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- EMDB-31515: Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5 -

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Basic information

Entry
Database: EMDB / ID: EMD-31515
TitleCryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5
Map data
Sample
  • Complex: Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5
    • Protein or peptide: 3A3 heavy chain
    • Protein or peptide: 3A3 light chain
    • Protein or peptide: Envelope glycoprotein B
    • Protein or peptide: 3A5 light chain
    • Protein or peptide: 3A5 heavy chain
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / membrane => GO:0016020 / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZheng Q / Li S / Zha Z / Hong J / Chen Y / Zhang X
CitationJournal: To Be Published
Title: Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5
Authors: Zheng Q / Li S / Zha Z / Hong J / Chen Y / Zhang X
History
DepositionJul 10, 2021-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJul 13, 2022-
Current statusJul 13, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31515.png

Downloads & links

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Map

FileDownload / File: emd_31515.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 3.2
Minimum - Maximum-19.151176 - 28.493126
Average (Standard dev.)0.001798083 (±0.9064687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5

EntireName: Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5
Components
  • Complex: Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5
    • Protein or peptide: 3A3 heavy chain
    • Protein or peptide: 3A3 light chain
    • Protein or peptide: Envelope glycoprotein B
    • Protein or peptide: 3A5 light chain
    • Protein or peptide: 3A5 heavy chain

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Supramolecule #1: Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5

SupramoleculeName: Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: 3A3 heavy chain

MacromoleculeName: 3A3 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 11.744192 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVKESGGRL VTPGTPLTLT CTVSGFSLSS YAMSWVRQAP GKGLEYIGVI YASGSTYYAS WAKGRFTISR TATTVDLKIT SPTTEDTAT YFCGRGVSTN MWGPGTLVTV SS

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Macromolecule #2: 3A3 light chain

MacromoleculeName: 3A3 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 11.572933 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DLVMTQTPSS VSAAVGGTVT IKCQASQSLG GGLAWYQQKP GQRPKLLIYS ASTLESGVPS RFRGSGSGTE FTLTISDLEC ADAATYYCQ SAYGPTSNGL FNAFGGGTKV VIK

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Macromolecule #3: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Strain: GD1
Molecular weightTheoretical: 73.456188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AQTPEQPAPP ATTVQPTATR QQTSFPFRVC ELSSHGDLFR FSSDIQCPSF GTRENHTEGL LMVFKDNIIP YSFKVRSYTK IVTNILIYN GHRADSVTNR HEEKFSVESY ETDQMDTIYQ CYNAVKMTKD GLTRVYVDRD GVNITVNLKP TGGLANGVRR Y ASQTELYD ...String:
AQTPEQPAPP ATTVQPTATR QQTSFPFRVC ELSSHGDLFR FSSDIQCPSF GTRENHTEGL LMVFKDNIIP YSFKVRSYTK IVTNILIYN GHRADSVTNR HEEKFSVESY ETDQMDTIYQ CYNAVKMTKD GLTRVYVDRD GVNITVNLKP TGGLANGVRR Y ASQTELYD APGRVEATYR TRTTVNCLIT DMMAKSNSPF DFFVTTTGQT VEMSPFYDGK NTETFHERAD SFHVRTNYKI VD YDNRGTN PQGERRAFLD KGTYTLSWKL ENRTAYCPLQ HWQTFDSTIA TETGKSIHFV TDEGTSSFVT NTTVGIELPD AFK CIEEQV NKTMHEKYEA VQDRYTKGQE AITYFITSGG LLLAWLPLTP RSLATVKNLT ELTTPTSSPP SSPSPPAPPA ARGS TSAAV LRRRRRNAGN ATTPVPPAAP GKSLGTLNNP ATVQIQFAYD SLRRQINRML GDLARAWCLE QKRQNMVLRE LTKIN PTTV MSSIYGKAVA AKRLGDVISV SQCVPVNQAT VTLRKSMRVP GSETMCYSRP LVSFSFINDT KTYEGQLGTD NEIFLT KKM TEVCQATSQY YFQSGNEIHV YNDYHHFKTI ELDGIATLQT FISLNTSLIE NIDFASLELY SRDEQRASNV FDLEGIF RE YNFQAQNIAG L

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Macromolecule #4: 3A5 light chain

MacromoleculeName: 3A5 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 11.672961 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ALVMTQTPSS VSEPVGGTVT IKCQASQSIS SYLAWYQRKP GQRPKLLIYG TSTLASGVPS RFIGSGSGTD YTLTISDLEC DDAATYYCQ QGFSTSNVYN SFGGGTKVDI K

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Macromolecule #5: 3A5 heavy chain

MacromoleculeName: 3A5 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 12.513935 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVKESGGRL VTPGTPLTLT CTVSGFSLSS YEMGWVRQAP GEGLEWIGTI STGGSSYYAS WAKGRFTISR TSTTVDLKMT SLTTADTAT YFCARGYGGY GIGAGYFNIW GPGTLVTVSS

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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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 367966
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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