[English] 日本語
Yorodumi
- EMDB-61049: Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61049
TitleApo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue
Map data
Sample
  • Complex: Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue
    • Protein or peptide: P2Y purinoceptor 14,Soluble cytochrome b562
    • Protein or peptide: Antibody 1b3 Fab Heavy chain
    • Protein or peptide: Antibody 1b3 Fab Light chain
KeywordsComplex / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


G protein-coupled UDP receptor activity / P2Y receptors / G protein-coupled purinergic nucleotide receptor activity / hematopoietic stem cell homeostasis / electron transport chain / G alpha (i) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding ...G protein-coupled UDP receptor activity / P2Y receptors / G protein-coupled purinergic nucleotide receptor activity / hematopoietic stem cell homeostasis / electron transport chain / G alpha (i) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / heme binding / membrane / plasma membrane
Similarity search - Function
P2Y14 purinoceptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Soluble cytochrome b562 / P2Y purinoceptor 14
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang TX / Tang WQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue
Authors: Wang TX / Tang WQ
History
DepositionAug 2, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61049.png

Downloads & links

-
Map

FileDownload / File: emd_61049.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-4.5468755 - 6.271559
Average (Standard dev.)-0.001998312 (±0.070822075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_61049_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61049_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61049_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue

EntireName: Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue
Components
  • Complex: Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue
    • Protein or peptide: P2Y purinoceptor 14,Soluble cytochrome b562
    • Protein or peptide: Antibody 1b3 Fab Heavy chain
    • Protein or peptide: Antibody 1b3 Fab Light chain

-
Supramolecule #1: Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue

SupramoleculeName: Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: P2Y purinoceptor 14,Soluble cytochrome b562

MacromoleculeName: P2Y purinoceptor 14,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.084027 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SFVIKKPINI PDYSYRPTIG RGSMKTIIAL SYIFCLVFAH HHHHHHHHHD YKDDDDKLEV LFQGPAINST STQPPDESCS QNLLITQQI IPVLYCMVFI AGILLNGVSG WIFFYVPSSK SFIIYLKNIV IADFVMSLTF PFKILGDSGL GPWQLNVFVC R VSAVLFYV ...String:
SFVIKKPINI PDYSYRPTIG RGSMKTIIAL SYIFCLVFAH HHHHHHHHHD YKDDDDKLEV LFQGPAINST STQPPDESCS QNLLITQQI IPVLYCMVFI AGILLNGVSG WIFFYVPSSK SFIIYLKNIV IADFVMSLTF PFKILGDSGL GPWQLNVFVC R VSAVLFYV NMYVSIVFFG LISFDRYYKI VKPLWTSFIQ SVSYSKLLSV IVWMLMLLLA VPNIILTNQS VREVTQIKCI EL KSELGRK WHKASNYIFV AIFWIVFLLL IVFYTAITKK IFKSHADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AAL DAQKAS GSGSPEMKDF RHGFDILVGQ IDDALKLANE GKVKEAQAAA EQLKTTRNAY IQKYLSVKKK SSRNIFSIVF VFFV CFVPY HIARIPYTKS QTEAHYSCQS KEILRYMKEF TLLLSAANVC LDPIIYFFLC QPFREILCKK LKIAALKEKI AALKE KIAA LKEAEEKRAS RLEEELRRRL TE

UniProtKB: P2Y purinoceptor 14, Soluble cytochrome b562, P2Y purinoceptor 14

-
Macromolecule #2: Antibody 1b3 Fab Heavy chain

MacromoleculeName: Antibody 1b3 Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.704461 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAMH HHHHHHHHHL EVLFQGPEIS EVQLVESGGG LVQPGGSLRL SCAASGFNI YYSSMHWVRQ APGKGLEWVA SISPYSGSTY YADSVKGRFT ISADTSKNTA YLQMNSLRAE DTAVYYCARP W YPWSYWSG ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAMH HHHHHHHHHL EVLFQGPEIS EVQLVESGGG LVQPGGSLRL SCAASGFNI YYSSMHWVRQ APGKGLEWVA SISPYSGSTY YADSVKGRFT ISADTSKNTA YLQMNSLRAE DTAVYYCARP W YPWSYWSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQ SSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKS

-
Macromolecule #3: Antibody 1b3 Fab Light chain

MacromoleculeName: Antibody 1b3 Fab Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.768082 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFASD IQMTQSPSSL SASVGDRVTI TCRASQSVSS AVAWYQQKPG KAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQQ PWSWGSALIT FGQGTKVEIK RTVAAPSVFI F PPSDSQLK ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFASD IQMTQSPSSL SASVGDRVTI TCRASQSVSS AVAWYQQKPG KAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQQ PWSWGSALIT FGQGTKVEIK RTVAAPSVFI F PPSDSQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV TH QGLSSPV TKSFNRGEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88888
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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