[English] 日本語
Yorodumi
- EMDB-38194: A35 of MPXV in complex with mAb981 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38194
TitleA35 of MPXV in complex with mAb981
Map data
Sample
  • Complex: A35 of MPXV in complex with mAb981
    • Protein or peptide: Protein OPG161
    • Protein or peptide: Heavy chain of mAb981
    • Protein or peptide: Light chain of mAb981
KeywordsRECOMBINATION / REPLICATION / VIRAL PROTEIN
Function / homologyChordopoxvirus A33R / Chordopoxvirus A33R protein / C-type lectin-like/link domain superfamily / C-type lectin fold / host cell membrane / carbohydrate binding / virion membrane / membrane / Protein OPG161
Function and homology information
Biological speciesMonkeypox virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsLi YN / Shi TH / Yan RH
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509301 China
CitationJournal: To Be Published
Title: Structure of MPXV A35 with a neutralizing and protective human monoclonal antibody
Authors: Li YN / Shi TH / Yan RH
History
DepositionDec 1, 2023-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38194.png

Downloads & links

-
Map

FileDownload / File: emd_38194.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.)
0.83 Å/pix.
x 288 pix.
= 239.904 Å		0.83 Å/pix.
x 288 pix.
= 239.904 Å		0.83 Å/pix.
x 288 pix.
= 239.904 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.78425854 - 1.6504273
Average (Standard dev.)0.0009943721 (±0.037325922)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.904 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_38194_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38194_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : A35 of MPXV in complex with mAb981

EntireName: A35 of MPXV in complex with mAb981
Components
  • Complex: A35 of MPXV in complex with mAb981
    • Protein or peptide: Protein OPG161
    • Protein or peptide: Heavy chain of mAb981
    • Protein or peptide: Light chain of mAb981

-
Supramolecule #1: A35 of MPXV in complex with mAb981

SupramoleculeName: A35 of MPXV in complex with mAb981 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Monkeypox virus

-
Macromolecule #1: Protein OPG161

MacromoleculeName: Protein OPG161 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 20.04342 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MMTPENDEEQ TSVFSATVYG DKIQGKNKRK RVIGLCIRIS MVISLLSMIT MSAFLIVRLN QCMSANEAAI TDSAVAVAAA SSTHRKVAS STTQYDHKES CNGLYYQGSC YILHSDYKSF EDAKANCAAE SSTLPNKSDV LTTWLIDYVE DTWGSDGNPI T KTTSDYQD SDVSQEVRKY FCT

UniProtKB: Protein OPG161

-
Macromolecule #2: Heavy chain of mAb981

MacromoleculeName: Heavy chain of mAb981 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.548179 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLQLQESGPG LVKPSETLSL TCTVSGGSIS SNNDYWGWIR QPPGKGLEWI GSIYYSGRTN GNPSLKSRVN ISADTSKNQF SLKLNSVTA ADTAVYYCAR LRLGSLLHRY RAVDPWGQGI LVAVSS

-
Macromolecule #3: Light chain of mAb981

MacromoleculeName: Light chain of mAb981 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.723094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERVT LSCRASQRVS STYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QHFDSSLLTF GGGTKVEIK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 986061
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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