[English] 日本語
Yorodumi
- EMDB-80132: Unknown entry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-80132
TitleStructure of mC5aR2 in complex with mC5a-desArg (Monomer)
Map data
Sample
  • Complex: mC5aR2 bound to mC5a-desArg (Monomer)
    • Protein or peptide: C5a anaphylatoxin chemotactic receptor 2
    • Protein or peptide: Complement C5
KeywordsG protein coupled receptor / G protein / Membrane protein / Immunite system / SIGNALING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsTiwari D / Ganguly M / Banerjee R / Shukla AK / Mishra S / Dalal A / Nureki O
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
DepositionApr 6, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileReleased
Voxel sizeX=Y=Z: 0.91094 Å
Density
Contour LevelBy AUTHOR: 7.36
Minimum - Maximum-28.242972999999999 - 72.885050000000007
Average (Standard dev.)-0.000000000001137 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 233.20064 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : mC5aR2 bound to mC5a-desArg (Monomer)

EntireName: mC5aR2 bound to mC5a-desArg (Monomer)
Components
  • Complex: mC5aR2 bound to mC5a-desArg (Monomer)
    • Protein or peptide: C5a anaphylatoxin chemotactic receptor 2
    • Protein or peptide: Complement C5

-
Supramolecule #1: mC5aR2 bound to mC5a-desArg (Monomer)

SupramoleculeName: mC5aR2 bound to mC5a-desArg (Monomer) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

-
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: Mus musculus (house mouse)
Molecular weightTheoretical: 44.13707 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSMNH TTSEYYDYEY DHEHYSDLPD VPVDCPAGT CFTSDVYLIV LLVLYAAVFL VGVPGNTLVA WVTWKESRHR LGASWFLHLT MADLLCCVSL PFLAVPIAQK G HWPYGAAG ...String:
MGKTIIALSY IFCLVFADYK DDDDAANFTP VNGSSGNQSV RLVTSSSLEV LFQGPGSMNH TTSEYYDYEY DHEHYSDLPD VPVDCPAGT CFTSDVYLIV LLVLYAAVFL VGVPGNTLVA WVTWKESRHR LGASWFLHLT MADLLCCVSL PFLAVPIAQK G HWPYGAAG CWLLSSITIL SMYASVLLLT GLSGDLFLLA FRPSWKGADH RTFGVRVVQA SSWMLGLLLT VPSAVYRRLL QE HYPPRLV CGIDYGGSVS AEVAITTVRF LFGFLGPLVF MAGCHGILQR QMARRHWPLG TAVVVGFFIC WTPYHVLRVI IAA APPHSL LLARVLEAEP LFNGLALAHS ALNPIMFLYF GRKQLCKSLQ AACHWALRDP QDEESAVTKV SISTSHEMVS EMPV

UniProtKB: C5a anaphylatoxin chemotactic receptor 2

-
Macromolecule #2: Complement C5

MacromoleculeName: Complement C5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 8.762245 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NLHLLRQKIE EQAAKYKHSV PKKCCYDGAR VNFYETCEER VARVTIGPLC IRAFNECCTI ANKIRKESPH KPVQLG

UniProtKB: Complement C5

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 75.0 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

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 285775
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.3)

-
Atomic model buiding 1

Initial modelPDB ID:

9wdi


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-25if:
Structure of mC5aR2 in complex with mC5a-desArg (Monomer)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more