[English] 日本語
Yorodumi
- PDB-8jps: Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jps
TitleStructure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Composite map)
Components
  • Atypical chemokine receptor 1
  • C-C motif chemokine 7
KeywordsIMMUNE SYSTEM / GPCR / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of chemokine production / CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway ...regulation of chemokine production / CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / cytoskeleton organization / Peptide ligand-binding receptors / neutrophil chemotaxis / G protein-coupled receptor activity / response to gamma radiation / recycling endosome / defense response / cellular response to type II interferon / intracellular calcium ion homeostasis / transmembrane signaling receptor activity / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / signaling receptor activity / heparin binding / regulation of cell shape / early endosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Duffy antigen/chemokine receptor / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like
Similarity search - Domain/homology
C-C motif chemokine 7 / Atypical chemokine receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsBanerjee, R. / Khanppnavar, B. / Maharana, J. / Saha, S. / Korkhov, V.M. / Shukla, A.K.
Funding support India, United Kingdom, 4items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR29041/BRB/10/1697/2018 India
Wellcome TrustIA/S/20/1/504916 United Kingdom
Science and Engineering Research Board (SERB)SPR/2020/000408 India
Science and Engineering Research Board (SERB)IPA/2020/000405 India
CitationJournal: Cell(Cambridge,Mass.) / Year: 2024
Title: Molecular mechanism of distinct chemokine engagement and functional divergence of the human Duffy antigen receptor
Authors: Saha, S. / Khanppnavar, B. / Maharana, J. / Kim, H. / Carino, C.M.C. / Daly, C. / Houston, S. / Sharma, S. / Zaidi, N. / Dalal, A. / Mishra, S. / Ganguly, M. / Tiwari, D. / Kumari, P. / ...Authors: Saha, S. / Khanppnavar, B. / Maharana, J. / Kim, H. / Carino, C.M.C. / Daly, C. / Houston, S. / Sharma, S. / Zaidi, N. / Dalal, A. / Mishra, S. / Ganguly, M. / Tiwari, D. / Kumari, P. / Jhingan, G.D. / Yadav, P.N. / Plouffe, B. / Inoue, A. / Chung, K.Y. / Banerjee, R. / Korkhov, V.M. / Shukla, A.K.
History
DepositionJun 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Atypical chemokine receptor 1
D: C-C motif chemokine 7
A: Atypical chemokine receptor 1
C: C-C motif chemokine 7


Theoretical massNumber of molelcules
Total (without water)71,3374
Polymers71,3374
Non-polymers00
Water00
1


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

-
Components

#1: Protein Atypical chemokine receptor 1


Mass: 28073.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACKR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16570
#2: Protein C-C motif chemokine 7 / Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small- ...Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small-inducible cytokine A7


Mass: 7594.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL7, MCP3, SCYA6, SCYA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P80098

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7COMPLEXall0RECOMBINANT
2Duffy Antigen Receptor for Chemokines (DARC)/ACKR1COMPLEX#11RECOMBINANT
3CCL7COMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
7Coot0.9.6model fitting
9PHENIX1.20.1model refinement
13cryoSPARC43D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 25479169
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 308174 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.014862
ELECTRON MICROSCOPYf_angle_d0.9936652
ELECTRON MICROSCOPYf_dihedral_angle_d5.102660
ELECTRON MICROSCOPYf_chiral_restr0.046817
ELECTRON MICROSCOPYf_plane_restr0.009805

+
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://pdbjlvh1.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