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- EMDB-34063: Cyro-EM structure of HCMV glycoprotein B in complex with 1B03 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-34063
TitleCyro-EM structure of HCMV glycoprotein B in complex with 1B03 Fab
Map data
Sample
  • Complex: HCMV glycoprotein B in complex with 1B03 Fab
    • Complex: HCMV glycoprotein B
      • Complex: 1B03 Fab
        • Protein or peptide: 1B03 Fab antibody Heavy Chain
        • Protein or peptide: 1B03 Fab antibody Light Chain
      • Protein or peptide: Envelope glycoprotein B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVIRAL PROTEN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / 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
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman betaherpesvirus 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsWang H / Zhu S / Liao H
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Cyro-EM structure of HCMV glycoprotein B in complex with 1B03 Fab
Authors: Wu C / Wang H / Zhu S / Liao H
History
DepositionAug 10, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34063.png

Downloads & links

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Map

FileDownload / File: emd_34063.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 308.16 Å		0.86 Å/pix.
x 360 pix.
= 308.16 Å		0.86 Å/pix.
x 360 pix.
= 308.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.030655902 - 0.06591142
Average (Standard dev.)0.00016856333 (±0.0014347692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 308.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34063_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_34063_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 : HCMV glycoprotein B in complex with 1B03 Fab

EntireName: HCMV glycoprotein B in complex with 1B03 Fab
Components
  • Complex: HCMV glycoprotein B in complex with 1B03 Fab
    • Complex: HCMV glycoprotein B
      • Complex: 1B03 Fab
        • Protein or peptide: 1B03 Fab antibody Heavy Chain
        • Protein or peptide: 1B03 Fab antibody Light Chain
      • Protein or peptide: Envelope glycoprotein B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HCMV glycoprotein B in complex with 1B03 Fab

SupramoleculeName: HCMV glycoprotein B in complex with 1B03 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: HCMV glycoprotein B

SupramoleculeName: HCMV glycoprotein B / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human betaherpesvirus 5

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Supramolecule #3: 1B03 Fab

SupramoleculeName: 1B03 Fab / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5 / Strain: Towne
Molecular weightTheoretical: 83.545547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MESRIWCLVV CVNLCIVCLG AAVSSSSTRG TSATHSHHSS HTTSAAHSRS GSVSQRVTSS QTVSHGVNET IYNTTLKYGD VVGVNTTKY PYRVCSMAQG TDLIRFERNI VCTSMKPINE DLDEGIMVVY KRNIVAHTFK VRVYQKVLTF RRSYAYHRTT Y LLGSNTEY ...String:
MESRIWCLVV CVNLCIVCLG AAVSSSSTRG TSATHSHHSS HTTSAAHSRS GSVSQRVTSS QTVSHGVNET IYNTTLKYGD VVGVNTTKY PYRVCSMAQG TDLIRFERNI VCTSMKPINE DLDEGIMVVY KRNIVAHTFK VRVYQKVLTF RRSYAYHRTT Y LLGSNTEY VAPPMWEIHH INSHSQCYSS YSRVIAGTVF VAYHRDSYEN KTMQLMPDDY SNTHSTRYVT VKDQWHSRGS TN LTRETSN LNCMVTITTA RSKYPYHFFA TSTGDVVDIS PFYNGTNRNA SYFGENADKF FIFPNYTIVS DFGRPNSALE THR LVAFLE RADSVISWDI QDEKNVTCQL TFWEASERTI RSEAEDSYHF SSAKMTATFL SKKQEVNMSD SALDCVRDEA INKL QQIFN TSYNQTYEKY GNVSVFETTG GLVVFWQGIK QKSLVELERL ANRSSLNLTH NETKESTDGN NATHLSNMES VHNLV YAQL QFTYDTLRGY INRALAQIAE AWCVDQRRTL EVFKELSKIN PSAILSAIYN KPIAARFMGD VLGLASCVTI NQTSVK VLR DMNVKESPGR CYSRPVVIFN FANSSYVQYG QLGEDNEILL GNHRTEECQL PSLKIFIAGN SAYEYVDYLF KRMIDLS SI STVDSMIALD IDPLENTDFR VLELYSQKEL RSINVFDLEE IMREFNSYKQ RVKYVEDKGL NDIFEAQKIE WHELEVLF Q GPGHHHHHHH

UniProtKB: Envelope glycoprotein B

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Macromolecule #2: 1B03 Fab antibody Heavy Chain

MacromoleculeName: 1B03 Fab antibody Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.851783 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGESLKI SCKGSGYTFT NYWIGWVRQM PGAGLEWMAI IFPRDSYSAY SPSFQGRVTI SVDKSISTAY LHWSSLEAS DTAVYYCAIY NDLRSGNSWG QGTPLIVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLVQSGAE VKKPGESLKI SCKGSGYTFT NYWIGWVRQM PGAGLEWMAI IFPRDSYSAY SPSFQGRVTI SVDKSISTAY LHWSSLEAS DTAVYYCAIY NDLRSGNSWG QGTPLIVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCDK

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Macromolecule #3: 1B03 Fab antibody Light Chain

MacromoleculeName: 1B03 Fab antibody Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.508117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSIT KYLNWYQQKP GRAPKLLIHT TSTLQSGVPS RFSGSGSGTD FTLTISSLQL EDFGTYYCQ QSFSTLWTFG QGTKLDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSIT KYLNWYQQKP GRAPKLLIHT TSTLQSGVPS RFSGSGSGTD FTLTISSLQL EDFGTYYCQ QSFSTLWTFG QGTKLDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185463
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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