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- EMDB-79526: HCMV gH/gK + D11L, B1L, G2L Fabs Composite Map -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-79526
TitleHCMV gH/gK + D11L, B1L, G2L Fabs Composite Map
Map dataHCMV gH/gK D11L, B1L, G2L Fabs Composite Map
Sample
  • Complex: HCMV gH/gK + D11L, B1L, G2L Fabs
    • Complex: HCMV gH/gK
      • Protein or peptide: HCMV gK
      • Protein or peptide: Envelope glycoprotein H
    • Complex: B1L Fab
      • Protein or peptide: B1L Fab Heavy Chain
      • Protein or peptide: B1L Fab Light Chain
    • Complex: D11L Fab
      • Protein or peptide: D11L Fab Heavy Chain
      • Protein or peptide: D11L Fab Light Chain
    • Complex: G2L Fab
      • Protein or peptide: G2L Fab Heavy Chain
      • Protein or peptide: G2L Fab Light Chain
KeywordsVIRAL PROTEIN-IMMUNE SYSTEM complex / HCMV glycoprotein / gH-gK complex / antibody Fab / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endosome membrane / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane
Similarity search - Function
: / Human cytomegalovirus UL116 protein / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain
Similarity search - Domain/homology
Envelope glycoprotein H / Uncharacterized protein UL116
Similarity search - Component
Biological speciesHuman herpesvirus 5 strain AD169, Homo sapiens / Human herpesvirus 5 strain AD169 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsRamamohan AR / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: B cell response to HCMV gH/UL116 elicits neutralizing and Fc gamma receptor-activating antibodies
Authors: Ramamohan AR / McLellan JS
History
DepositionOct 12, 2026-
Header (metadata) releaseOct 28, 2026-
Map releaseOct 28, 2026-
UpdateOct 28, 2026-
Current statusOct 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_79526.png

Downloads & links

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Map

FileDownload / File: emd_79526.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHCMV gH/gK D11L, B1L, G2L Fabs Composite Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 416 pix.
= 346.611 Å		0.83 Å/pix.
x 416 pix.
= 346.611 Å		0.83 Å/pix.
x 416 pix.
= 346.611 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-44.198112000000002 - 62.074286999999998
Average (Standard dev.)0.0065177516 (±1.010991)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 346.6112 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HCMV gH/gK + D11L, B1L, G2L Fabs

EntireName: HCMV gH/gK + D11L, B1L, G2L Fabs
Components
  • Complex: HCMV gH/gK + D11L, B1L, G2L Fabs
    • Complex: HCMV gH/gK
      • Protein or peptide: HCMV gK
      • Protein or peptide: Envelope glycoprotein H
    • Complex: B1L Fab
      • Protein or peptide: B1L Fab Heavy Chain
      • Protein or peptide: B1L Fab Light Chain
    • Complex: D11L Fab
      • Protein or peptide: D11L Fab Heavy Chain
      • Protein or peptide: D11L Fab Light Chain
    • Complex: G2L Fab
      • Protein or peptide: G2L Fab Heavy Chain
      • Protein or peptide: G2L Fab Light Chain

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Supramolecule #1: HCMV gH/gK + D11L, B1L, G2L Fabs

SupramoleculeName: HCMV gH/gK + D11L, B1L, G2L Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human herpesvirus 5 strain AD169, Homo sapiens

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Supramolecule #2: HCMV gH/gK

SupramoleculeName: HCMV gH/gK / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Human herpesvirus 5 strain AD169

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Supramolecule #3: B1L Fab

SupramoleculeName: B1L Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: D11L Fab

SupramoleculeName: D11L Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: G2L Fab

SupramoleculeName: G2L Fab / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: B1L Fab Heavy Chain

