[English] 日本語
Yorodumi
- EMDB-68429: Structure of neutralizing antibody G4 with MPXV M1R -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-68429
TitleStructure of neutralizing antibody G4 with MPXV M1R
Map dataDimerised M1R-G4Fab complex
Sample
  • Complex: G4 FAB_M1R COMPLEX
    • Protein or peptide: Entry-fusion complex associated protein OPG095
    • Protein or peptide: G4 heavy chain
    • Protein or peptide: G4 light chain
KeywordsCryo-EM / Complex / ANTIVIRAL PROTEIN
Function / homologyVirion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / Entry-fusion complex associated protein OPG095
Function and homology information
Biological speciesMacaca fascicularis (crab-eating macaque) / Monkeypox virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZai XD / Chen L
Funding support China, 2 items
OrganizationGrant numberCountry
Other private2023QNRC001 China
National Natural Science Foundation of China (NSFC)32571110 China
CitationJournal: To Be Published
Title: Structure of neutralizing antibody G4 with MPXV M1R
Authors: Zai XD / Chen L
History
DepositionJan 15, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_68429.png

Downloads & links

-
Map

FileDownload / File: emd_68429.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDimerised M1R-G4Fab complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 320 pix.
= 256.96 Å		0.8 Å/pix.
x 320 pix.
= 256.96 Å		0.8 Å/pix.
x 320 pix.
= 256.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.803 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.00093704707 - 2.010841
Average (Standard dev.)0.0032946502 (±0.045613788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 256.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_68429_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_68429_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_68429_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : G4 FAB_M1R COMPLEX

EntireName: G4 FAB_M1R COMPLEX
Components
  • Complex: G4 FAB_M1R COMPLEX
    • Protein or peptide: Entry-fusion complex associated protein OPG095
    • Protein or peptide: G4 heavy chain
    • Protein or peptide: G4 light chain

-
Supramolecule #1: G4 FAB_M1R COMPLEX

SupramoleculeName: G4 FAB_M1R COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1-#2
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)

-
Macromolecule #1: G4 heavy chain

MacromoleculeName: G4 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 23.797732 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQFGGSLRL SCAASRFTFS SYGLSWVRQA PGKGLEWIST INSGGGRTYY KDSVKGRFTI SRDNSKNTLS LQMNSLRAE DTAVYYCAKV PPGTGTWGFV DFWGQGLRVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
EVQLVESGGG LVQFGGSLRL SCAASRFTFS SYGLSWVRQA PGKGLEWIST INSGGGRTYY KDSVKGRFTI SRDNSKNTLS LQMNSLRAE DTAVYYCAKV PPGTGTWGFV DFWGQGLRVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSC

-
Macromolecule #2: G4 light chain

MacromoleculeName: G4 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 23.219723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQLTQSPSS LSASVGDRVT ITCRASQGIS SYLAWYQQKP GKAPKLLIYE ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QGKSDPFTFG PGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQLTQSPSS LSASVGDRVT ITCRASQGIS SYLAWYQQKP GKAPKLLIYE ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QGKSDPFTFG PGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #3: Entry-fusion complex associated protein OPG095

MacromoleculeName: Entry-fusion complex associated protein OPG095 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 20.16251 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HHHHHHGAAA SIQTTVNTLS ERISSKLEQE ANASAQTKCD IEIGNFYIRQ NHGCNITVKN MCSADADAQL DAVLSAATET YSGLTPEQK AYVPAMFTAA LNIQTSVNTV VRDFENYVKQ TCNSSAVVDN KLKIQNVIID ECYGAPGSPT NLEFINTGSS K GNCAIKAL MQLTTKATTQ IAPRQVAGTG

UniProtKB: Entry-fusion complex associated protein OPG095

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.4 / Details: PBS
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: CryoSMART / Number images used: 17196
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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