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- EMDB-46761: Cryo-EM structure of neutralizing human antibody D48 in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-46761
TitleCryo-EM structure of neutralizing human antibody D48 in complex with HSV-1 glycoprotein B trimer gB-Ecto.516P.531E
Map data
Sample
  • Complex: D48 in complex with HSV-1 gB ectodomain trimer
    • Complex: D48 Fab heavy chain, D48 Fab light chain
      • Protein or peptide: D48 heavy chain
      • Protein or peptide: D48 light chain
    • Complex: HSV-1 gB ectodomain trimer gB-Ecto.516P.531E
      • Protein or peptide: Glycoprotein B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsimmune complex / neutralization / herpes fusogen / VIRAL PROTEIN
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 speciesHomo sapiens (human) / Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsRoark RS / Shapiro LS / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Herpes simplex virus 1 evades prefusion gB neutralization
Authors: Roark RS / Shapiro L / Kwong PD
History
DepositionAug 27, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46761.png

Downloads & links

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Map

FileDownload / File: emd_46761.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.12172278 - 0.28858557
Average (Standard dev.)0.0016848457 (±0.0101050455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46761_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_46761_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 : D48 in complex with HSV-1 gB ectodomain trimer

EntireName: D48 in complex with HSV-1 gB ectodomain trimer
Components
  • Complex: D48 in complex with HSV-1 gB ectodomain trimer
    • Complex: D48 Fab heavy chain, D48 Fab light chain
      • Protein or peptide: D48 heavy chain
      • Protein or peptide: D48 light chain
    • Complex: HSV-1 gB ectodomain trimer gB-Ecto.516P.531E
      • Protein or peptide: Glycoprotein B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: D48 in complex with HSV-1 gB ectodomain trimer

SupramoleculeName: D48 in complex with HSV-1 gB ectodomain trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: D48 Fab heavy chain, D48 Fab light chain

SupramoleculeName: D48 Fab heavy chain, D48 Fab light chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: HSV-1 gB ectodomain trimer gB-Ecto.516P.531E

SupramoleculeName: HSV-1 gB ectodomain trimer gB-Ecto.516P.531E / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)

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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 alphaherpesvirus 1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 90.320102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHQGAPSWGR RWFVVWALLG LTLGVLVASA APSSPGTPGV AAATQAANGG PATPAPPALG AAPTGDPKPK KNKKPKNPTP PRPAGDNAT VAAGHATLRE HLRDIKAENT DANFYVCPPP TGATVVQFEQ PRRCPTRPEG QNYTEGIAVV FKENIAPYKF K ATMYYKDV ...String:
MHQGAPSWGR RWFVVWALLG LTLGVLVASA APSSPGTPGV AAATQAANGG PATPAPPALG AAPTGDPKPK KNKKPKNPTP PRPAGDNAT VAAGHATLRE HLRDIKAENT DANFYVCPPP TGATVVQFEQ PRRCPTRPEG QNYTEGIAVV FKENIAPYKF K ATMYYKDV TVSQVWFGHR YSQFMGIFED RAPVPFEEVI DKINAKGVCR STAKYVRNNL ETTAFHRDDH ETDMELKPAN AA TRTSRGW HTTDLKYNPS RVEAFHRYGT TVNCIVEEVD ARSVYPYDEF VLATGDFVYM SPFYGYREGS HTEHTSYAAD RFK QVDGFY ARDLTTKARA TAPTTRNLLT TPKFTVAWDW VPKRPSVCTM TKWQEVDEML RSEYGGSFRF SSDAISTTFT TNLT EYPLS RVDLGDCIGK DARDAMDRIF ARRYNATHIK VGQPQYYLAN GGFLIAYQPL LSNTLAELYV REHLREQSRK PPNPT PPPP GASANASVER IKTTSSIEFA RLQFTYNHIQ RPVNDMLGRV AIAWCEEQNH ELTLWNEARK LNPNAIASVT VGRRVS ARM LGDVMAVSTC VPVAADNVIV QNSMRISSRP GACYSRPLVS FRYEDQGPLV EGQLGENNEL RLTRDAIEPC TVGHRRY FT FGGGYVYFEE YAYSHQLSRA DITTVSTFID LNITMLEDHE FVPLEVYTRH EIKDSGLLDY TEVQRRNQLH DLRFADID T VIHADANGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGRSL EVLFQGPGHH HHHHHHSAWS HPQFEKGGGS GGGGSGGSA WSHPQFEK

UniProtKB: Glycoprotein B

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Macromolecule #2: D48 heavy chain

MacromoleculeName: D48 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.59041 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVETGGGV VRPGRSLRLS CTTSGFSFSG SAMHWVRQAP GKGLEWVAVI SHDGNIIQYH DSVKGRFTIS RDNSKNVLLL QMNSLRVDD TAMYYCARDV WLLPATISYA FDFWGQGTMV TVSS

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Macromolecule #3: D48 light chain

MacromoleculeName: D48 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.716142 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VIWMTQSPPS LSASIGDTVT ITCRASQGIS NSIAWYQRRP GKAPELLVYA AYRLQSGVPS RLSGSGSGAE YTLTIKNMQP EDFATYYCQ QYYDNPLTFG GGTKVEIK

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / 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: 7.5 / Details: PBS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2gum

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43574
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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