resolution 1.77 Å R-free 0.218
8RO9 Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Open/closed P-loop conformation Deposited 2024-01-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 558–629（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide; 0.1 M Bis-Tris propane pH 6.5; 20% w/v PEG 3350	Resolution 1.77 Å R-free 0.218
8ROA Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ADP-bound conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium formate; 20% w/v PEG 3350	Resolution 2.44 Å R-free 0.250
8ROA Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ADP-bound conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 558–629（72 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium formate; 20% w/v PEG 3350	Resolution 2.44 Å R-free 0.250
8ROB Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ATPgS-Mg-bound conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MMT pH 7.0; 25% w/v PEG 1500	Resolution 2.50 Å R-free 0.299
8ROC Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - Apo closed P-loop conformation Deposited 2024-01-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium nitrate pH 6.3; 20% w/v PEG 3350	Resolution 1.85 Å R-free 0.222
8ROD Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - Open/closed P-loop conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium sulfate; 20 % w/v PEG 3350	Resolution 1.50 Å R-free 0.232
8ROE Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-bound conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium malonate; 0.1 M Bis Tris propane pH 6.5; 20 % w/v PEG 3350	Resolution 1.36 Å R-free 0.219
8ROF Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-Mg-bound conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M magnesium chloride; 0.1 M MES pH 6.0; 20 % w/v PEG 6000	Resolution 1.65 Å R-free 0.228
8ROG Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ATPgS-Mg-bound conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 558–629（72 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium formate; 0.1 M Bis Tris propane pH 6.5; 20 % w/v PEG 3350	Resolution 1.94 Å R-free 0.253
8ROH Human cohesin SMC3-HD(EQ)/RAD21-N complex - Apo conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–102（102 aa）	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.21M NaSO4 ; 0.1M Bis-tris propane pH 7; 16% w/v PEG3350	Resolution 2.60 Å R-free 0.255
8ROI Human cohesin SMC3-HD(EQ)/RAD21-N complex - ADP-bound conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–102（102 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Na/K phosphate pH 7.5; 0.1 M HEPES pH 7.5; 15% v/v PEG Smear High; 10% v/v ethylene glycol	Resolution 2.45 Å R-free 0.239
8ROJ Human cohesin SMC3-HD/RAD21-N complex - ADP-Mg-bound conformation Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–102（102 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.075 M magnesium chloride; 0.075 M Sodium citrate tribasic dehydrate; 0.1 M Bis-Tris pH 6.0; 18% v/v PEG Smear Broad	Resolution 3.00 Å R-free 0.264
8ROK Human cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 1 Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–102（102 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.3 M NaCl; 0.05 M L-Arginine; 0.1 M Tris pH7.5; 22.5 % v/v PEG Smear Broad; 0.05 M L-Glutamic acid monosodium salt hydrate	Resolution 2.25 Å R-free 0.253
8ROK Human cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 1 Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–102（102 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.3 M NaCl; 0.05 M L-Arginine; 0.1 M Tris pH7.5; 22.5 % v/v PEG Smear Broad; 0.05 M L-Glutamic acid monosodium salt hydrate	Resolution 2.25 Å R-free 0.253
8ROL Human cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 2 Deposited 2024-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–102（102 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium chloride; 0.1 M Bicine pH 9.0; 20% w/v PEG 550 MME	Resolution 3.11 Å R-free 0.238
9EP3 Structure of the SA2/SCC1/WAPL complex Deposited 2024-03-16	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 281–420（140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K	Resolution 3.08 Å R-free 0.268
9HMS Cryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2 Deposited 2024-12-09	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 310–550（241 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9HMV Cryo-EM structure of SA2-SCC1 complex at 2.9 angstrom Deposited 2024-12-09	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 310–550（241 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9HN0 Cryo-EM structure of human separase bound to SCC1 (310-550 aa) Deposited 2024-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 310–550（241 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9HN4 Cryo-EM structure of human separase bound to phosphorylated SCC1 (310-550 aa) Deposited 2024-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 310–550（241 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.93 Å
9HN5 Cryo-EM structure of human separase bound to phosphorylated SCC1 (100-320 aa) Deposited 2024-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 100–320（221 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9HVY Cryo-EM structure of human separase-SCC1 (1-631) fusion protein Deposited 2025-01-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–631（631 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

35 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAD21_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–140； UniProt 281–420

