SMTL ID : 9d9z.1

Structure of human UBR4-KCMF1-CaM E3 ligase complex (Silencing Factor of the Integrated stress response, SiFI)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

20 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.1684, T.1685, C.1713, C.1716, C.1736 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.1684, A:C.1713, A:C.1716, A:C.1736 ZN.2: 4 residues within 4Å: Chain A: C.1701, C.1704, H.1721, H.1724 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.1701, A:C.1704, A:H.1721, A:H.1724 ZN.3: 4 residues within 4Å: Chain A: C.3682, C.3685, C.3696, C.3699 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.3682, A:C.3685, A:C.3696, A:C.3699 ZN.4: 5 residues within 4Å: Chain A: C.3706, C.3709, S.3711, C.3722, C.3725 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.3706, A:C.3709, A:C.3722, A:C.3725 ZN.5: 5 residues within 4Å: Chain A: C.3554, C.3557, S.3890, C.3894, C.3897 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.3554, A:C.3557, A:C.3894, A:C.3897 ZN.6: 4 residues within 4Å: Chain A: C.1716, C.1720, C.1738, C.1746 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.1716, A:C.1720, A:C.1738, A:C.1746 ZN.7: 5 residues within 4Å: Chain B: C.1684, C.1713, C.1716, C.1736 Ligands: ZN.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1684, B:C.1713, B:C.1716, B:C.1736 ZN.8: 5 residues within 4Å: Chain B: C.1701, T.1703, C.1704, H.1721, H.1724 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1701, B:C.1704, B:H.1721, B:H.1724 ZN.9: 4 residues within 4Å: Chain B: C.3682, C.3685, C.3696, C.3699 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.3682, B:C.3685, B:C.3696, B:C.3699 ZN.10: 5 residues within 4Å: Chain B: C.3706, C.3709, S.3711, C.3722, C.3725 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.3706, B:C.3709, B:C.3722, B:C.3725 ZN.11: 4 residues within 4Å: Chain B: C.3554, C.3557, C.3894, C.3897 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.3554, B:C.3557, B:C.3894, B:C.3897 ZN.12: 6 residues within 4Å: Chain B: C.1716, C.1720, C.1738, C.1746, A.1748 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1716, B:C.1720, B:C.1738, B:C.1746 ZN.17: 5 residues within 4Å: Chain E: C.9, C.12, C.33, S.35, C.36 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.9, E:C.12, E:C.33, E:C.36 ZN.18: 6 residues within 4Å: Chain E: C.24, C.27, R.45, H.46, T.47, H.50 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.24, E:C.27, E:H.46, E:H.50 ZN.19: 4 residues within 4Å: Chain E: C.80, C.83, H.96, H.101 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.80, E:C.83, E:H.96, E:H.101 ZN.20: 4 residues within 4Å: Chain E: C.110, C.113, H.131, H.136 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.110, E:C.113, E:H.131, E:H.136 ZN.21: 5 residues within 4Å: Chain F: C.9, C.12, C.33, S.35, C.36 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.9, F:C.12, F:C.33, F:C.36 ZN.22: 6 residues within 4Å: Chain F: C.24, C.27, R.45, H.46, T.47, H.50 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.24, F:C.27, F:H.46, F:H.50 ZN.23: 4 residues within 4Å: Chain F: C.80, C.83, H.96, H.101 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.80, F:C.83, F:H.96, F:H.101 ZN.24: 4 residues within 4Å: Chain F: C.110, C.113, H.131, H.136 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.110, F:C.113, F:H.131, F:H.136

4 x CA: CALCIUM ION(Non-covalent)

CA.13: 6 residues within 4Å: Chain C: D.130, D.132, D.134, Q.136, E.140, E.141 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.132, C:E.141 CA.14: 5 residues within 4Å: Chain C: D.94, D.96, Y.100, S.102, E.105 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:Y.100 CA.15: 6 residues within 4Å: Chain D: Y.100, D.132, D.134, Q.136, E.140, E.141 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.141 CA.16: 5 residues within 4Å: Chain D: D.94, D.96, N.98, S.102, E.105 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.96, D:E.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Molecular basis of SIFI activity in the integrated stress response. Nature (2025)

Release Date

2025-06-11

Peptides

UBR4 (endogenously FLAG-tagged at the N-terminus),E3 ubiquitin-protein ligase UBR4,E3 ubiquitin-protein ligase UBR4,E3 ubiquitin-protein ligase UBR4: AB
Calmodulin-1: CD
E3 ubiquitin-protein ligase KCMF1: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

UBR4 (endogenously FLAG-tagged at the N-terminus),E3 ubiquitin-protein ligase UBR4,E3 ubiquitin-protein ligase UBR4,E3 ubiquitin-protein ligase UBR4

Calmodulin-1

E3 ubiquitin-protein ligase KCMF1

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