[English] 日本語
Yorodumi
- EMDB-71586: Negative stain EM map of EBV glycoprotein gH/gL in complex with g... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71586
TitleNegative stain EM map of EBV glycoprotein gH/gL in complex with glycoprotein gp42 and FAB ATX-42-2 Open conformation
Map data
Sample
  • Complex: Coexpressed EBV surface glycoprotein gH/gL complex 1:1 with glucoprotein gp42 and then 1:1 with FAB ATX-42-2
    • Protein or peptide: EBV surface glycoprotein gL
    • Protein or peptide: EBV surface glycoprotein gH
    • Protein or peptide: EBV surface glycoprotein gp42
    • Protein or peptide: FAB ATX-42-2 heavy chain
    • Protein or peptide: FAB ATX-42-2 light chain
KeywordsViral protein / Complex / Antibody / EBV / IMMUNE SYSTEM
Function / homology
Function and homology information


host cell membrane / host cell endosome membrane / carbohydrate binding / host cell Golgi apparatus / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Glycoprotein 42 / Envelope glycoprotein L / Envelope glycoprotein H
Similarity search - Component
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus) / Mus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 8.45 Å
AuthorsLang K / Kher G / Chan CB / Pancera M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA285227 United States
CitationJournal: To Be Published
Title: Transgenic Mouse-Derived Human Monoclonal Antibodies Targeting EBV gp350 and gp42 Provide Basis for Therapeutic Development
Authors: Chan CB / Lang K / Davis AR / Wan YH / Aldridge NT / Kher G / Scharffenberger SC / Hardy SR / Iureniev R / Giltiay NV / Edwards KR / Radtke S / Kiem HP / Pancera M / McGuire A
History
DepositionJul 3, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71586.png

Downloads & links

-
Map

FileDownload / File: emd_71586.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.49 Å/pix.
x 90 pix.
= 404.48 Å		4.49 Å/pix.
x 90 pix.
= 404.48 Å		4.49 Å/pix.
x 90 pix.
= 404.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.49422 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.534
Minimum - Maximum-1.6095151 - 12.994946000000001
Average (Standard dev.)-0.0025445765 (±0.28053954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 404.47998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_71586_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_71586_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Coexpressed EBV surface glycoprotein gH/gL complex 1:1 with gluco...

EntireName: Coexpressed EBV surface glycoprotein gH/gL complex 1:1 with glucoprotein gp42 and then 1:1 with FAB ATX-42-2
Components
  • Complex: Coexpressed EBV surface glycoprotein gH/gL complex 1:1 with glucoprotein gp42 and then 1:1 with FAB ATX-42-2
    • Protein or peptide: EBV surface glycoprotein gL
    • Protein or peptide: EBV surface glycoprotein gH
    • Protein or peptide: EBV surface glycoprotein gp42
    • Protein or peptide: FAB ATX-42-2 heavy chain
    • Protein or peptide: FAB ATX-42-2 light chain

-
Supramolecule #1: Coexpressed EBV surface glycoprotein gH/gL complex 1:1 with gluco...

SupramoleculeName: Coexpressed EBV surface glycoprotein gH/gL complex 1:1 with glucoprotein gp42 and then 1:1 with FAB ATX-42-2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 173 KDa

-
Macromolecule #1: EBV surface glycoprotein gL

MacromoleculeName: EBV surface glycoprotein gL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: B95-8
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MRAVGVFLAI CLVTIFVLPT WGNWAYPCCH VTQLRAQHLL ALENISDIYL VSNQTCDGFS LASLNSPKNG SNQLVISRCA NGLNVVSFFI SILKRSSSAL TGHLRELLTT LETLYGSFSV EDLFGANLNR YAWHRGG