Transcriptional repressor CTCF

OrganismNot specified

UniProt P49711

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 222–231	Not recorded	Cohesin subunit SA-2 × 1 （Q8N3U4） 64-kDa C-terminal product × 1 （O60216）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K	Resolution 2.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6QNX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1X6H Solution structures of the C2H2 type zinc finger domain of human Transcriptional repressor CTCF Deposited 2005-05-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 515–587（73 aa） Fragment：C2H2 type zinc finger domain	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.5mM C2H2 type zinc finger domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 5mM d-DTT; 0.02% NaN3; 10uM ZnCl2; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2CT1 Solution Structure of the zinc finger domain of Transcriptional repressor CTCF protein Deposited 2005-05-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 399–462（64 aa） Fragment：zinc finger domain	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 2.46mM zinc finger domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZnCl2; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
5K5H Homo sapiens CCCTC-binding factor (CTCF) ZnF4-7 and DNA complex structure Deposited 2016-05-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 348–464（117 aa） Fragment：unp residues 348-464	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；25% (w/v) polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M bis-tris HCl, pH 5.5	Resolution 3.11 Å R-free 0.264
5K5I Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P65 Deposited 2016-05-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 378–489（112 aa） Fragment：unp residues 378-489	Not recorded	ZN ZINC ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；20% (w/v) polyethylene glycol 3350, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5	Resolution 2.19 Å R-free 0.245
5K5J Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P41212 Deposited 2016-05-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 378–489（112 aa） Fragment：unp residues 378-489	Not recorded	ZN ZINC ION × 4 SO4 SULFATE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；25% (w/v) polyethylene glycol 3350, 0.2 M ammonium sulfate, and 0.1 M bis-tris HCl, pH 5.5	Resolution 2.29 Å R-free 0.254
5K5L Homo sapiens CCCTC-binding factor (CTCF) ZnF6-8 and H19 sequence DNA complex structure Deposited 2016-05-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: heptameric	Chain E 405–492（88 aa） Fragment：unp residues 405-492 Chain F 405–492（88 aa） Fragment：unp residues 405-492 Chain G 405–492（88 aa） Fragment：unp residues 405-492	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；289 K；20% (w/v) polyethylene glycol 8,000 0.1 M CHES-NaOH pH 9.5	Resolution 3.12 Å R-free 0.270
5KKQ Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure Deposited 2016-06-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 321–465（145 aa）	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M Bis-tris, pH 6.5	Resolution 1.74 Å R-free 0.199
5KKQ Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure Deposited 2016-06-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 321–465（145 aa）	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M Bis-tris, pH 6.5	Resolution 1.74 Å R-free 0.199
5T00 Human CTCF ZnF3-7 and methylated DNA complex Deposited 2016-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 321–465（145 aa） Fragment：UNP residues 321-465	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M HEPES-NaOH, pH 7.5	Resolution 2.19 Å R-free 0.243
5T00 Human CTCF ZnF3-7 and methylated DNA complex Deposited 2016-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 321–465（145 aa） Fragment：UNP residues 321-465	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M HEPES-NaOH, pH 7.5	Resolution 2.19 Å R-free 0.243
5T0U CTCF ZnF2-7 and DNA complex structure Deposited 2016-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 294–465（172 aa） Fragment：UNP residues 294-465	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% PEG 4000, 0.2 M ammonium acetate, 0.2 M Na-Citrate pH 5.6	Resolution 3.20 Å R-free 0.266
5T0U CTCF ZnF2-7 and DNA complex structure Deposited 2016-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 294–465（172 aa） Fragment：UNP residues 294-465	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% PEG 4000, 0.2 M ammonium acetate, 0.2 M Na-Citrate pH 5.6	Resolution 3.20 Å R-free 0.266
5UND Crystal Structure of CTCF(ZnF 4-10) With 28-mer DNA Deposited 2017-01-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 348–547（200 aa）	Not recorded	ZN ZINC ION × 7 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；28% PEG 2000 MME 100mM Bis-Tris, pH 6.5	Resolution 2.55 Å R-free 0.237
5UND Crystal Structure of CTCF(ZnF 4-10) With 28-mer DNA Deposited 2017-01-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 348–547（200 aa）	Not recorded	ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；28% PEG 2000 MME 100mM Bis-Tris, pH 6.5	Resolution 2.55 Å R-free 0.237
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 292–490（199 aa） Fragment：UNP residues 292-490	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.81 Å R-free 0.254
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 292–490（199 aa） Fragment：UNP residues 292-490	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.81 Å R-free 0.254
