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- PDB-9u4j: Cryo-EM structure of the hGPR4-apo Receptor in pH 7.8 -

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Basic information

Entry
Database: PDB / ID: 9u4j
TitleCryo-EM structure of the hGPR4-apo Receptor in pH 7.8
ComponentsG-protein coupled receptor 4,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / pH7.8 / hGPR4 / apo / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM
Function / homology
Function and homology information


glomerular mesangial cell development / Class A/1 (Rhodopsin-like receptors) / regulation of vascular permeability / angiogenesis involved in wound healing / response to acidic pH / positive regulation of Rho protein signal transduction / regulation of cell adhesion / cellular response to acidic pH / negative regulation of angiogenesis / electron transport chain ...glomerular mesangial cell development / Class A/1 (Rhodopsin-like receptors) / regulation of vascular permeability / angiogenesis involved in wound healing / response to acidic pH / positive regulation of Rho protein signal transduction / regulation of cell adhesion / cellular response to acidic pH / negative regulation of angiogenesis / electron transport chain / G protein-coupled receptor activity / positive regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / periplasmic space / electron transfer activity / iron ion binding / G protein-coupled receptor signaling pathway / 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. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Soluble cytochrome b562 / G-protein coupled receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli O157:H7 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhong, Y.N. / Liu, Z.L. / Guo, L.L. / Sun, J.P. / Yang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81773704 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the hGPR4 apo-BRIL Fab Receptor in pH 7.8
Authors: Zhong, Y.N. / Liu, Z.L. / Yang, F. / Sun, J.P. / Yang, F.
History
DepositionMar 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: G-protein coupled receptor 4,Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)33,1181
Polymers33,1181
Non-polymers00
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: Protein G-protein coupled receptor 4,Soluble cytochrome b562 / G-protein coupled receptor 6C.l / GPR6C.l / Cytochrome b-562


Mass: 33117.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli O157:H7 (bacteria)
Gene: GPR4, cybC, Z5846, ECs5213
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
References: UniProt: P46093, UniProt: P0ABE8
Has protein modificationN

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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: Cryo-EM structure of the receptor of the hGPR4 apo-BRIL Fab complex in pH 7.8
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Escherichia coli O157:H7 (bacteria)83334
Source (recombinant)Organism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
Buffer solutionpH: 7.8
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: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1274935 / Symmetry type: POINT

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