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- EMDB-79524: HCMV gH/gK + D11L, B1L, G2L Fabs Local Refinement Map -

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Basic information

Entry
Database: EMDB / ID: EMD-79524
TitleHCMV gH/gK + D11L, B1L, G2L Fabs Local Refinement Map
Map dataHCMV gH/gK D11L, B1L, G2L Fabs Local Refinement Map
Sample
  • Complex: HCMV gH/gK + D11L, B1L, G2L Fabs
    • Complex: HCMV gH/gK
      • Protein or peptide: HCMV gK
      • Protein or peptide: HCMV gH
    • 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
Biological speciesHuman herpesvirus 5 strain AD169, Homo sapiens / Human herpesvirus 5 strain AD169 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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_79524.png

Downloads & links

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Map

FileDownload / File: emd_79524.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHCMV gH/gK D11L, B1L, G2L Fabs Local Refinement Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (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: 0.0375
Minimum - Maximum-0.13718876 - 0.23108843
Average (Standard dev.)0.00015124961 (±0.0044158413)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: Half map A

Fileemd_79524_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_79524_half_map_2.map
AnnotationHalf map B
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 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: HCMV gH
    • 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: 13.928717 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AVHLVESGGG LVKPGGSLRL SCAASGFSFS NTWMSWVRQA PGKGPEYIGR IKTKVDGATV DSAAPVKGRF TISRDDSKNT LYLQMKRLTT EDTAMYYCAT VKYYGSGTPP FGYSYFDYWG QGTLVTVSPA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW ...String:
AVHLVESGGG LVKPGGSLRL SCAASGFSFS NTWMSWVRQA PGKGPEYIGR IKTKVDGATV DSAAPVKGRF TISRDDSKNT LYLQMKRLTT EDTAMYYCAT VKYYGSGTPP FGYSYFDYWG QGTLVTVSPA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCD

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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: 11.428567 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLSQAPSA SGTPGQRVSI ACSGSNSNIG NNYVNWYQRL PGTAPKLLIH RNDQRPSGVP DRFSGSKSGT SGSLAISGLR SEDEGDYYCA VWDDSLLTWV FGGGTRLAVL RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD ...String:
QSVLSQAPSA SGTPGQRVSI ACSGSNSNIG NNYVNWYQRL PGTAPKLLIH RNDQRPSGVP DRFSGSKSGT SGSLAISGLR SEDEGDYYCA VWDDSLLTWV FGGGTRLAVL RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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: 13.337002 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVKPGGSLRL SCAASGFSFS RYTMNWVRQA PGKGLEWVSS ITSSSAYISY ADSLRGRFSI SRDNAKSSLY LQMYTLRAED TAIYYCARAR MGTATAPGPY YFDFWGLGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA ...String:
EVQLVESGGG LVKPGGSLRL SCAASGFSFS RYTMNWVRQA PGKGLEWVSS ITSSSAYISY ADSLRGRFSI SRDNAKSSLY LQMYTLRAED TAIYYCARAR MGTATAPGPY YFDFWGLGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCD

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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: 10.949197 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTVVTHEVSF SVSPGGTVTL TCGLNSDSVS ANYYPSWYQQ TPGQTPRTLI YNTNIRFSGV PERFSGSILG NKAALTIAGA QADDEGKYYC ALHLRSGVWV FGGGTKVTVL RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD ...String:
QTVVTHEVSF SVSPGGTVTL TCGLNSDSVS ANYYPSWYQQ TPGQTPRTLI YNTNIRFSGV PERFSGSILG NKAALTIAGA QADDEGKYYC ALHLRSGVWV FGGGTKVTVL RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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: 12.888192 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGSE LRKPGASVTV SCKASGYTFT AYGINWVRQA PGQGPEWLGW INTFTGKPTY AQDFIGRLVF SLDTSVDTAY LQISSLQAED SALYFCARES NWNYDHWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF ...String:
QVQLVQSGSE LRKPGASVTV SCKASGYTFT AYGINWVRQA PGQGPEWLGW INTFTGKPTY AQDFIGRLVF SLDTSVDTAY LQISSLQAED SALYFCARES NWNYDHWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC D

