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7w1m

Cryo-EM structure of human cohesin-CTCF-DNA complex

Method: ELECTRON MICROSCOPY Dmax: 234.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Structural maintenance of chromosomes protein 1A

Homo sapiens

UniProt Q14683

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain A； UniProt 1–1233 Not recorded Structural maintenance of chromosomes protein 3 × 1 （Q9UQE7） Double-strand-break repair protein rad21 homolog × 1 （O60216） Cohesin subunit SA-1 × 1 （Q8WVM7） Nipped-B-like protein × 1 （Q6KC79） DNA (118-MER) × 1 DNA (118-MER) × 1 Transcriptional repressor CTCF × 1 （P49711） 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

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 7W1M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WG3 Cryo-EM structure of human Cohesin-NIPBL-DNA complex Deposited 2020-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain A 1–1233（1233 aa）
Mutation：E1157Q 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 mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–1233（1233 aa）
Mutation：E1157Q 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
8P0A Human Cohesin ATPase module Deposited 2023-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–200（200 aa）
Chain A 992–1233（242 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
8RO8 Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Apo closed P-loop conformation Deposited 2024-01-11 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 1–200（200 aa）
Chain A 992–1233（242 aa）
Mutation：E1157Q Mutation：E1157Q 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 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 1–200（200 aa）
Chain A 992–1233（242 aa）
Mutation：E1157Q Mutation：E1157Q 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–200（200 aa）
Chain C 992–1233（242 aa）
Mutation：E1157Q Mutation：E1157Q 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 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 1–200（200 aa）
Chain A 992–1233（242 aa）
Mutation：E1157Q Mutation：E1157Q 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–200（200 aa）
Chain C 992–1233（242 aa）
Mutation：E1157Q Mutation：E1157Q 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 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 1–200（200 aa）
Chain A 992–1233（242 aa）
Mutation：E1157Q Mutation：E1157Q 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 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 1–175（175 aa）
Chain A 1057–1233（177 aa）
Mutation：E1157Q Mutation：E1157Q 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 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 1–175（175 aa）
Chain A 1057–1233（177 aa）
Mutation：E1157Q Mutation：E1157Q 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 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 1–175（175 aa）
Chain A 1057–1233（177 aa）
Mutation：E1157Q Mutation：E1157Q 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 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 1–175（175 aa）
Chain A 1057–1233（177 aa）
Mutation：E1157Q Mutation：E1157Q 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 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 1–175（175 aa）
Chain A 1057–1233（177 aa）
Mutation：E1157Q Mutation：E1157Q 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

12 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMC1A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1233； UniProt 1–1233

Structural maintenance of chromosomes protein 3

Homo sapiens

UniProt Q9UQE7

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain B； UniProt 1–1217 Not recorded Structural maintenance of chromosomes protein 1A × 1 （Q14683） Double-strand-break repair protein rad21 homolog × 1 （O60216） Cohesin subunit SA-1 × 1 （Q8WVM7） Nipped-B-like protein × 1 （Q6KC79） DNA (118-MER) × 1 DNA (118-MER) × 1 Transcriptional repressor CTCF × 1 （P49711） 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

