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SMTL ID : 7ykd.1

Cryo-EM structure of the human chemerin receptor 1 complex with the C-terminal nonapeptide of chemerin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x TYR- PHE- PRO- GLY- GLN- PHE- ALA- PHE- SER: Retinoic acid receptor responder protein 2(Non-covalent)

TYR-PHE-PRO-GLY-GLN-PHE-ALA-PHE-SER.1:

23 residues within 4Å:

Chain A: F.88, H.95, Y.103, N.116, L.119, I.120, M.123, S.174, R.178, L.183, S.188, C.189, F.190, N.191, R.224, Y.276, E.283, H.286, F.294, S.295, L.298, T.302, I.306

28 PLIP interactions:

28 interactions with chain A

Hydrophobic interactions: A:F.88, A:Y.103, A:L.119, A:I.120, A:L.183, A:F.190, A:F.190, A:F.190, A:Y.276, A:E.283, A:H.286, A:F.294, A:L.298, A:L.298, A:T.302, A:I.306
Hydrogen bonds: A:S.174, A:R.178, A:R.178, A:S.188, A:N.191, A:N.191, A:R.224, A:R.224, A:Y.276, A:Y.276, A:E.283, A:E.283

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.2:	9 residues within 4Å: Chain A: K.260, V.263, T.264, I.267, T.268, L.271, C.272, L.304 Ligands: CLR.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.260, A:V.263, A:I.267, A:L.271
CLR.3:	5 residues within 4Å: Chain A: S.135, I.139, L.143, W.146 Ligands: CLR.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.139, A:L.143, A:W.146, A:W.146, A:W.146
CLR.4:	5 residues within 4Å: Chain A: F.128, I.132, M.158, A.159 Ligands: CLR.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.128, A:F.128, A:I.132, A:M.158, A:A.159
CLR.5:	10 residues within 4Å: Chain A: L.79, N.80, V.83, L.87, F.117, L.118, H.121, Y.157, M.161, W.164 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.79, A:V.83, A:L.87, A:F.117, A:L.118, A:Y.157, A:W.164 Hydrogen bonds: A:N.80, A:Y.157
CLR.6:	6 residues within 4Å: Chain A: K.257, K.260, I.261, M.311, I.314 Ligands: CLR.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.260, A:I.261, A:I.314

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Wang, J. et al., Cryo-EM structure of the human chemerin receptor 1-Gi protein complex bound to the C-terminal nonapeptide of chemerin. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-04-19

Peptides

Chemerin-like receptor 1: A
Guanine nucleotide-binding protein G(i) subunit alpha-1: B
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: C
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: D
scFV16: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
G

E
S

Membrane

We predict this structure to be a membrane protein.
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Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Chemerin-like receptor 1

Guanine nucleotide-binding protein G(i) subunit alpha-1

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

scFV16

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
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Extreme

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