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- EMDB-63220: Cryo-EM structure of antagonist-bounded inactive human GPR4 -

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Basic information

Entry
Database: EMDB / ID: EMD-63220
TitleCryo-EM structure of antagonist-bounded inactive human GPR4
Map data
Sample
  • Organelle or cellular component: antagonist-bounded inactive GPR4
    • Protein or peptide: Heavy chain of anti-Bril Fab
    • Protein or peptide: Light chain of anti-Bril Fab
    • Protein or peptide: G-protein coupled receptor 4,Soluble cytochrome b562
  • Ligand: NE52-QQ57
KeywordsGPCR / class A / GPR4 / cryo-EM / protein sensing / inactive state / antagonist-bounded / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


glomerular mesangial cell development / regulation of vascular permeability / Class A/1 (Rhodopsin-like receptors) / response to acidic pH / angiogenesis involved in wound healing / positive regulation of Rho protein signal transduction / regulation of cell adhesion / negative regulation of angiogenesis / electron transport chain / G protein-coupled receptor activity ...glomerular mesangial cell development / regulation of vascular permeability / Class A/1 (Rhodopsin-like receptors) / response to acidic pH / angiogenesis involved in wound healing / positive regulation of Rho protein signal transduction / regulation of cell adhesion / negative regulation of angiogenesis / electron transport chain / G protein-coupled receptor activity / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsChen LN / Zhou H / Xi K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of antagonist-bounded inactive human GPR4
Authors: Chen LN / Zhou H / Xi K
History
DepositionJan 19, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63220.png

Downloads & links

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Map

FileDownload / File: emd_63220.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 224 pix.
= 208.32 Å		0.93 Å/pix.
x 224 pix.
= 208.32 Å		0.93 Å/pix.
x 224 pix.
= 208.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.33433053 - 0.7778094
Average (Standard dev.)0.00069635245 (±0.017571846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 208.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63220_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63220_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : antagonist-bounded inactive GPR4

EntireName: antagonist-bounded inactive GPR4
Components
  • Organelle or cellular component: antagonist-bounded inactive GPR4
    • Protein or peptide: Heavy chain of anti-Bril Fab
    • Protein or peptide: Light chain of anti-Bril Fab
    • Protein or peptide: G-protein coupled receptor 4,Soluble cytochrome b562
  • Ligand: NE52-QQ57

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Supramolecule #1: antagonist-bounded inactive GPR4

SupramoleculeName: antagonist-bounded inactive GPR4 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Heavy chain of anti-Bril Fab

MacromoleculeName: Heavy chain of anti-Bril Fab / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.00885 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDKTHT

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Macromolecule #2: Light chain of anti-Bril Fab

MacromoleculeName: Light chain of anti-Bril Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.586205 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #3: G-protein coupled receptor 4,Soluble cytochrome b562

MacromoleculeName: G-protein coupled receptor 4,Soluble cytochrome b562 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.274223 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGNHTWEGCH VDSRVDHLFP PSLYIFVIGV GLPTNCLALW AAYRQVQQRN ELGVYLMNLS IADLLYICTL PLWVDYFLHH DNWIHGPGS CKLFGFIFYT NIYISIAFLC CISVDRYLAV AHPLRFARLR RVKTAVAVSS VVWATELGAN SAPLFHDELF R DRYNHTFC ...String:
MGNHTWEGCH VDSRVDHLFP PSLYIFVIGV GLPTNCLALW AAYRQVQQRN ELGVYLMNLS IADLLYICTL PLWVDYFLHH DNWIHGPGS CKLFGFIFYT NIYISIAFLC CISVDRYLAV AHPLRFARLR RVKTAVAVSS VVWATELGAN SAPLFHDELF R DRYNHTFC FEKFPMEGWV AWMNLYRVFV GFLFPWALML LSYRGILRAV DKRKADLEDN WETLNDNLKV IEKADNAAQV KD ALTKMRA AALDAQKATD KSPDSPEMKD FRHGFDILVG QIDDALKLAN EGKVKEAQAA AEQLKTTRNA YIQKYLEYLD GLE RIKRLA LSLIAIVLVC FAPYHVLLLS RSAIYLGRPW DCGFEERVFS AYHSSLAFTS LNCVADPILY CLVNEGARSD VAKA LHNLL RFLASDKPQE MANASLTLET PLTSKRNSTA KAMTGSWAAT PPSQGDQVQL KMLPPAQ

UniProtKB: G-prodeshotein coupled receptor 4, Soluble cytochrome b562, G-prodeshotein coupled receptor 4

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Macromolecule #4: NE52-QQ57

MacromoleculeName: NE52-QQ57 / type: ligand / ID: 4 / Number of copies: 1 / Formula: A1L1E
Molecular weightTheoretical: 416.519 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 469564
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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