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 7W1M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WG3 Cryo-EM structure of human Cohesin-NIPBL-DNA complex Deposited 2020-04-04 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain B 1–1217（1217 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6WG4 Crystal structure of human SMC1-SMC3 hinge domain heterodimer in south-open conformation Deposited 2020-04-04 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 B 493–685（193 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；2% 1,4-dioxane, 0.1 Tris pH 8.0, 15% polyethylene glycol 3350
Resolution 2.31 Å R-free 0.235
6WG6 Crystal structure of human SMC1-SMC3 hinge domain heterodimer in north-open conformation Deposited 2020-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain B 466–713（248 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293.15 K；0.1 M sodium acetate pH 4.0, 15% polyethylene glycol 400
Resolution 3.54 Å R-free 0.288
6WG6 Crystal structure of human SMC1-SMC3 hinge domain heterodimer in north-open conformation Deposited 2020-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain D 466–713（248 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293.15 K；0.1 M sodium acetate pH 4.0, 15% polyethylene glycol 400
Resolution 3.54 Å R-free 0.288
6WG6 Crystal structure of human SMC1-SMC3 hinge domain heterodimer in north-open conformation Deposited 2020-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 466–713（248 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293.15 K；0.1 M sodium acetate pH 4.0, 15% polyethylene glycol 400
Resolution 3.54 Å R-free 0.288
6WG6 Crystal structure of human SMC1-SMC3 hinge domain heterodimer in north-open conformation Deposited 2020-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 466–713（248 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293.15 K；0.1 M sodium acetate pH 4.0, 15% polyethylene glycol 400
Resolution 3.54 Å R-free 0.288
6WG6 Crystal structure of human SMC1-SMC3 hinge domain heterodimer in north-open conformation Deposited 2020-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 466–713（248 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293.15 K；0.1 M sodium acetate pH 4.0, 15% polyethylene glycol 400
Resolution 3.54 Å R-free 0.288
6WG6 Crystal structure of human SMC1-SMC3 hinge domain heterodimer in north-open conformation Deposited 2020-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 466–713（248 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293.15 K；0.1 M sodium acetate pH 4.0, 15% polyethylene glycol 400
Resolution 3.54 Å R-free 0.288
6WGE Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1 Deposited 2020-04-05 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–1217（1217 aa）
Mutation：E1144Q 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
8P0A Human Cohesin ATPase module Deposited 2023-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–211（211 aa）
Chain B 979–1217（239 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
8ROH Human cohesin SMC3-HD(EQ)/RAD21-N complex - Apo conformation Deposited 2024-01-11 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 1–219（219 aa）
Chain A 971–1217（247 aa）
Mutation：E1144Q Mutation：E1144Q 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 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 1–211（211 aa）
Chain A 979–1217（239 aa）
Mutation：E1144Q Mutation：E1144Q 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 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 1–211（211 aa）
Chain A 979–1217（239 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 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 1–211（211 aa）
Chain A 979–1217（239 aa）
Mutation：E1144Q Mutation：E1144Q 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–211（211 aa）
Chain C 979–1217（239 aa）
Mutation：E1144Q Mutation：E1144Q 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 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 1–211（211 aa）
Chain A 979–1217（239 aa）
Mutation：E1144Q Mutation：E1144Q 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

10 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMC3_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–1217； UniProt 1–1217

Double-strand-break repair protein rad21 homolog

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain C； UniProt 1–631 Mutation：R172A, D279A, R450A Structural maintenance of chromosomes protein 1A × 1 （Q14683） Structural maintenance of chromosomes protein 3 × 1 （Q9UQE7） Cohesin subunit SA-1 × 1 （Q8WVM7） Nipped-B-like protein × 1 （Q6KC79） DNA (118-MER) × 1 DNA (118-MER) × 1 Transcriptional repressor CTCF × 1 （P49711） 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

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 7W1M 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 ligand/ion Different experimental method 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 method 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 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 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
6QNX Structure of the SA2/SCC1/CTCF complex Deposited 2019-02-12 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 × 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；293 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K
Resolution 2.70 Å
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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11 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 × 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 × 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 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 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 × 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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 3
Chains and sequence ranges Author chain C； PDBConstruct 1–631； UniProt 1–631

Cohesin subunit SA-1

Homo sapiens

UniProt Q8WVM7

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain D； UniProt 1–1258 Not recorded Structural maintenance of chromosomes protein 1A × 1 （Q14683） Structural maintenance of chromosomes protein 3 × 1 （Q9UQE7） Double-strand-break repair protein rad21 homolog × 1 （O60216） Nipped-B-like protein × 1 （Q6KC79） DNA (118-MER) × 1 DNA (118-MER) × 1 Transcriptional repressor CTCF × 1 （P49711） 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

