[English] 日本語
Yorodumi
- EMDB-80806: Structure of a human monoclonal neutralizing antibody S54 targeti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-80806
TitleStructure of a human monoclonal neutralizing antibody S54 targeting Epstein-Barr virus major glycoprotein gp350
Map data
Sample
  • Complex: complex of gp350 with antibody S54
    • Protein or peptide: Fab S54 H chain
    • Protein or peptide: Fab S54 L chain
    • Protein or peptide: BLLF1
KeywordsEBV / Antibody / gp350 / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Herpesvirus major outer envelope glycoprotein / : / : / : / : / Herpes virus envelope glycoprotein gp350, N-terminal A domain / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal
Similarity search - Domain/homology
Biological speciesEpstein-Barr virus (Epstein-Barr virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSun C / Fang XY / Liu Z / Zeng MS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: Science China Life Sciences / Year: 2026
Title: A potent human neutralizing antibody targeting the receptor binding site in the glycoprotein gp350 of Epstein-Barr virus
Authors: Sun C / Fang XY / Liu Z / Zeng MS
History
DepositionMay 9, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_80806.png

Downloads & links

-
Map

FileDownload / File: emd_80806.map.gz / Format: CCP4 / Size: 209.3 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 380 pix.
= 314.26 Å		0.83 Å/pix.
x 380 pix.
= 314.26 Å		0.83 Å/pix.
x 380 pix.
= 314.26 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: 0.09
Minimum - Maximum-0.34379932 - 0.6412355
Average (Standard dev.)-0.00004046364 (±0.009240105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 314.26 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_80806_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_80806_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_80806_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : complex of gp350 with antibody S54

EntireName: complex of gp350 with antibody S54
Components
  • Complex: complex of gp350 with antibody S54
    • Protein or peptide: Fab S54 H chain
    • Protein or peptide: Fab S54 L chain
    • Protein or peptide: BLLF1

-
Supramolecule #1: complex of gp350 with antibody S54

SupramoleculeName: complex of gp350 with antibody S54 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Epstein-Barr virus (Epstein-Barr virus)

-
Macromolecule #1: Fab S54 H chain

MacromoleculeName: Fab S54 H chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.859342 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVQSGAEV KKPGASVKVS CKASGYTFTT YYLHWMRQAP GEGLEWVGLI NPSVGSASSA QKFKGRVTMT SDTSTSIAYL EVNSLTSED TAVYYCARVG PSRYSTSSPY WGQGTLVTVS S

-
Macromolecule #2: Fab S54 L chain

MacromoleculeName: Fab S54 L chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.192152 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QPVLTQSPSA SGTPGQRVTI SCSGSSSNIG SNTVNWYQQL PGTAPKLLIY GNNQRPSGVP DRFSGSKSGT SASLAISGLQ SDDEADYYC SSYTSSSSLV FGGGTKLTVL

-
Macromolecule #3: BLLF1

MacromoleculeName: BLLF1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (Epstein-Barr virus)
Molecular weightTheoretical: 90.96225 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARGSHHH HHHHHHHEAA LLVCQYTIQS LIHLTGEDPG FFNVEIPEFP FYPTCNVCT ADVNVTINFD VGGKKHQLDL DFGQLTPHTK AVYQPRGAFG GSENATNLFL LELLGAGELA LTMRSKKLPI N VTTGEEQQ ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARGSHHH HHHHHHHEAA LLVCQYTIQS LIHLTGEDPG FFNVEIPEFP FYPTCNVCT ADVNVTINFD VGGKKHQLDL DFGQLTPHTK AVYQPRGAFG GSENATNLFL LELLGAGELA LTMRSKKLPI N VTTGEEQQ VSLESVDVYF QDVFGTMWCH HAEMQNPVYL IPETVPYIKW DNCNSTNITA VVRAQGLDVT LPLSLPTSAQ DS NFSVKTQ MLGNEIDIEC IMEDGEISQV LPGDNKFNIT CSGYESHVPS GGILTSTSPV ATPIPGTGYA YSLRLTPRPV SRF LGNNSI LYVFYSGNGP KASGGDYCIQ SNIVFSDEIP ASQDMPTNTT DITYVGDNAT YSVPMVTSED ANSPNVTVTA FWAW PNNTE TDFKCKWTLT SGTPSGCENI SGAFASNRTF DITVSGLGTA PKTLIITRTA TNATTTTHKV IFSKAPESTT TSPTL NTTG FADPNTTTGL PSSTHVPTNL TAPASTGPTV STADVTSPTP AGTTSGASPV TPSPSPRDNG TESKAPDMTS PTSAVT TPT PNGTSPTPAM TTPTPNATSP TLGKTSPTSA VTTPTPNATS PTPAVTTPTP NATSPTVGET SPQANATNHT LGGTSPT PV VTSPPKNATS DVTTGQHNRT SSSTSSMSLR PSSIPETTSH MPLLTSAHPT GGENITQVTP ASISTHHVST SSPAPRPG T TSQASGPGNS STSTKPGEVN VTKGTPPKNA TSPQAPSGQK TAVPTVTSTG GKANSTTGGK HTTGHGARTS TEPTTDYGD DSTTPRPRYN ATTYLPPSTS SKLRPRWTFT SPPVTTAQAT VPVPPTSQPR FSNLHHHHHH HHHH

UniProtKB: BLLF1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 390971
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER

+
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