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- EMDB-61596: Cryo-EM structure of HSV-2 gB and FAB 16F9 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61596
TitleCryo-EM structure of HSV-2 gB and FAB 16F9 complex
Map data
Sample
  • Complex: HSV-2 gB and FAB 16F9 complex
    • Protein or peptide: Glycoprotein B
    • Protein or peptide: 16F9 VH
    • Protein or peptide: 16F9 VL
KeywordsCryo-EM / HSV-2 gB / FAB 16F9 / Herpes virus / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / 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
Biological speciesHuman alphaherpesvirus 2 / Human herpesvirus 2 / Mus musculus (house mouse)
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 HSV-2 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_61596.png

Downloads & links

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Map

FileDownload / File: emd_61596.map.gz / Format: CCP4 / Size: 729 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 576 pix.
= 374.4 Å		0.65 Å/pix.
x 576 pix.
= 374.4 Å		0.65 Å/pix.
x 576 pix.
= 374.4 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: 0.08
Minimum - Maximum-0.1794871 - 0.49651372
Average (Standard dev.)0.00006567221 (±0.0102037545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61596_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61596_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 : HSV-2 gB and FAB 16F9 complex

EntireName: HSV-2 gB and FAB 16F9 complex
Components
  • Complex: HSV-2 gB and FAB 16F9 complex
    • Protein or peptide: Glycoprotein B
    • Protein or peptide: 16F9 VH
    • Protein or peptide: 16F9 VL

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Supramolecule #1: HSV-2 gB and FAB 16F9 complex

SupramoleculeName: HSV-2 gB and FAB 16F9 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human alphaherpesvirus 2

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Macromolecule #1: Glycoprotein B

MacromoleculeName: Glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2
Molecular weightTheoretical: 81.529953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRGGGLICAL VVGALVAAVA SAAPAAPAAP RASGGVAATV AANGGPASRP PPVPSPATTK ARKRKTKKPP KRPEATPPPD ANATVAAGH ATLRAHLREI KVENADAQFY VCPPPTGATV VQFEQPRRCP TRPEGQNYTE GIAVVFKENI APYKFKATMY Y KDVTVSQV ...String:
MRGGGLICAL VVGALVAAVA SAAPAAPAAP RASGGVAATV AANGGPASRP PPVPSPATTK ARKRKTKKPP KRPEATPPPD ANATVAAGH ATLRAHLREI KVENADAQFY VCPPPTGATV VQFEQPRRCP TRPEGQNYTE GIAVVFKENI APYKFKATMY Y KDVTVSQV WFGHRYSQFM GIFEDRAPVP FEEVIDKINA KGVCRSTAKY VRNNMETTAF HRDDHETDME LKPAKVATRT SR GWHTTDL KYNPSRVEAF HRYGTTVNCI VEEVDARSVY PYDEFVLATG DFVYMSPFYG YREGSHTEHT SYAADRFKQV DGF YARDLT TKARATSPTT RNLLTTPKFT VAWDWVPKRP AVCTMTKWQE VDEMLRAEYG GSFRFSSDAI STTFTTNLTE YSLS RVDLG DCIGRDAREA IDRMFARKYN ATHIKVGQPQ YYLATGGFLI AYQPLLSNTL AELYVREYMR EQDRKPRNAT PAPLR EAPS ANASVERIKT TSSIEFARLQ FTYNHIQRHV NDMLGRIAVA WCELQNHELT LWNEARKLNP NAIASATVGR RVSARM LGD VMAVSTCVPV APDNVIVQNS MRVSSRPGTC YSRPLVSFRY EDQGPLIEGQ LGENNELRLT RDALEPCTVG HRRYFIF GG GYVYFEEYAY SHQLSRADVT TVSTFIDLNI TMLEDHEFVP LEVYTRHEIK DSGLLDYTEV QRRNQLHDLR FADIDTVI R ADANAA

UniProtKB: Glycoprotein B

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Macromolecule #2: 16F9 VH

MacromoleculeName: 16F9 VH / type: protein_or_peptide / ID: 2 / 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 #3: 16F9 VL

MacromoleculeName: 16F9 VL / type: protein_or_peptide / ID: 3 / 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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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: 77359
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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