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 7W1M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5QSM PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z57261895 Deposited 2019-05-25 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 459–915（457 aa）
Not recorded O2D 2-cyclohexyl-N-(4H-1,2,4-triazol-4-yl)acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.74 Å R-free 0.299
5QSM PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z57261895 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–915（457 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.74 Å R-free 0.299
5QSN PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z1272480091 Deposited 2019-05-25 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 459–915（457 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.66 Å R-free 0.288
5QSN PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z1272480091 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–915（457 aa）
Not recorded O2J (2R)-2-(methoxymethyl)-4-(pyridin-2-yl)morpholine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.66 Å R-free 0.288
5QSO PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z466628048 Deposited 2019-05-25 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 459–915（457 aa）
Not recorded O2M N-[(4-methyl-1,3-thiazol-2-yl)methyl]-1H-pyrazole-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.70 Å R-free 0.295
5QSO PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z466628048 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–915（457 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.70 Å R-free 0.295
5QSP PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434929 Deposited 2019-05-25 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 459–915（457 aa）
Not recorded LVV 4-[(4-methylphenyl)methyl]-1,4-thiazinane 1,1-dioxide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.89 Å R-free 0.263
5QSP PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434929 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–915（457 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.89 Å R-free 0.263
5QSQ PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z396380540 Deposited 2019-05-25 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 459–915（457 aa）
Not recorded HR5 ~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.48 Å R-free 0.289
5QSQ PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z396380540 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–915（457 aa）
Not recorded HR5 ~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.48 Å R-free 0.289
5QSR PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z136583524 Deposited 2019-05-25 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 459–915（457 aa）
Not recorded NU4 2-methyl-N-(pyridin-4-yl)furan-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 3.28 Å R-free 0.294
5QSR PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z136583524 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–915（457 aa）
Not recorded NU4 2-methyl-N-(pyridin-4-yl)furan-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 3.28 Å R-free 0.294
5QSS PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z33452282 Deposited 2019-05-25 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 459–915（457 aa）
Not recorded O2P N-(2-hydroxy-4-methylphenyl)-2-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 3.08 Å R-free 0.296
5QSS PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z33452282 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–915（457 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 3.08 Å R-free 0.296
5QST PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2447286438 Deposited 2019-05-25 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 C 86–420（335 aa）
Not recorded O3A (3S)-N-methyl-N-phenylpyrrolidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.58 Å R-free 0.271
5QST PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2447286438 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.58 Å R-free 0.271
5QST PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2447286438 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.58 Å R-free 0.271
5QST PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2447286438 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.58 Å R-free 0.271
5QSU PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434926 Deposited 2019-05-25 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 C 86–420（335 aa）
Not recorded O3D 4-[(furan-2-yl)methyl]-1lambda~6~,4-thiazinane-1,1-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.73 Å R-free 0.263
5QSU PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434926 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.73 Å R-free 0.263
5QSU PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434926 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.73 Å R-free 0.263
5QSU PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434926 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.73 Å R-free 0.263
5QSV PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434783 Deposited 2019-05-25 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 C 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.76 Å R-free 0.264
5QSV PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434783 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.76 Å R-free 0.264
5QSV PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434783 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.76 Å R-free 0.264
5QSV PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434783 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 86–420（335 aa）
Not recorded O3G N-benzyl-1-(4-fluorophenyl)methanamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.76 Å R-free 0.264
5QSW PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434884 Deposited 2019-05-25 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 C 86–420（335 aa）
Not recorded O3J 1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 3.03 Å R-free 0.267
5QSW PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434884 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 86–420（335 aa）
Not recorded O3J 1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 3.03 Å R-free 0.267
5QSW PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434884 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 86–420（335 aa）
Not recorded O3J 1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 3.03 Å R-free 0.267
5QSW PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434884 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 86–420（335 aa）
Not recorded O3J 1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 3.03 Å R-free 0.267
5QSX PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434812 Deposited 2019-07-16 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 C 86–420（335 aa）
Not recorded O3M 4-[(3,4-dihydroisoquinolin-2(1H)-yl)methyl]phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.34 Å R-free 0.275
5QSX PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434812 Deposited 2019-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.34 Å R-free 0.275
5QSX PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434812 Deposited 2019-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 86–420（335 aa）
Not recorded O3M 4-[(3,4-dihydroisoquinolin-2(1H)-yl)methyl]phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.34 Å R-free 0.275
5QSX PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434812 Deposited 2019-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 86–420（335 aa）
Not recorded O3M 4-[(3,4-dihydroisoquinolin-2(1H)-yl)methyl]phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.34 Å R-free 0.275
5QSY PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z755044716 Deposited 2019-05-25 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 459–915（457 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.40 Å R-free 0.297
5QSY PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z755044716 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–915（457 aa）
Not recorded K0J N-ethyl-1H-1,2,3-triazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.40 Å R-free 0.297
5QSZ PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z1267773786 Deposited 2019-05-25 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 459–915（457 aa）
Not recorded K3J N-ethyl-6-methylpyridazin-3-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 3.08 Å R-free 0.292
5QSZ PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z1267773786 Deposited 2019-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–915（457 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 3.08 Å R-free 0.292
6QB5 Crystal structure of the N-terminal region of human cohesin subunit STAG1 Deposited 2018-12-20 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 C 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Na/K Phosphate pH 6.0, 0.2 M NaCl, 34% PEG200
Resolution 2.02 Å R-free 0.245
6QB5 Crystal structure of the N-terminal region of human cohesin subunit STAG1 Deposited 2018-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Na/K Phosphate pH 6.0, 0.2 M NaCl, 34% PEG200
Resolution 2.02 Å R-free 0.245
6QB5 Crystal structure of the N-terminal region of human cohesin subunit STAG1 Deposited 2018-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 86–420（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Na/K Phosphate pH 6.0, 0.2 M NaCl, 34% PEG200
Resolution 2.02 Å R-free 0.245
6QB5 Crystal structure of the N-terminal region of human cohesin subunit STAG1 Deposited 2018-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 86–420（335 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Na/K Phosphate pH 6.0, 0.2 M NaCl, 34% PEG200
Resolution 2.02 Å R-free 0.245
6R7O Crystal structure of the central region of human cohesin subunit STAG1 Deposited 2019-03-29 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 459–915（457 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.31 Å R-free 0.264
6R7O Crystal structure of the central region of human cohesin subunit STAG1 Deposited 2019-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 459–915（457 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol
Resolution 2.31 Å R-free 0.264
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 86–420（335 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 86–420（335 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 459–915（457 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 459–915（457 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain D 1–1258（1258 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å

