SMTL ID : 7w1m.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: K.13, S.14, G.35, S.36, G.37, K.38, S.39, N.40, R.57, I.65, H.66, G.67, P.69, V.1211 Chain B: F.1102, R.1110, Q.1114, S.1116, Q.1119 Ligands: BEF.2 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:K.13, A:K.13, A:K.13, A:S.14, A:G.35, A:G.37, A:K.38, A:S.39, A:S.39, A:G.67, B:R.1110, B:Q.1114, B:S.1116, B:Q.1119, B:Q.1119 Salt bridges: A:K.38, A:R.57, A:R.57 ADP.3: 21 residues within 4Å: Chain A: K.1120, R.1121, R.1123, N.1127, S.1129, E.1132 Chain B: R.12, S.13, G.35, G.37, K.38, S.39, N.40, A.63, L.65, H.66, E.67, G.68, Q.141, F.1191 Ligands: BEF.4 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.12, B:G.37, B:K.38, B:S.39, B:S.39, B:S.39, B:N.40, B:L.65, B:E.67, B:Q.141, A:R.1121, A:R.1123, A:N.1127, A:S.1129 Salt bridges: B:R.12

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 9 residues within 4Å: Chain A: P.33, N.34, G.35, S.36, K.38, E.1157 Chain B: S.1116, G.1117 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) BEF.4: 8 residues within 4Å: Chain A: S.1129 Chain B: R.33, G.35, S.36, G.37, K.38, Q.141 Ligands: ADP.3 No protein-ligand interaction detected (PLIP)

11 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain H: C.268, L.270, C.271, H.284, H.288 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.268, H:C.271, H:H.284, H:H.288 ZN.6: 4 residues within 4Å: Chain H: C.296, C.299, H.312, H.316 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.296, H:C.299, H:H.312, H:H.316 ZN.7: 4 residues within 4Å: Chain H: C.324, C.327, H.340, H.345 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.324, H:C.327, H:H.340, H:H.345 ZN.8: 4 residues within 4Å: Chain H: C.353, C.356, H.369, H.373 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.353, H:C.356, H:H.369, H:H.373 ZN.9: 5 residues within 4Å: Chain H: C.381, L.383, C.384, H.397, H.401 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.381, H:C.384, H:H.397, H:H.401 ZN.10: 4 residues within 4Å: Chain H: C.409, C.412, H.425, H.430 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.409, H:C.412, H:H.425, H:H.430 ZN.11: 4 residues within 4Å: Chain H: C.439, C.442, H.455, H.460 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.439, H:C.442, H:H.455, H:H.460 ZN.12: 5 residues within 4Å: Chain H: C.469, Y.471, C.472, H.485, H.489 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.469, H:C.472, H:H.485, H:H.489 ZN.13: 5 residues within 4Å: Chain H: C.497, Q.499, C.500, H.513, H.517 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.497, H:C.500, H:H.513, H:H.517 ZN.14: 4 residues within 4Å: Chain H: C.525, C.528, H.541, H.546 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.525, H:C.528, H:H.541, H:H.546 ZN.15: 5 residues within 4Å: Chain H: C.557, C.560, G.561, H.573, C.577 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.557, H:C.560, H:H.573, H:C.577

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., CTCF and R-loops are boundaries of cohesin-mediated DNA looping. Mol.Cell (2023)

Release Date

2023-05-31

Peptides

Structural maintenance of chromosomes protein 1A: A
Structural maintenance of chromosomes protein 3: B
Double-strand-break repair protein rad21 homolog: C
Cohesin subunit SA-1: D
Nipped-B-like protein: E
Transcriptional repressor CTCF: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

H
H

Structural maintenance of chromosomes protein 1A

Structural maintenance of chromosomes protein 3

Double-strand-break repair protein rad21 homolog

Cohesin subunit SA-1

Nipped-B-like protein

Transcriptional repressor CTCF

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