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- PDB-9lmp: Cryo-EM structure of antagonist-bounded inactive human GPR4 -

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Basic information

Entry
Database: PDB / ID: 9lmp
TitleCryo-EM structure of antagonist-bounded inactive human GPR4
Components
  • G-protein coupled receptor 4,Soluble cytochrome b562
  • Heavy chain of anti-Bril Fab
  • Light chain of anti-Bril Fab
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / GPCR / class A / GPR4 / cryo-EM / protein sensing / inactive state / antagonist-bounded / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


glomerular mesangial cell development / regulation of vascular permeability / response to acidic pH / Class A/1 (Rhodopsin-like receptors) / angiogenesis involved in wound healing / positive regulation of Rho protein signal transduction / regulation of cell adhesion / negative regulation of angiogenesis / G protein-coupled receptor activity / electron transport chain ...glomerular mesangial cell development / regulation of vascular permeability / response to acidic pH / Class A/1 (Rhodopsin-like receptors) / angiogenesis involved in wound healing / positive regulation of Rho protein signal transduction / regulation of cell adhesion / negative regulation of angiogenesis / G protein-coupled receptor activity / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of inflammatory response / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / heme binding / plasma membrane
Similarity search - Function
G protein-coupled receptor 4 orphan / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
: / Soluble cytochrome b562 / G-prodeshotein coupled receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsChen, L.N. / Zhou, H. / Xi, K. / Cheng, S.Z. / Liu, Y.F. / Fu, Y.F. / Ma, X.Y. / Xu, P. / Ji, S.Y. / Wang, W.W. ...Chen, L.N. / Zhou, H. / Xi, K. / Cheng, S.Z. / Liu, Y.F. / Fu, Y.F. / Ma, X.Y. / Xu, P. / Ji, S.Y. / Wang, W.W. / Shen, D.D. / Zhang, H.B. / Shen, Q.Y. / Chai, R. / Zhang, M. / Yang, L. / Han, F. / Mao, C.Y. / Cai, X.J. / Zhang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of antagonist-bounded inactive human GPR4
Authors: Chen, L.N. / Zhou, H. / Xi, K.
History
DepositionJan 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Structure summary / Category: audit_author / em_admin / em_author_list / Item: _em_admin.last_update
Revision 1.1Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_author_list / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of anti-Bril Fab
L: Light chain of anti-Bril Fab
R: G-protein coupled receptor 4,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2864
Polymers100,8693
Non-polymers4171
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody Heavy chain of anti-Bril Fab


Mass: 25008.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Light chain of anti-Bril Fab


Mass: 23586.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein G-protein coupled receptor 4,Soluble cytochrome b562 / G-protein coupled receptor 6C.l / GPR6C.l / Cytochrome b-562


Mass: 52274.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPR4, cybC / Production host: Homo sapiens (human) / References: UniProt: P46093, UniProt: P0ABE7
#4: Chemical ChemComp-A1L1E / NE52-QQ57 / 2-[4-[(2-ethyl-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-3-yl)methyl]phenyl]-5-piperidin-4-yl-1,3,4-oxadiazole


Mass: 416.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28N6O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: antagonist-bounded inactive GPR4 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 469564 / Symmetry type: POINT
RefinementHighest resolution: 2.65 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0186382
ELECTRON MICROSCOPYf_angle_d1.5878695
ELECTRON MICROSCOPYf_dihedral_angle_d11.6922223
ELECTRON MICROSCOPYf_chiral_restr0.076981
ELECTRON MICROSCOPYf_plane_restr0.0091096

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