19 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STAG1_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–1258； UniProt 1–1258

Nipped-B-like protein

Homo sapiens

UniProt Q6KC79

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain E； UniProt 1164–2630 Not recorded Structural maintenance of chromosomes protein 1A × 1 （Q14683） Structural maintenance of chromosomes protein 3 × 1 （Q9UQE7） Double-strand-break repair protein rad21 homolog × 1 （O60216） Cohesin subunit SA-1 × 1 （Q8WVM7） DNA (118-MER) × 1 DNA (118-MER) × 1 Transcriptional repressor CTCF × 1 （P49711） 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

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 7W1M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WG3 Cryo-EM structure of human Cohesin-NIPBL-DNA complex Deposited 2020-04-04 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain E 1163–2804（1642 aa）
Not recorded 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain E 1163–2804（1642 aa）
Not recorded 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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NIPBL_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 1–1467； UniProt 1164–2630

Transcriptional repressor CTCF

Homo sapiens

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain H； UniProt 1–727 Not recorded Structural maintenance of chromosomes protein 1A × 1 （Q14683） Structural maintenance of chromosomes protein 3 × 1 （Q9UQE7） Double-strand-break repair protein rad21 homolog × 1 （O60216） Cohesin subunit SA-1 × 1 （Q8WVM7） Nipped-B-like protein × 1 （Q6KC79） DNA (118-MER) × 1 DNA (118-MER) × 1 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

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 7W1M 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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
6QNX Structure of the SA2/SCC1/CTCF complex Deposited 2019-02-12 Different construct Different oligomeric state 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 222–231（10 aa）
Not recorded No recorded non-water small molecule 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
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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 8
Chains and sequence ranges Author chain H； PDBConstruct 1–727； UniProt 1–727

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

SAXS profile for 7w1m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7w1m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7w1m
Deposition date deposition_date2021-11-19
Structure title titleCryo-EM structure of human cohesin-CTCF-DNA complex
Keywords keywords;Cohesin, NIPBL, CTCF, DNA, chromosome folding, topologically associating domain, chromatin loops, DNA loop extrusion, sister chromatid cohesion, complex, ATPase, HEAT repeat protein, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex ;; DNA BINDING PROTEIN/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier82.29 Å
Radius of gyration Rg (electron density) rg_electron80.47 Å
Forward intensity I(0) i04030010000.00
Molecular weight molecular_weight492450.0 kDa
Excluded volume excluded_volume598230 ų
Envelope volume envelope_volume1058200 ų
Hydration-shell volume shell_volume122900 ų
Envelope diameter envelope_diameter325.8 Å
Shell Rg shell_rg68.20 Å
Envelope Rg envelope_rg83.39 Å
Shape Rg shape_rg80.24 Å
Total Rg total_rg81.01 Å
Total atoms total_atoms34251
Residues n_residues3904
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax234.6 Å
Rg (real space) rg_real76.05 Å
Rg uncertainty (real space) rg_real_error1.34 Å
I(0) (real space) i0_real3.8720e+09
I(0) uncertainty (real space) i0_real_error7.7030e+07
Rg (reciprocal space) rg_reciprocal76.87 Å
I(0) (reciprocal space) i0_reciprocal3971000000.0000
Solution quality estimate total_estimate0.9155
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary74.1 Å
Skewness Skewness skewness0.567
Kurtosis Kurtosis kurtosis-0.303
Angular range angular_range— – 0.0950 Å−1
Current regularization parameter α current_alpha0.2650
Highest regularization parameter α highest_alpha172400000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 0.986; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.226
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

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8. Citations (1)

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9. Files and Curves (10)