[English] 日本語
Yorodumi
- EMDB-37203: Cryo-EM structure of HSV-1 gB with D48 Fab complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37203
TitleCryo-EM structure of HSV-1 gB with D48 Fab complex
Map data
Sample
  • Complex: Cryo-EM structure of HSV-1 gB with D48 Fab complex
    • Protein or peptide: D48 heavy chain
    • Protein or peptide: D48 light chain
    • Protein or peptide: Envelope glycoprotein B
KeywordsHSV-1 gB / fab / neutralizing antibody / complex / Cryo-EM / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHomo sapiens (human) / Human herpesvirus 1 (strain KOS)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsYang J / Sun C / Fang X / Zeng M / Liu Z
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82070329 China
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: hlife / Year: 2023
Title: The structure of HSV-1 gB bound to a potent neutralizing antibody reveals a conservative antigenic domain across herpesviruses
Authors: Sun C / Yang JW / Xie C / Fang XY / Bu GL / Zhao GX / Dai DL / Liu Z / Zeng MS
History
DepositionAug 15, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_37203.png

Downloads & links

-
Map

FileDownload / File: emd_37203.map.gz / Format: CCP4 / Size: 325 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 440 pix.
= 363.88 Å		0.83 Å/pix.
x 440 pix.
= 363.88 Å		0.83 Å/pix.
x 440 pix.
= 363.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.20085397 - 0.43246728
Average (Standard dev.)0.00009981576 (±0.011389267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 363.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_37203_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37203_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of HSV-1 gB with D48 Fab complex

EntireName: Cryo-EM structure of HSV-1 gB with D48 Fab complex
Components
  • Complex: Cryo-EM structure of HSV-1 gB with D48 Fab complex
    • Protein or peptide: D48 heavy chain
    • Protein or peptide: D48 light chain
    • Protein or peptide: Envelope glycoprotein B

-
Supramolecule #1: Cryo-EM structure of HSV-1 gB with D48 Fab complex

SupramoleculeName: Cryo-EM structure of HSV-1 gB with D48 Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: D48 heavy chain

MacromoleculeName: D48 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.742861 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVETGGG VVRPGRSLRL SCTTSGFSFS GSAMHWVRQA PGKGLEWVAV ISHDGNIIQY HDSVKGRFTI SRDNSKNVLL LQMNSLRVD DTAMYYCARD VWLLPATISY AFDFWGQGTM VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
EVQLVETGGG VVRPGRSLRL SCTTSGFSFS GSAMHWVRQA PGKGLEWVAV ISHDGNIIQY HDSVKGRFTI SRDNSKNVLL LQMNSLRVD DTAMYYCARD VWLLPATISY AFDFWGQGTM VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKRVGSHHHH HH

-
Macromolecule #2: D48 light chain

MacromoleculeName: D48 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.476164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VIWMTQSPPS LSASIGDTVT ITCRASQGIS NSIAWYQRRP GKAPELLVYA AYRLQSGVPS RLSGSGSGAE YTLTIKNMQP EDFATYYCQ QYYDNPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
VIWMTQSPPS LSASIGDTVT ITCRASQGIS NSIAWYQRRP GKAPELLVYA AYRLQSGVPS RLSGSGSGAE YTLTIKNMQP EDFATYYCQ QYYDNPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #3: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 (strain KOS)
Molecular weightTheoretical: 70.337844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ANFYVCPPPT GATVVQFEQP RRCPTRPEGQ NYTEGIAVVF KENIAPYKFK ATMYYKDVTV SQVWFGHRYS QFMGIFEDRA PVPFEEVID KINAKGVCRS TAKYVRNNLE TTAFHRDDHE TDMELKPANA ATRTSRGWHT TDLKYNPSRV EAFHRYGTTV N CIVEEVDA ...String:
ANFYVCPPPT GATVVQFEQP RRCPTRPEGQ NYTEGIAVVF KENIAPYKFK ATMYYKDVTV SQVWFGHRYS QFMGIFEDRA PVPFEEVID KINAKGVCRS TAKYVRNNLE TTAFHRDDHE TDMELKPANA ATRTSRGWHT TDLKYNPSRV EAFHRYGTTV N CIVEEVDA RSVYPYDEFV LATGDFVYMS PFYGYREGSH TEHTTYAADR FKQVDGFYAR DLTTKARATA PTTRNLLTTP KF TVAWDWV PKRPSVCTMT KWQEVDEMLR SEYGGSFRFS SDAISTTFTT NLTEYPLSRV DLGDCIGKDA RDAMDRIFAR RYN ATHIKV GQPQYYQANG GFLIAYQPLL SNTLAELYVR EHLREQSRKP PNPTPPPPGA SANASVERIK TTSSIEFARL QFTY NHIQR HVNDMLGRVA IAWCELQNHE LTLWNEARKL NPNAIASVTV GRRVSARMLG DVMAVSTCVP VAADNVIVQN SMRIS SRPG ACYSRPLVSF RYEDQGPLVE GQLGENNELR LTRDAIEPCT VGHRRYFTFG GGYVYFEEYA YSHQLSRADI TTVSTF IDL NITMLEDHEF VPLEVYTRHE IKDSGLLDYT EVQRRNQLHD LRFADIDTVI HA

UniProtKB: Envelope glycoprotein B

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.56 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168888
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
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