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SMTL ID : 8yn7.1

Cryo-EM structure of histamine H3 receptor in complex with immethridine and miniGo

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x 01: 4-(1H-imidazol-4-ylmethyl)pyridine

01.1:

8 residues within 4Å:

Chain E: D.167, Y.168, C.171, E.259, Y.427, F.451, L.454, W.455

7 PLIP interactions:

7 interactions with chain E

Hydrophobic interactions: E:Y.168, E:Y.427, E:L.454
pi-Stacking: E:Y.168, E:Y.427, E:F.451, E:W.455

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.2:	6 residues within 4Å: Chain E: L.93, L.96, V.148, E.448, T.449, W.452 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.93, E:L.96, E:V.148, E:E.448, E:E.448, E:W.452, E:W.452
CLR.3:	7 residues within 4Å: Chain E: I.131, V.206, M.209, L.210, W.213 Ligands: CLR.5, CLR.6 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.131, E:I.131, E:V.206, E:W.213, E:W.213
CLR.4:	8 residues within 4Å: Chain E: F.176, V.179, L.180, Y.183, K.208, L.215, L.258, T.262 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.176, E:F.176, E:V.179, E:L.180, E:Y.183, E:L.215, E:L.215, E:L.258, E:T.262 Hydrogen bonds: E:K.208
CLR.5:	7 residues within 4Å: Chain E: M.109, F.112, V.113, L.127, I.131, L.135 Ligands: CLR.3 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.112, E:L.127, E:I.131, E:L.135
CLR.6:	8 residues within 4Å: Chain E: G.158, K.161, L.162, V.165, W.213, F.217, L.225 Ligands: CLR.3 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:K.161, E:L.162, E:V.165, E:F.217, E:F.217, E:F.217, E:L.225, E:L.225

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Zhang, X. et al., Structural basis of ligand recognition and activation of the histamine receptor family. Nat Commun (2024)

Release Date

2024-10-16

Peptides

Engineered guanine nucleotide-binding protein G(o) subunit alpha,Guanine nucleotide-binding protein G(o) subunit alpha: A
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: B
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: C
Antibody fragment scFv16: D
Histamine H3 receptor: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
R

Membrane

We predict this structure to be a membrane protein.
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Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Engineered guanine nucleotide-binding protein G(o) subunit alpha,Guanine nucleotide-binding protein G(o) subunit alpha

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

Antibody fragment scFv16

Histamine H3 receptor

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

Background

Transparent

Resolution

Low
Medium
High
Extreme

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