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- EMDB-61939: The glycoprotein E of Varicella-Zoster Virus in complex with WLL-... -

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Basic information

Entry
Database: EMDB / ID: EMD-61939
TitleThe glycoprotein E of Varicella-Zoster Virus in complex with WLL-1/WLL-28 Fab
Map data
Sample
  • Complex: Ternary complex of VZV gE with neutralizing antibodies Fab WLL-1 and WLL-28
    • Protein or peptide: Envelope glycoprotein E
    • Protein or peptide: WLL-1 Fab heavy chain
    • Protein or peptide: WLL-1 Fab light chain
    • Protein or peptide: WLL-28 Fab heavy chain
    • Protein or peptide: WLL-28 Fab light chain
KeywordsVZV / glycoprotein E / single B cell / monoclonal antibodies / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell junction / host cell Golgi membrane / host cell endosome membrane / entry receptor-mediated virion attachment to host cell / viral envelope / symbiont entry into host cell / virion membrane / enzyme binding / membrane
Similarity search - Function
Envelope glycoprotein E, Fc-binding domain / Envelope glycoprotein E, N-terminal / Alphaherpesvirus glycoprotein E / Alphaherpesvirus glycoprotein E N-terminal / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Envelope glycoprotein E
Similarity search - Component
Biological speciesVaricella-zoster virus (strain Oka vaccine) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsWang L / Zhang N / Guo Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Protein Cell / Year: 2025
Title: Discovery and structural investigation of Varicella-Zoster virus gE-neutralizing antibodies isolated from a convalescent patient.
Authors: Lulu Wang / Zihan Jia / Xiaohan Ye / Chunxiao Chen / Baofa Sun / Xiangshuai Zhao / Ruiqi Zhang / Ying Li / Wenya Wang / Zixian Sun / Lushuai Zhou / Zhiyu Ni / Nan Zhang / Yu Guo /
History
DepositionOct 14, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61939.png

Downloads & links

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Map

FileDownload / File: emd_61939.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.)
0.69 Å/pix.
x 380 pix.
= 262.2 Å		0.69 Å/pix.
x 380 pix.
= 262.2 Å		0.69 Å/pix.
x 380 pix.
= 262.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0135
Minimum - Maximum-0.11282379 - 0.21648073
Average (Standard dev.)0.00012290129 (±0.005228729)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 262.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61939_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_61939_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 : Ternary complex of VZV gE with neutralizing antibodies Fab WLL-1 ...

EntireName: Ternary complex of VZV gE with neutralizing antibodies Fab WLL-1 and WLL-28
Components
  • Complex: Ternary complex of VZV gE with neutralizing antibodies Fab WLL-1 and WLL-28
    • Protein or peptide: Envelope glycoprotein E
    • Protein or peptide: WLL-1 Fab heavy chain
    • Protein or peptide: WLL-1 Fab light chain
    • Protein or peptide: WLL-28 Fab heavy chain
    • Protein or peptide: WLL-28 Fab light chain

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Supramolecule #1: Ternary complex of VZV gE with neutralizing antibodies Fab WLL-1 ...

SupramoleculeName: Ternary complex of VZV gE with neutralizing antibodies Fab WLL-1 and WLL-28
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Varicella-zoster virus (strain Oka vaccine)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Envelope glycoprotein E

