[English] 日本語
Yorodumi
- EMDB-37212: Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37212
TitleStructure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Receptor original map)
Map data
Sample
  • Complex: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Receptor original map)
    • Complex: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1
    • Complex: CCL7
KeywordsGPCR / SIGNALING PROTEIN / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsBanerjee R / Khanppnavar B / Maharana J / Saha S / Korkhov VM / Shukla AK
Funding support India, United Kingdom, 4 items
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 CMC / Daly C / Houston S / Sharma S / Zaidi N / Dalal A / Mishra S / Ganguly M / Tiwari D / Kumari P / Jhingan GD / Yadav PN / Plouffe B ...Authors: Saha S / Khanppnavar B / Maharana J / Kim H / Carino CMC / Daly C / Houston S / Sharma S / Zaidi N / Dalal A / Mishra S / Ganguly M / Tiwari D / Kumari P / Jhingan GD / Yadav PN / Plouffe B / Inoue A / Chung KY / Banerjee R / Korkhov VM / Shukla AK
History
DepositionAug 17, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37212.png

Downloads & links

-
Map

FileDownload / File: emd_37212.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 288 pix.
= 270.4 Å		0.94 Å/pix.
x 288 pix.
= 270.4 Å		0.94 Å/pix.
x 288 pix.
= 270.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-2.0499685 - 2.6357322
Average (Standard dev.)-0.0018620354 (±0.049385358)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 270.40033 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_37212_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_37212_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex wit...

EntireName: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Receptor original map)
Components
  • Complex: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Receptor original map)
    • Complex: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1
    • Complex: CCL7

-
Supramolecule #1: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex wit...

SupramoleculeName: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CCL7 (Receptor original map)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #2: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1

SupramoleculeName: Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

-
Supramolecule #3: CCL7

SupramoleculeName: CCL7 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

-
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 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 25479169
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 308174
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

+
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