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- EMDB-72061: HCMV trimer in complex with G1L (II), G1L (A), B5L, C4K, B1K, A7K... -

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Basic information

Entry
Database: EMDB / ID: EMD-72061
TitleHCMV trimer in complex with G1L (II), G1L (A), B5L, C4K, B1K, A7K, A12K, and C5K Fabs
Map dataEM map for HCMV trimer in complex with G1L, B5L, C4K, B1K, A7K, A12K, and C5K Fabs
Sample
  • Complex: HCMV trimer in complex with G1L (II), G1L (A), B5L, C4K, B1K, A7K, A12K, and C5K Fabs
    • Protein or peptide: x 16 types
  • Ligand: x 1 types
KeywordsVirus / glycoprotein / antibody / VIRAL PROTEIN
Biological speciesHuman betaherpesvirus 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGoldsmith JA / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: To Be Published
Title: Structural characterization of antibodies for synergistic HCMV neutralization
Authors: Ashurov A / Goldsmith JA / McLellan JS / Zehner M / Klein F
History
DepositionAug 9, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72061.png

Downloads & links

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Map

FileDownload / File: emd_72061.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map for HCMV trimer in complex with G1L, B5L, C4K, B1K, A7K, A12K, and C5K Fabs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 400 pix.
= 376. Å		0.94 Å/pix.
x 400 pix.
= 376. Å		0.94 Å/pix.
x 400 pix.
= 376. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.28601664 - 0.6843887
Average (Standard dev.)-0.00012556552 (±0.018322563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 376.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map for HCMV trimer in complex with...

Fileemd_72061_additional_1.map
AnnotationSharpened map for HCMV trimer in complex with G1L, B5L, C4K, B1K, A7K, A12K, and C5K Fabs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B for HCMV trimer in complex with...

Fileemd_72061_half_map_1.map
AnnotationHalf-map B for HCMV trimer in complex with G1L, B5L, C4K, B1K, A7K, A12K, and C5K Fabs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A for HCMV trimer in complex with...

Fileemd_72061_half_map_2.map
AnnotationHalf-map A for HCMV trimer in complex with G1L, B5L, C4K, B1K, A7K, A12K, and C5K Fabs
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 trimer in complex with G1L (II), G1L (A), B5L, C4K, B1K, A7K...

EntireName: HCMV trimer in complex with G1L (II), G1L (A), B5L, C4K, B1K, A7K, A12K, and C5K Fabs
Components
  • Complex: HCMV trimer in complex with G1L (II), G1L (A), B5L, C4K, B1K, A7K, A12K, and C5K Fabs
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
    • Protein or peptide: Immunoglobulin lambda variable 1-51
    • Protein or peptide: G1L Fab heavy chain
    • Protein or peptide: Immunoglobulin heavy variable 1-46
    • Protein or peptide: Immunoglobulin kappa variable 3-20
    • Protein or peptide: A12K Fab heavy chain
    • Protein or peptide: Immunoglobulin heavy variable 4-34
    • Protein or peptide: A12K Fab light chain
    • Protein or peptide: Immunoglobulin kappa variable 1-39
    • Protein or peptide: Immunoglobulin heavy variable 4-39
    • Protein or peptide: B5L Fab light chain
    • Protein or peptide: C5K Fab light chain
    • Protein or peptide: Immunoglobulin heavy variable 1-46
    • Protein or peptide: C4K Fab heavy chain
    • Protein or peptide: C4K Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HCMV trimer in complex with G1L (II), G1L (A), B5L, C4K, B1K, A7K...