MacromoleculeName: B1L Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.68283 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AVHLVESGGG LVKPGGSLRL SCAASGFSFS NTWMSWVRQA PGKGPEYIGR IKTKVDGATV DSAAPVKGRF TISRDDSKNT LYLQMKRLT TEDTAMYYCA TVKYYGSGTP PFGYSYFDYW GQGTLVTVSP ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String:
AVHLVESGGG LVKPGGSLRL SCAASGFSFS NTWMSWVRQA PGKGPEYIGR IKTKVDGATV DSAAPVKGRF TISRDDSKNT LYLQMKRLT TEDTAMYYCA TVKYYGSGTP PFGYSYFDYW GQGTLVTVSP ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSCD

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Macromolecule #2: B1L Fab Light Chain

MacromoleculeName: B1L Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.403797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLSQAPSA SGTPGQRVSI ACSGSNSNIG NNYVNWYQRL PGTAPKLLIH RNDQRPSGVP DRFSGSKSGT SGSLAISGLR SEDEGDYYC AVWDDSLLTW VFGGGTRLAV LRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
QSVLSQAPSA SGTPGQRVSI ACSGSNSNIG NNYVNWYQRL PGTAPKLLIH RNDQRPSGVP DRFSGSKSGT SGSLAISGLR SEDEGDYYC AVWDDSLLTW VFGGGTRLAV LRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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Macromolecule #3: D11L Fab Heavy Chain

MacromoleculeName: D11L Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.293322 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVKPGGSLRL SCAASGFSFS RYTMNWVRQA PGKGLEWVSS ITSSSAYISY ADSLRGRFSI SRDNAKSSLY LQMYTLRAE DTAIYYCARA RMGTATAPGP YYFDFWGLGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
EVQLVESGGG LVKPGGSLRL SCAASGFSFS RYTMNWVRQA PGKGLEWVSS ITSSSAYISY ADSLRGRFSI SRDNAKSSLY LQMYTLRAE DTAIYYCARA RMGTATAPGP YYFDFWGLGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC D

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Macromolecule #4: D11L Fab Light Chain

MacromoleculeName: D11L Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.50508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTVVTHEVSF SVSPGGTVTL TCGLNSDSVS ANYYPSWYQQ TPGQTPRTLI YNTNIRFSGV PERFSGSILG NKAALTIAGA QADDEGKYY CALHLRSGVW VFGGGTKVTV LRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
QTVVTHEVSF SVSPGGTVTL TCGLNSDSVS ANYYPSWYQQ TPGQTPRTLI YNTNIRFSGV PERFSGSILG NKAALTIAGA QADDEGKYY CALHLRSGVW VFGGGTKVTV LRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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Macromolecule #5: G2L Fab Heavy Chain

MacromoleculeName: G2L Fab Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.571221 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGSE LRKPGASVTV SCKASGYTFT AYGINWVRQA PGQGPEWLGW INTFTGKPTY AQDFIGRLVF SLDTSVDTAY LQISSLQAE DSALYFCARE SNWNYDHWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
QVQLVQSGSE LRKPGASVTV SCKASGYTFT AYGINWVRQA PGQGPEWLGW INTFTGKPTY AQDFIGRLVF SLDTSVDTAY LQISSLQAE DSALYFCARE SNWNYDHWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCD

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Macromolecule #6: G2L Fab Light Chain

MacromoleculeName: G2L Fab Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.0874 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSGQGSQSSV SVPPGGTITL TCGLSSGSVS SSDYPSWYQQ TPGQAPRTLI YSTNIRSFGV PDRFSGSILG NKAALTITGA QAEDESDYF CLVYAGSNTW VFGGGTKLTV LRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
GSGQGSQSSV SVPPGGTITL TCGLSSGSVS SSDYPSWYQQ TPGQAPRTLI YSTNIRSFGV PDRFSGSILG NKAALTITGA QAEDESDYF CLVYAGSNTW VFGGGTKLTV LRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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Macromolecule #7: HCMV gK

