[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleA Rapid and Universal Pipeline for High-Resolution GPCR Structure Determination through In Silico Construct Optimization and de novo Protein Design
Journal, issue, pagesBiorxiv, Year 2026
Publish dateMay 11, 2025 (structure data deposition date)
AuthorsKojima A / Kawakami K / Kobayashi N / Kobayashi K / Matsui TE / Uemoto K / Gu Y / Fukuda M / Kato HE
External linksBiorxiv / Search PubMed
MethodsEM (single particle)
Resolution2.89 - 3.69 Å
Structure data

64536

9uvt

EMDB-64536, PDB-9uvt:
Cryo-EM structure of bradykinin B2 receptor (B2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with icatibant
Method: EM (single particle) / Resolution: 3.29 Å

64537

9uvu

EMDB-64537, PDB-9uvu:
Cryo-EM structure of bradykinin B2 receptor (B2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with icatibant, focused on receptor
Method: EM (single particle) / Resolution: 3.69 Å

64538

9uvv

EMDB-64538, PDB-9uvv:
Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with tolvaptan
Method: EM (single particle) / Resolution: 3.02 Å

64539

9uvw

EMDB-64539, PDB-9uvw:
Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with tolvaptan, focused on receptor
Method: EM (single particle) / Resolution: 2.89 Å

64540

9uvx

EMDB-64540, PDB-9uvx:
Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with OPC51803, focused on receptor
Method: EM (single particle) / Resolution: 3.31 Å

64541

9uvy

EMDB-64541, PDB-9uvy:
Cryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan
Method: EM (single particle) / Resolution: 2.98 Å

64542

9uvz

EMDB-64542, PDB-9uvz:
Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425
Method: EM (single particle) / Resolution: 2.99 Å

Chemicals

PDB-1it8:
Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0

PDB-1l9o:
CRYSTAL STRUCTURE OF NITRITE SOAKED I257A VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS

ChemComp-HOH:
WATER

PDB-1l9p:
CRYSTAL STRUCTURE OF NITRITE SOAKED I257G VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIES S-6

ChemComp-NA:
Unknown entry

Source
  • homo sapiens (human)
  • mus musculus (house mouse)
  • synthetic construct (others)
  • escherichia coli (E. coli)
KeywordsMEMBRANE PROTEIN / GPCR / B2R / bradykinin / icatibant / V2R / vasopressin / tolvaptan / OPC51803 / ARK1 / LPA2 / Lysophosphatidic acid receptor 2 / Ki16425

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more