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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: 10.853939 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSGQGSQSSV SVPPGGTITL TCGLSSGSVS SSDYPSWYQQ TPGQAPRTLI YSTNIRSFGV PDRFSGSILG NKAALTITGA QAEDESDYFC LVYAGSNTWV FGGGTKLTVL RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD ...String:
GSGQGSQSSV SVPPGGTITL TCGLSSGSVS SSDYPSWYQQ TPGQAPRTLI YSTNIRSFGV PDRFSGSILG NKAALTITGA QAEDESDYFC LVYAGSNTWV FGGGTKLTVL RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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: 12.571927 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRRRRWRGW LLFPALCFCL LCEAVETNAT TVTSTTAAAA TTNTTVATTG TTTTSPNVTS TTSNTVTTPT TVSSVSNLTS STTSIPISTS TVSGTRNTGN NNTTTIGTNA TSPSPSVSIL TTVTPAATST ISVDGVVTAS DYTPTFDDLE NITTTRAPTR PPAQDLCSHN ...String:
MKRRRRWRGW LLFPALCFCL LCEAVETNAT TVTSTTAAAA TTNTTVATTG TTTTSPNVTS TTSNTVTTPT TVSSVSNLTS STTSIPISTS TVSGTRNTGN NNTTTIGTNA TSPSPSVSIL TTVTPAATST ISVDGVVTAS DYTPTFDDLE NITTTRAPTR PPAQDLCSHN LSIILYEEES QSSVDIAVDE EEPELEDDDE YDELWFPLYF EAECNRNYTL HVNHSCDYSV RQSSVSFPPW RDIDSVTFVP RNLSNCSAHG LAVIVAGNQT WYVNPFSLAH LLDAIYNVLG IEDLSANFRR QLAPYRHTLI VPQTAAASWS HPQFEKGGAS GGGGSGGSAW SHPQFEK

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Macromolecule #8: HCMV gH

MacromoleculeName: HCMV gH / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 5 strain AD169
Molecular weightTheoretical: 71.676047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSVPTQVLGL LLLWLTDARC RYGADAASEA LDPHAFHLLL NTYGRPIRFL RENTTQCTYN SSLRNSTVVR ENAISFNFFQ SYNQYYVFHM PRCLFAGPLA EQFLNQVDLT ETLERYQQRL NTYALVSKDL ASYRSFSQQL KAQDSLGQQP TTVPPPIDLS IPHVWMPPQT ...String:
MSVPTQVLGL LLLWLTDARC RYGADAASEA LDPHAFHLLL NTYGRPIRFL RENTTQCTYN SSLRNSTVVR ENAISFNFFQ SYNQYYVFHM PRCLFAGPLA EQFLNQVDLT ETLERYQQRL NTYALVSKDL ASYRSFSQQL KAQDSLGQQP TTVPPPIDLS IPHVWMPPQT TPHDWKGSHT TSGLHRPHFN QTCILFDGHD LLFSTVTPCL HQGFYLMDEL RYVKITLTED FFVVTVSIDD DTPMLLIFGH LPRVLFKAPY QRDNFILRQT EKHELLVLVK KAQLNRHSYL KDSDFLDAAL DFNYLDLSAL LRNSFHRYAV DVLKSGRCQM LDRRTVEMAF AYALALFAAA RQEEAGTEIS IPRALDRQAA LLQIQEFMIT CLSQTPPRTT LLLYPTAVDL AKRALWTPDQ ITDITSLVRL VYILSKQNQQ HLIPQWALRQ IADFALQLHK THLASFLSAF ARQELYLMGS LVHSMLVHTT ERREIFIVET GLCSLAELSH FTQLLAHPHH EYLSDLYTPC SSSGRRDHSL ERLTRLFPDA TVPATVPAAL SILSTMQPST LETFPDLFCL PLGESFSALT VSEHVSYVVT NQYLIKGISY PVSTTVVGQS LIITQTDSQT KCELTRNMHT THSITAALNI SLENCAFCQS ALLEYDDTQG VINIMYMHDS DDVLFALDPY NEVVVSSPRT HYLMLLKNGT VLEVTDVVVD ATDSRHHHHH 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: Global refinement map from the same dataset used as the starting volume
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 14324
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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