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 292–490（199 aa） Fragment：UNP residues 292-490	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.81 Å R-free 0.254
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain J 292–490（199 aa） Fragment：UNP residues 292-490	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.81 Å R-free 0.254
5YEG Crystal structure of CTCF ZFs4-8-Hs5-1a complex Deposited 2017-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 349–490（142 aa） Fragment：UNP residues 349-490	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289.15 K；0.1M Bis-tris pH 5.6-6.0, 0.2M Sodium chloride, 17-24% PEG3350	Resolution 2.00 Å R-free 0.204
5YEG Crystal structure of CTCF ZFs4-8-Hs5-1a complex Deposited 2017-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 349–489（141 aa） Fragment：UNP residues 349-489	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289.15 K；0.1M Bis-tris pH 5.6-6.0, 0.2M Sodium chloride, 17-24% PEG3350	Resolution 2.00 Å R-free 0.204
5YEH Crystal structure of CTCF ZFs4-8-eCBS Deposited 2017-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 349–490（142 aa） Fragment：UNP residues 349-490	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.33 Å R-free 0.270
5YEH Crystal structure of CTCF ZFs4-8-eCBS Deposited 2017-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 349–490（142 aa） Fragment：UNP residues 349-490	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.33 Å R-free 0.270
5YEL Crystal structure of CTCF ZFs6-11-gb7CSE Deposited 2017-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 405–580（176 aa） Fragment：UNP residues 405-580	Mutation：C504S	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1M Bis-tris pH 5.6-6.0, 0.1M Sodium chloride, 17-20% PEG3350	Resolution 2.96 Å R-free 0.286
5YEL Crystal structure of CTCF ZFs6-11-gb7CSE Deposited 2017-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 405–580（176 aa） Fragment：UNP residues 405-580	Mutation：C504S	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1M Bis-tris pH 5.6-6.0, 0.1M Sodium chloride, 17-20% PEG3350	Resolution 2.96 Å R-free 0.286
7W1M Cryo-EM structure of human cohesin-CTCF-DNA complex Deposited 2021-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain H 1–727（727 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 ZN ZINC ION × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
8SSQ ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4 Deposited 2023-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 319–606（288 aa） Fragment：Zinc finger domains 3-11	Not recorded	ZN ZINC ION × 9 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium malonate pH 5.0, 15-22% w/v PEG 3,350	Resolution 3.12 Å R-free 0.271
8SSQ ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4 Deposited 2023-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 319–606（288 aa） Fragment：Zinc finger domains 3-11	Not recorded	ZN ZINC ION × 8 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium malonate pH 5.0, 15-22% w/v PEG 3,350	Resolution 3.12 Å R-free 0.271
8SSR ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-20 Deposited 2023-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 319–606（288 aa） Fragment：Zinc finger domains 3-11	Not recorded	ZN ZINC ION × 9 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20-25%% w/v PEG 3,350, 0.1 M BIS-TRIS pH 5.0-6.5, 0.05-0.20M NaCl	Resolution 3.14 Å R-free 0.284
8SSR ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-20 Deposited 2023-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 319–606（288 aa） Fragment：Zinc finger domains 3-11	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20-25%% w/v PEG 3,350, 0.1 M BIS-TRIS pH 5.0-6.5, 0.05-0.20M NaCl	Resolution 3.14 Å R-free 0.284
8SSS ZnFs 1-7 of CCCTC-binding factor (CTCF) Complexed with 23mer Deposited 2023-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 263–465（203 aa） Fragment：Zinc finger domains 1-7	Not recorded	ZN ZINC ION × 7 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；26.5% PEG3350, 0.26M DL-Malic acid 7.0	Resolution 2.30 Å R-free 0.231
8SSS ZnFs 1-7 of CCCTC-binding factor (CTCF) Complexed with 23mer Deposited 2023-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 263–465（203 aa） Fragment：Zinc finger domains 1-7	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；26.5% PEG3350, 0.26M DL-Malic acid 7.0	Resolution 2.30 Å R-free 0.231
8SST ZnFs 1-7 of CCCTC-binding factor (CTCF) K365T Mutant Complexed with 23mer Deposited 2023-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 263–465（203 aa） Fragment：Zinc finger domains 1-7	Mutation：K365T	ZN ZINC ION × 7 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.243
8SST ZnFs 1-7 of CCCTC-binding factor (CTCF) K365T Mutant Complexed with 23mer Deposited 2023-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 263–465（203 aa） Fragment：Zinc finger domains 1-7	Mutation：K365T	ZN ZINC ION × 7 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.243
8SSU ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA Deposited 2023-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: trimeric	Chain A 320–582（263 aa） Fragment：Zinc finger domains 3-11 of CTCF, Residues 195-258 of LDB1	Not recorded	EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.04 M Citric acid, 0.06 M BIS-TRIS propane/pH 6.4, 20% w/v Polyethylene glycol 3,350	Resolution 2.89 Å R-free 0.240

