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Basic information

Entry
Database: EMDB / ID: EMD-64749
TitleStructure of C5a anaphylatoxin chemotactic receptor 2, C5aR2 in the Apo state
Map data
Sample
  • Complex: C5aR2 in the Apo state
    • Protein or peptide: C5a anaphylatoxin chemotactic receptor 2
KeywordsG protein coupled receptor / G protein / Membrane protein / Immunite system / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsTiwari D / Sano FK / Yadav MK / Sawada K / Ganguly M / Mishra S / Dalal A / Banerjee R / Nureki O / Shukla AK
Funding support United Kingdom, India, 3 items
OrganizationGrant numberCountry
Wellcome TrustIA/S/20/1/504916 United Kingdom
Science and Engineering Research Board (SERB)IPA/2020/000405 India
Science and Engineering Research Board (SERB)CRG/2022/002646 India
CitationJournal: Mol.Cell / Year: 2026
Title: Molecular mechanisms of naturally encoded signaling bias at the complement anaphylatoxin receptors.
Authors: Tiwari D / Sawada K / Dalal A / Mishra S / Li XX / Dent JC / Kim K / Yadav MK / Roy N / Ganguly M / Banerjee N / Stepniewski TM / Ahn D / Yamaguchi K / Oshima HS / Hashimoto K / Fung JN / ...Authors: Tiwari D / Sawada K / Dalal A / Mishra S / Li XX / Dent JC / Kim K / Yadav MK / Roy N / Ganguly M / Banerjee N / Stepniewski TM / Ahn D / Yamaguchi K / Oshima HS / Hashimoto K / Fung JN / Lerskiatiphanich T / Cui CS / Lee JD / Selent J / Inoue A / Clark RJ / Chung KY / Banerjee R / Sano FK / Woodruff TM / Nureki O / Shukla AK
History
DepositionMay 21, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64749.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 0.94857 Å
Density
Contour LevelBy AUTHOR: 0.043
Minimum - Maximum-0.6562327 - 0.965259
Average (Standard dev.)0.000292647 (±0.010428907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 265.5996 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : C5aR2 in the Apo state

EntireName: C5aR2 in the Apo state
Components
  • Complex: C5aR2 in the Apo state
    • Protein or peptide: C5a anaphylatoxin chemotactic receptor 2

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Supramolecule #1: C5aR2 in the Apo state

SupramoleculeName: C5aR2 in the Apo state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: C5a anaphylatoxin chemotactic receptor 2

MacromoleculeName: C5a anaphylatoxin chemotactic receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.014789 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSGND SVSYEYGDYS DLSDRPVDCL DGACLAIDP LRVAPLPLYA AIFLVGVPGN AMVAWVAGKV ARRRVGATWL LHLAVADLLC CLSLPILAVP IARGGHWPYG A VGCRALPS ...String:
MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSGND SVSYEYGDYS DLSDRPVDCL DGACLAIDP LRVAPLPLYA AIFLVGVPGN AMVAWVAGKV ARRRVGATWL LHLAVADLLC CLSLPILAVP IARGGHWPYG A VGCRALPS IILLTMYASV LLLAALSADL CFLALGPAWW STVQRACGVQ VACGAAWTLA LLLTVPSAIY RRLHQEHFPA RL QCVVDYG GSSSTENAVT AIRFLFGFLG PLVAVASCHS ALLCWAARRC RPLGTAIVVG FFVCWAPYHL LGLVLTVAAP NSA LLARAL RAEPLIVGLA LAHSCLNPML FLYFGRAQLR RSLPAACHWA LRESQGQDES VDSKKSTSHD LVSEMEV

UniProtKB: C5a anaphylatoxin chemotactic receptor 2

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 117521
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9v35:
Structure of C5a anaphylatoxin chemotactic receptor 2, C5aR2 in the Apo state

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