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- EMDB-61599: Cryo-EM structure of BV gB and FAB 16F9 complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61599
TitleCryo-EM structure of BV gB and FAB 16F9 complex
Map data
Sample
  • Complex: BV gB and FAB 16F9 complex
    • Protein or peptide: 16F9 VH
    • Protein or peptide: 16F9 VL
    • Protein or peptide: Virion glycoprotein B
KeywordsCryo-EM / MBV gB protein / FAB 16F9 / Hepes virus / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology: / 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 / Virion glycoprotein B
Function and homology information
Biological speciesMacacine alphaherpesvirus 1 (monkey B virus) / Mus musculus (house mouse) / Cercopithecine herpesvirus 1 (monkey B virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.18 Å
AuthorsLi Y / Zheng Q / Li S / Wu Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of BV gB and FAB 16F9 complex
Authors: Li Y / Zheng Q / Li S
History
DepositionSep 20, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61599.png

Downloads & links

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Map

FileDownload / File: emd_61599.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 480 pix.
= 312. Å		0.65 Å/pix.
x 480 pix.
= 312. Å		0.65 Å/pix.
x 480 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.078
Minimum - Maximum-0.65456617 - 1.1371108
Average (Standard dev.)0.00072104175 (±0.028144311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61599_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61599_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BV gB and FAB 16F9 complex

EntireName: BV gB and FAB 16F9 complex
Components
  • Complex: BV gB and FAB 16F9 complex
    • Protein or peptide: 16F9 VH
    • Protein or peptide: 16F9 VL
    • Protein or peptide: Virion glycoprotein B

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Supramolecule #1: BV gB and FAB 16F9 complex

SupramoleculeName: BV gB and FAB 16F9 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Macacine alphaherpesvirus 1 (monkey B virus)

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Macromolecule #1: 16F9 VH

MacromoleculeName: 16F9 VH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 52.536238 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGRLTSSFLL LIVPAYVLSE VQLQQSGPEL VKPGASVKIS CKASGYTFAD YTMHWVKQSH GKSLEWIGYI NPYSLFIDSN QKFKNKATL TVDNSSYTAY MELRSLTSED SAVYYCARFP PYYGFDSHFD YWGQGTALTV SSAKTTPPSV YPLAPGCGDT T GSSVTLGC ...String:
MGRLTSSFLL LIVPAYVLSE VQLQQSGPEL VKPGASVKIS CKASGYTFAD YTMHWVKQSH GKSLEWIGYI NPYSLFIDSN QKFKNKATL TVDNSSYTAY MELRSLTSED SAVYYCARFP PYYGFDSHFD YWGQGTALTV SSAKTTPPSV YPLAPGCGDT T GSSVTLGC LVKGYFPESV TVTWNSGSLS SSVHTFPALL QSGLYTMSSS VTVPSSTWPS QTVTCSVAHP ASSTTVDKKL EP SGPISTI NPCPPCKECH KCPAPNLEGG PSVFIFPPNI KDVLMISLTP KVTCVVVDVS EDDPDVRISW FVNNVEVHTA QTQ THREDY NSTIRVVSAL PIQHQDWMSG KEFKCKVNNK DLPSPIERTI SKIKGLVRAP QVYILPPPAE QLSRKDVSLT CLVV GFNPG DISVEWTSNG HTEENYKDTA PVLDSDGSYF IYSKLDIKTS KWEKTDSFSC NVRHEGLKNY YLKKTISRSP GK

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Macromolecule #2: 16F9 VL

MacromoleculeName: 16F9 VL / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.464201 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ IVLSQSPAIL SASPGEKVTM TCRASSSVSY IYWYQQKPES SPKPWIYATS NLASGVPGRF SGSGSGTSY SLTISRVEAE DAATYYCQQW SYNPYTFGGG TKLEIRRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP K DINVKWKI ...String:
MGWSCIILFL VATATGVHSQ IVLSQSPAIL SASPGEKVTM TCRASSSVSY IYWYQQKPES SPKPWIYATS NLASGVPGRF SGSGSGTSY SLTISRVEAE DAATYYCQQW SYNPYTFGGG TKLEIRRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP K DINVKWKI DGSERQNGVL NSWTDQDSKD STYSMSSTLT LTKDEYERHN SYTCEATHKT STSPIVKSFN RNEC

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Macromolecule #3: Virion glycoprotein B

MacromoleculeName: Virion glycoprotein B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cercopithecine herpesvirus 1 (monkey B virus)
Molecular weightTheoretical: 98.79368 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPRAGPLPL PSPLVPLLAL ALLAATRPLG PAAATPVVSP RASPAPPVPA ATPTFPDDDN DGEAGAAPGA PGTNASVEAG HATLRENLR DIKALDGDAT FYVCPPPTGA TVVQFEQPRP CPRAPDGQNY TEGIAVIFKE NIAPYKFKAT MYYKDVTVSQ V WFGHRYSQ ...String:
MRPRAGPLPL PSPLVPLLAL ALLAATRPLG PAAATPVVSP RASPAPPVPA ATPTFPDDDN DGEAGAAPGA PGTNASVEAG HATLRENLR DIKALDGDAT FYVCPPPTGA TVVQFEQPRP CPRAPDGQNY TEGIAVIFKE NIAPYKFKAT MYYKDVTVSQ V WFGHRYSQ FMGIFEDRAP VPFEEVIDKI NARGVCRSTA KYVRNNMEST AFHRDDDESD MKLKPAKAAT RTSRGWHTTD LK YNPSRIE AFHRYGTTVN CIVEEVEARS VYPYDEFVLA TGDFVYMSPF YGYRDGAHAE HTAYAADRFR QVDGYYERDL STG RRASTP ATRNLLTTPK FTVGWDWAPK RPSVCTLTKW QEVDEMLRAE YGPSFRFSSS ALSTTFTTNR TEYALSRVDL GDCV GREAR EAVDRIFLRR YNGTHVKVGQ VQYYLATGGF LIAYQPLLSN ALVELYVREL LREQERRPGD AAATPKPSAD PPDVE RIKT TSSVEFARLQ FTYDHIQRHV NDMLGRIAIA WCELQNHELT LWNEARKLNP NAIASATVGR RVSARMLGDV MAVSTC VPV TPDNVIMQNS MRVPARPGTC YSRPLVSFRY EEGGPLVEGQ LGEDNEIRLE RDALEPCTVG HRRYFTFGAG YVYFEDY AY SHQLGRADVT TVSTFINLNL TMLEDHEFVP LEVYTRQEIK DSGLLDYTEV QRRNQLHALR FADIDTVIKA DAHAALFA G LYSFFEGLGD VGRAVGKVVM GIVGGVVSAV SGVSSFLSNP FGALAVGLLV LAGLAAAFFA FRYVMRLQRN PMKALYPLT TKELKSDGPS PAGDGGDGAS GGGEEDFDEA KLAQAREMIR YMALVSAMER TEHKARKKGT SALLSAKVTN MVMRKRAKPR YSPLGDTDE EEL

UniProtKB: Virion glycoprotein B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: 0.9 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109849
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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