20 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CTCF_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 222–231

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6qnx
Deposition date deposition_date	2019-02-12
Structure title title	Structure of the SA2/SCC1/CTCF complex
Keywords keywords	Cohesin, CTCF, TAD, Chromatin folding, genome regulation, SA2, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	39.78 Å
Radius of gyration Rg (electron density) rg_electron	39.17 Å
Forward intensity I(0) i0	201092000.00
Molecular weight molecular_weight	117170.0 kDa
Excluded volume excluded_volume	147550 Å³
Envelope volume envelope_volume	206950 Å³
Hydration-shell volume shell_volume	44372 Å³
Envelope diameter envelope_diameter	137.5 Å
Shell Rg shell_rg	44.70 Å
Envelope Rg envelope_rg	38.44 Å
Shape Rg shape_rg	39.17 Å
Total Rg total_rg	39.52 Å
Total atoms total_atoms	16463
Residues n_residues	1011
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	132.8 Å
Rg (real space) rg_real	39.83 Å
Rg uncertainty (real space) rg_real_error	1.05 Å
I(0) (real space) i0_real	2.0110e+08
I(0) uncertainty (real space) i0_real_error	3.4620e+06
Rg (reciprocal space) rg_reciprocal	39.81 Å
I(0) (reciprocal space) i0_reciprocal	201100000.0000
Solution quality estimate total_estimate	0.8835
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.8 Å
Skewness Skewness skewness	0.250
Kurtosis Kurtosis kurtosis	-0.580
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21970000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.842

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Cohesin subunit SA-2
Molecular weight formula_weight	113610.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	16469

ENMMLFEVVKMGKSAMQSVVDDWIESYKHDRDIALLDLINFFIQCSGCKGVVTAEMFRHMQNSEIIRKMTEEFDEDSGDYPLTMAGPQWKKFKSSFCEFIGVLVRQCQYSIIYDEYMMDTVISLLTGLSDSQVRAFRHTSTLAAMKLMTALVNVALNLSINMDNTQRQYEAERNKMIGKRANERLELLLQKRKELQENQDEIENMMNAIFKGVFVHRYRDAIAEIRAICIEEIGIWMKMYSDAFLNDSYLKYVGWTMHDKQGEVRLKCLTALQGLYYNKELNSKLELFTSRFKDRIVSMTLDKEYDVAVQAIKLLTLVLQSSEEVLTAEDCENVYHLVYSAHRPVAVAAGEFLYKKLFSRRDPEEDGMMKRRGRQGPNANLVKTLVFFFLESELHEHAAYLVDSMWDCATELLKDWECMNSLLLEEPLSGEEALTDRQESALIEIMLCTIRQAAECHPPVGRGTGKRVLTAKEKKTQLDDRTKITELFAVALPQLLAKYSVDAEKVTNLLQLPQYFDLEIYTTGRLEKHLDALLRQIRNIVEKHTDTDVLEACSKTYHALCNEEFTIFNRVDISRSQLIDELADKFNRLLEDFLQEGEEPDEDDAYQVLSTLKRITAFHNAHDLSKWDLFACNYKLLKTGIENGDMPEQIVIHALQCTHYVILWQLAKITESSSTKEDLLRLKKQMRVFCQICQHYLTNVNTTVKEQAFTILCDILMIFSHQIMSGGRDMLEPLVYTPDSSLQSELLSFILDHVFIEQDDDNNSADGQQEDEASKIEALHKRRNLLAAFCKLIVYTVVEMNTAADIFKQYMKYYNDYGDIIKETMSKTRQIDKIQCAKTLILSLQQLFNEMIQENGYNFDRSSSTFSGIKELARRFALTFGLDQLKTREAIAMLHKDGIEFAFKEPNPQGESHPPLNLAFLDILSEFSSKLLRQDKRTVYVYLEKFMTFQMSLRREDVWLPLMSYRNSLLAGGDDDTMSVI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	64-kDa C-terminal product
Molecular weight formula_weight	16049.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

VDPVEPMPTMTDQTTLVPNEEEAFALEPIDITVKETKAKRKRKLIVDSVKELDSKTIRAQLSDYSDIVTTLDLAPPTKKLMMWKETGGVEKLFSLPAQPLWNNRLLKLFTRCLTPLVPEDLRKRRKGGEADNLDEFLKEF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Transcriptional repressor CTCF
Molecular weight formula_weight	1231.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DVSVYDFEEE

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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8. Citations (1)

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Unit-cell length a length_a	79.029 Å
Unit-cell length b length_b	107.255 Å
Unit-cell length c length_c	176.490 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	45.800 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/qn/6qnx/6qnx.fit
pddf	/app/data/pr_computation/qn/6qnx/6qnx.pr.out
profile	/app/data/saxs_computation/qn/6qnx/6qnx.dat

Structure of the SA2/SCC1/CTCF complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cohesin subunit SA-2

State in the Current Structure

Other States of the Same Protein in the Database

64-kDa C-terminal product

State in the Current Structure

Other States of the Same Protein in the Database

Transcriptional repressor CTCF

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)