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- EMDB-61612: Cryo-EM structure of VZV gB and FAB 16F9 complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61612
TitleCryo-EM structure of VZV gB and FAB 16F9 complex
Map data
Sample
  • Complex: DSR2 H171A
    • Protein or peptide: Glycoprotein B
    • Protein or peptide: 16F9 VH
    • Protein or peptide: 16F9 VL
KeywordsCryo-EM / VZV 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 speciesBacillus sp. DSM 5850 (bacteria) / Human herpesvirus 3 (Varicella-zoster virus) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 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 VZV gB and FAB 16F9 complex
Authors: Li Y / Zheng Q / Li S
History
DepositionSep 21, 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_61612.png

Downloads & links

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Map

FileDownload / File: emd_61612.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: 0.08
Minimum - Maximum-0.5297658 - 0.7275187
Average (Standard dev.)0.0004315285 (±0.017867777)
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: #2

Fileemd_61612_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_61612_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 : DSR2 H171A

EntireName: DSR2 H171A
Components
  • Complex: DSR2 H171A
    • Protein or peptide: Glycoprotein B
    • Protein or peptide: 16F9 VH
    • Protein or peptide: 16F9 VL

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Supramolecule #1: DSR2 H171A

SupramoleculeName: DSR2 H171A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus sp. DSM 5850 (bacteria)

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Macromolecule #1: Glycoprotein B

MacromoleculeName: Glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 3 (Varicella-zoster virus)
Molecular weightTheoretical: 86.20882 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSPCGYYSKW RNRDRPEYRR NLRFRRFFSS IHPNAAAGSG FNGPGVFITS VTGVWLCFLC IFSMFVTAVV SVSPSSFYES LQVEPTQSE DITRSAHLGD GDEIREAIHK SQDAETKPTF YVCPPPTGST IVRLEPTRTC PDYHLGKNFT EGIAVVYKEN I AAYKFKAT ...String:
MSPCGYYSKW RNRDRPEYRR NLRFRRFFSS IHPNAAAGSG FNGPGVFITS VTGVWLCFLC IFSMFVTAVV SVSPSSFYES LQVEPTQSE DITRSAHLGD GDEIREAIHK SQDAETKPTF YVCPPPTGST IVRLEPTRTC PDYHLGKNFT EGIAVVYKEN I AAYKFKAT VYYKDVIVST AWAGSSYTQI TNRYADRVPI PVSEITDTID KFGKCSSKAT YVRNNHKVEA FNEDKNPQDM PL IASKYNS VGSKAWHTTN DTYMVAGTPG TYRTGTSVNC IIEEVEARSI FPYDSFGLST GDIIYMSPFF GLRDGAYREH SNY AMDRFH QFEGYRQRDL DTRALLEPAA RNFLVTPHLT VGWNWKPKRT EVCSLVKWRE VEDVVRDEYA HNFRFTMKTL STTF ISETN EFNLNQIHLS QCVKEEARAI INRIYTTRYN SSHVRTGDIQ TYLARGGFVV VFQPLLSNSL ARLYLQELVR ENTNH SPQK HPTRNTGSAS SVPVELRANR TITTTSSVEF AMLQFTYDHI QEHVNEMLAR ISSSWCQLQN RERALWSGLF PINPSA LAS TILDQRVKAR ILGDVISVSN CPELGSDTRI ILQNSMRVSG STTRCYSRPL ISIVSLNGSG TVEGQLGTDN ELIMSRD LL EPCVANHKRY FLFGHHYVYY EDYRYVREIA VHDVGMISTY VDLNLTLLKD REFMPLQVYT RDELRDTGLL DYSEIQRR N QMHSLRFYDI DKVVQYDSGT AHHHHHHHHH H

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: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118987
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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