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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ynf
TitleStructure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8
Components
  • Atypical chemokine receptor 1
  • IL-8(9-77)
KeywordsIMMUNE SYSTEM / GPCR / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of chemokine production / regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / negative regulation of cell adhesion molecule production / CXCR chemokine receptor binding / ATF4 activates genes in response to endoplasmic reticulum stress / embryonic digestive tract development / neutrophil activation / induction of positive chemotaxis ...regulation of chemokine production / regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / negative regulation of cell adhesion molecule production / CXCR chemokine receptor binding / ATF4 activates genes in response to endoplasmic reticulum stress / embryonic digestive tract development / neutrophil activation / induction of positive chemotaxis / chemokine-mediated signaling pathway / C-C chemokine binding / positive regulation of neutrophil chemotaxis / chemokine activity / Chemokine receptors bind chemokines / negative regulation of G protein-coupled receptor signaling pathway / Interleukin-10 signaling / cellular response to interleukin-1 / regulation of cell adhesion / cellular response to fibroblast growth factor stimulus / neutrophil chemotaxis / Peptide ligand-binding receptors / response to endoplasmic reticulum stress / calcium-mediated signaling / response to molecule of bacterial origin / defense response / G protein-coupled receptor activity / recycling endosome / receptor internalization / positive regulation of angiogenesis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to tumor necrosis factor / transmembrane signaling receptor activity / signaling receptor activity / heparin binding / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / angiogenesis / Interleukin-4 and Interleukin-13 signaling / G alpha (i) signalling events / early endosome / intracellular signal transduction / G protein-coupled receptor signaling pathway / inflammatory response / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Duffy antigen/chemokine receptor / CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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
Interleukin-8 / 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: To Be Published
Title: Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8
Authors: Banerjee, R. / Khanppnavar, B. / Maharana, J. / Saha, S. / Korkhov, V.M. / Shukla, A.K.
History
DepositionMar 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Atypical chemokine receptor 1
D: IL-8(9-77)
E: IL-8(9-77)
A: Atypical chemokine receptor 1
G: IL-8(9-77)
H: IL-8(9-77)


Theoretical massNumber of molelcules
Total (without water)119,5516
Polymers119,5516
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 / Duffy antigen/chemokine receptor / Fy glycoprotein / GpFy / Glycoprotein D / Plasmodium vivax receptor


Mass: 41524.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACKR1, DARC, FY, GPD / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16570
#2: Protein
IL-8(9-77) / GCP/IL-8 protein III / IL8/NAP1 form VI


Mass: 9125.646 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL8, IL8 / Production host: Escherichia coli (E. coli) / References: UniProt: P10145
Has protein modificationY

-
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, CXCL8COMPLEXall0RECOMBINANT
2Duffy Antigen Receptor for Chemokines (DARC)/ACKR1COMPLEX#11RECOMBINANT
3CXCL8COMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Escherichia 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: 57.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
7Coot0.9.6model fitting
12cryoSPARC43D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 26196039
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 473012 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8JPS

8jps


Accession code: 8JPS / Source name: PDB / Type: experimental model

+
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