UniProtKB: Envelope glycoprotein L

-
Macromolecule #2: EBV surface glycoprotein gH

MacromoleculeName: EBV surface glycoprotein gH / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: B95-8
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQLLCVFCLV LLWEVGAASL SEVKLHLDIE GHASHYTIPW TELMAKVPGL SPEALWREAN VTEDLASMLN RYKLIYKTSG TLGIALAEPV DIPAVSEGSM QVDASKVHPG VISGLNSPAC MLSAPLEKQL FYYIGTMLPN TRPHSYVFYQ LRCHLSYVAL SINGDKFQYT ...String:
MQLLCVFCLV LLWEVGAASL SEVKLHLDIE GHASHYTIPW TELMAKVPGL SPEALWREAN VTEDLASMLN RYKLIYKTSG TLGIALAEPV DIPAVSEGSM QVDASKVHPG VISGLNSPAC MLSAPLEKQL FYYIGTMLPN TRPHSYVFYQ LRCHLSYVAL SINGDKFQYT GAMTSKFLMG TYKRVTEKGD EHVLSLVFGK TKDLPDLRGP FSYPSLTSAQ SGDYSLVIVT TFVHYANFHN YFVPNLKDMF SRAVTMTAAS YARYVLQKLV LLEMKGGCRE PELDTETLTT MFEVSVAFFK VGHAVGETGN GCVDLRWLAK SFFELTVLKD IIGICYGATV KGMQSYGLER LAAMLMATVK MEELGHLTTE KQEYALRLAT VGYPKAGVYS GLIGGATSVL LSAYNRHPLF QPLHTVMRET LFIGSHVVLR ELRLNVTTQG PNLALYQLLS TALCSALEIG EVLRGLALGT ESGLFSPCYL SLRFDLTRDK LLSMAPQEAT LDQAAVSNAV DGFLGRLSLE REDRDAWHLP AYKCVDRLDK VLMIIPLINV TFIISSDREV RGSALYEAST TYLSSSLFLS PVIMNKCSQG AVAGEPRQIP KIQNFTRTQK SCIFCGFALL SYDEKEGLET TTYITSQEVQ NSILSSNYFD FDNLHVHYLL LTTNGTVMEI AGLYEERAHV VLAIILYFIA FALGIFLVHK IVMFFLHHHH HH

UniProtKB: Envelope glycoprotein H

-
Macromolecule #3: EBV surface glycoprotein gp42

MacromoleculeName: EBV surface glycoprotein gp42 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: B95-8
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVSFKQVRVP LFTAIALVIV LLLAYFLPPR VRGGGRVAAA AITWVPKPNV EVWPVDPPPP VNFNKTAEQE YGDKEVKLPH WTPTLHTFQV PQNYTKANCT YCNTREYTFS YKGCCFYFTK KKHTWNGCFQ ACAELYPCTY FYGPTPDILP VVTRNLNAIE SLWVGVYRVG ...String:
MVSFKQVRVP LFTAIALVIV LLLAYFLPPR VRGGGRVAAA AITWVPKPNV EVWPVDPPPP VNFNKTAEQE YGDKEVKLPH WTPTLHTFQV PQNYTKANCT YCNTREYTFS YKGCCFYFTK KKHTWNGCFQ ACAELYPCTY FYGPTPDILP VVTRNLNAIE SLWVGVYRVG EGNWTSLDGG TFKVYQIFGS HCTYVSKFST VPVSHHECSF LKPCLCVSQR SNSHHHHHH

UniProtKB: Glycoprotein 42

-
Macromolecule #4: FAB ATX-42-2 heavy chain

MacromoleculeName: FAB ATX-42-2 heavy chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSSALLCCL VLLTGVRAEV QLVQSGAEVK KPGESLKISC KGSGYSFSNY WIAWVRQMPG KGLEWMGIIY PDDSDTRYSP SFQGQVTISA DKSISTAYLS WSSLKASDTA MYYCAREGDY YYGSGTYYKV WFDPWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL ...String:
MHSSALLCCL VLLTGVRAEV QLVQSGAEVK KPGESLKISC KGSGYSFSNY WIAWVRQMPG KGLEWMGIIY PDDSDTRYSP SFQGQVTISA DKSISTAYLS WSSLKASDTA MYYCAREGDY YYGSGTYYKV WFDPWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPK

-
Macromolecule #5: FAB ATX-42-2 light chain

MacromoleculeName: FAB ATX-42-2 light chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSSALLCCL VLLTGVRAEI VLTQSPATLS LSPGERATLS CRASQSVSTY LAWYQQKPGQ APRLLIYDTS NRATGIPARF SGSGSGTDFT LTISSLEPED FAVYYCQQRS NWPLTFGGGT KVEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ...String:
MHSSALLCCL VLLTGVRAEI VLTQSPATLS LSPGERATLS CRASQSVSTY LAWYQQKPGQ APRLLIYDTS NRATGIPARF SGSGSGTDFT LTISSLEPED FAVYYCQQRS NWPLTFGGGT KVEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ALQSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 1x TBS
StainingType: NEGATIVE / Material: Uranyl Formate / Details: 2% Uranyl Formate

-
Electron microscopy

MicroscopeTFS TALOS L120C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 96000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos L120C / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 12554
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
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