MacromoleculeName: HCMV gK / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 5 strain AD169
Molecular weightTheoretical: 37.405863 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRRRRWRGW LLFPALCFCL LCEAVETNAT TVTSTTAAAA TTNTTVATTG TTTTSPNVTS TTSNTVTTPT TVSSVSNLTS STTSIPIST STVSGTRNTG NNNTTTIGTN ATSPSPSVSI LTTVTPAATS TISVDGVVTA SDYTPTFDDL ENITTTRAPT R PPAQDLCS ...String:
MKRRRRWRGW LLFPALCFCL LCEAVETNAT TVTSTTAAAA TTNTTVATTG TTTTSPNVTS TTSNTVTTPT TVSSVSNLTS STTSIPIST STVSGTRNTG NNNTTTIGTN ATSPSPSVSI LTTVTPAATS TISVDGVVTA SDYTPTFDDL ENITTTRAPT R PPAQDLCS HNLSIILYEE ESQSSVDIAV DEEEPELEDD DEYDELWFPL YFEAECNRNY TLHVNHSCDY SVRQSSVSFP PW RDIDSVT FVPRNLSNCS AHGLAVIVAG NQTWYVNPFS LAHLLDAIYN VLGIEDLSAN FRRQLAPYRH TLIVPQTAAA SWS HPQFEK GGASGGGGSG GSAWSHPQFE K

UniProtKB: Uncharacterized protein UL116

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Macromolecule #8: Envelope glycoprotein H

MacromoleculeName: Envelope glycoprotein H / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 5 strain AD169
Molecular weightTheoretical: 82.101461 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSVPTQVLGL LLLWLTDARC RYGADAASEA LDPHAFHLLL NTYGRPIRFL RENTTQCTYN SSLRNSTVVR ENAISFNFFQ SYNQYYVFH MPRCLFAGPL AEQFLNQVDL TETLERYQQR LNTYALVSKD LASYRSFSQQ LKAQDSLGQQ PTTVPPPIDL S IPHVWMPP ...String:
MSVPTQVLGL LLLWLTDARC RYGADAASEA LDPHAFHLLL NTYGRPIRFL RENTTQCTYN SSLRNSTVVR ENAISFNFFQ SYNQYYVFH MPRCLFAGPL AEQFLNQVDL TETLERYQQR LNTYALVSKD LASYRSFSQQ LKAQDSLGQQ PTTVPPPIDL S IPHVWMPP QTTPHDWKGS HTTSGLHRPH FNQTCILFDG HDLLFSTVTP CLHQGFYLMD ELRYVKITLT EDFFVVTVSI DD DTPMLLI FGHLPRVLFK APYQRDNFIL RQTEKHELLV LVKKAQLNRH SYLKDSDFLD AALDFNYLDL SALLRNSFHR YAV DVLKSG RCQMLDRRTV EMAFAYALAL FAAARQEEAG TEISIPRALD RQAALLQIQE FMITCLSQTP PRTTLLLYPT AVDL AKRAL WTPDQITDIT SLVRLVYILS KQNQQHLIPQ WALRQIADFA LQLHKTHLAS FLSAFARQEL YLMGSLVHSM LVHTT ERRE IFIVETGLCS LAELSHFTQL LAHPHHEYLS DLYTPCSSSG RRDHSLERLT RLFPDATVPA TVPAALSILS TMQPST LET FPDLFCLPLG ESFSALTVSE HVSYVVTNQY LIKGISYPVS TTVVGQSLII TQTDSQTKCE LTRNMHTTHS ITAALNI SL ENCAFCQSAL LEYDDTQGVI NIMYMHDSDD VLFALDPYNE VVVSSPRTHY LMLLKNGTVL EVTDVVVDAT DSRHHHHH H

UniProtKB: Envelope glycoprotein H

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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 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 74.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Composite map generated from the global and local refinement maps using phenix.combine_focused_maps
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: OTHER / Software - Name: PHENIX (ver. 1.21rc1_5127)
Details: No resolution determined for the composite map; average of inputs reported (FSC 0.143 Gold Standard)
Number images used: 73502
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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