MacromoleculeName: Envelope glycoprotein E / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Varicella-zoster virus (strain Oka vaccine)
Molecular weightTheoretical: 63.17116 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGTVNKPVVG VLMGFGIITG TLRITNPVRA SVLRYDDFHI DEDKLDTNSV YEPYYHSDHA ESSWVNRGES SRKAYDHNSP YIWPRNDYD GFLENAHEHH GVYNQGRGID SGERLMQPTQ MSAQEDLGDD TGIHVIPTLN GDDRHKIVNV DQRQYGDVFK G DLNPKPQG ...String:
MGTVNKPVVG VLMGFGIITG TLRITNPVRA SVLRYDDFHI DEDKLDTNSV YEPYYHSDHA ESSWVNRGES SRKAYDHNSP YIWPRNDYD GFLENAHEHH GVYNQGRGID SGERLMQPTQ MSAQEDLGDD TGIHVIPTLN GDDRHKIVNV DQRQYGDVFK G DLNPKPQG QRLIEVSVEE NHPFTLRAPI QRIYGVRYTE TWSFLPSLTC TGDAAPAIQH ICLKHTTCFQ DVVVDVDCAE NT KEDQLAE ISYRFQGKKE ADQPWIVVNT STLFDELELD PPEIEPGVLK VLRTEKQYLG VYIWNMRGSD GTSTYATFLV TWK GDEKTR NPTPAVTPQP RGAEFHMWNY HSHVFSVGDT FSLAMHLQYK IHEAPFDLLL EWLYVPIDPT CQPMRLYSTC LYHP NAPQC LSHMNSGCTF TSPHLAQRVA STVYQNCEHA DNYTAYCLGI SHMEPSFGLI LHDGGTTLKF VDTPESLSGL YVFVV YFNG HVEAVAYTVV STVDHFVNAI EERGFPPTAG QPPATTKPKE ITPVNPGTSP LLRGSGSDYK DDDDKAAAHH HHHHHH

UniProtKB: Envelope glycoprotein E

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Macromolecule #2: WLL-1 Fab heavy chain

MacromoleculeName: WLL-1 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.313678 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QITLKESGPT LVKPTQTLTL TCTFSGFSLT NTEMTVGWIR RPPGKALEWL ALIYWDDDKR YSPSLRSRLT ITKDTSKNQV VLKMTNMDP VDTATYYCAR LSLRLLTFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
QITLKESGPT LVKPTQTLTL TCTFSGFSLT NTEMTVGWIR RPPGKALEWL ALIYWDDDKR YSPSLRSRLT ITKDTSKNQV VLKMTNMDP VDTATYYCAR LSLRLLTFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCD

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Macromolecule #3: WLL-1 Fab light chain

MacromoleculeName: WLL-1 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.816195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SYVVTQPPSV SVAPRQTARI TCGGSNIGSK SVHWHQQKPG QAPVLVVYDD SDRPSGIPER FSGSNSGNTA TLTITRVEAG DEADYYCQV WDSSGDHPLF GGGTKLTVLG QPKANPTVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADGSPVKA G VETTKPSK ...String:
SYVVTQPPSV SVAPRQTARI TCGGSNIGSK SVHWHQQKPG QAPVLVVYDD SDRPSGIPER FSGSNSGNTA TLTITRVEAG DEADYYCQV WDSSGDHPLF GGGTKLTVLG QPKANPTVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADGSPVKA G VETTKPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS

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Macromolecule #4: WLL-28 Fab heavy chain

MacromoleculeName: WLL-28 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.929906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVQSGAE VKKPGEPLKI SCKASGYNFA NFWVGWVRQM PGRGLEWMGV IFPADSDTRY SPSFQGQVII SADKSTNTAY LQWSSLKAS DSAMYYCARH VRGSLWGGGG YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
EVQLVQSGAE VKKPGEPLKI SCKASGYNFA NFWVGWVRQM PGRGLEWMGV IFPADSDTRY SPSFQGQVII SADKSTNTAY LQWSSLKAS DSAMYYCARH VRGSLWGGGG YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCD

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Macromolecule #5: WLL-28 Fab light chain

MacromoleculeName: WLL-28 Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.316805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVMTQSPST LSVSPGEGAT LSCRASQSVN NDLAWYQQKP GQAPRLLING ASTRATGIPA RFTGSGSGTE FTLTISSLQP EDFAVYFCQ QYNDWPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVMTQSPST LSVSPGEGAT LSCRASQSVN NDLAWYQQKP GQAPRLLING ASTRATGIPA RFTGSGSGTE FTLTISSLQP EDFAVYFCQ QYNDWPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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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: 2.2 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 324054
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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