SupramoleculeName: HCMV trimer in complex with G1L (II), G1L (A), B5L, C4K, B1K, A7K, A12K, and C5K Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Human betaherpesvirus 5

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Macromolecule #1: Envelope glycoprotein H

MacromoleculeName: Envelope glycoprotein H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 84.538617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPGLPPYLT VFTVYLLSHL PSQRYGADAA SEALDPHAFH LLLNTYGRPI RFLRENTTQC TYNSSLRNST VVRENAISFN FFQSYNQYY VFHMPRCLFA GPLAEQFLNQ VDLTETLERY QQRLNTYALV SKDLASYRSF SQQLKAQDSL GQQPTTVPPP I DLSIPHVW ...String:
MRPGLPPYLT VFTVYLLSHL PSQRYGADAA SEALDPHAFH LLLNTYGRPI RFLRENTTQC TYNSSLRNST VVRENAISFN FFQSYNQYY VFHMPRCLFA GPLAEQFLNQ VDLTETLERY QQRLNTYALV SKDLASYRSF SQQLKAQDSL GQQPTTVPPP I DLSIPHVW MPPQTTPHDW KGSHTTSGLH RPHFNQTCIL FDGHDLLFST VTPCLHQGFY LMDELRYVKI TLTEDFFVVT VS IDDDTPM LLIFGHLPRV LFKAPYQRDN FILRQTEKHE LLVLVKKAQL NRHSYLKDSD FLDAALDFNY LDLSALLRNS FHR YAVDVL KSGRCQMLDR RTVEMAFAYA LALFAAARQE EAGTEISIPR ALDRQAALLQ IQEFMITCLS QTPPRTTLLL YPTA VDLAK RALWTPDQIT DITSLVRLVY ILSKQNQQHL IPQWALRQIA DFALQLHKTH LASFLSAFAR QELYLMGSLV HSMLV HTTE RREIFIVETG LCSLAELSHF TQLLAHPHHE YLSDLYTPCS SSGRRDHSLE RLTRLFPDAT VPATVPAALS ILSTMQ PST LETFPDLFCL PLGESFSALT VSEHVSYVVT NQYLIKGISY PVSTTVVGQS LIITQTDSQT KCELTRNMHT THSITAA LN ISLENCAFCQ SALLEYDDTQ GVINIMYMHD SDDVLFALDP YNEVVVSSPR THYLMLLKNG TVLEVTDVVV DATDSRLL M MSVYALSAII GIYLLYRMLK TC

UniProtKB: Envelope glycoprotein H

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Macromolecule #2: Envelope glycoprotein L

MacromoleculeName: Envelope glycoprotein L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 29.877336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSVPTQVLGL LLLWLTDARC VAVSVAPTAA EKVPAECPEL TRRCLLGEVF QGDKYESWLR PLVNVTRRDG PLSQLIRYRP VTPEAANSV LLDDAFLDTL ALLYNNPDQL RALLTLLSSD TAPRWMTVMR GYSECGDGSP AVYTCVDDLC RGYDLTRLSY G RSIFTEHV ...String:
MSVPTQVLGL LLLWLTDARC VAVSVAPTAA EKVPAECPEL TRRCLLGEVF QGDKYESWLR PLVNVTRRDG PLSQLIRYRP VTPEAANSV LLDDAFLDTL ALLYNNPDQL RALLTLLSSD TAPRWMTVMR GYSECGDGSP AVYTCVDDLC RGYDLTRLSY G RSIFTEHV LGFELVPPSL FNVVVAIRNE ATRTNRAVRL PVSTAAAPEG ITLFYGLYNA VKEFCLRHQL DPPLLRHLDK YY AGLPPEL KQTRVNLPAH SRYGPQAVDA R

UniProtKB: Envelope glycoprotein L

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Macromolecule #3: Immunoglobulin lambda variable 1-51

MacromoleculeName: Immunoglobulin lambda variable 1-51 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.542777 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSL SAAPGQRVTI SCTGSTSNIV NNYVSWYQHL PGTAPKLLIY DNVKRPSGIS DRFSGSKSGT TATLTITGLQ TGDESDYYC GTWDSSLSLG VFGGGTKVTV L

UniProtKB: Immunoglobulin lambda variable 1-51

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Macromolecule #4: G1L Fab heavy chain

MacromoleculeName: G1L Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.754686 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGGE VKKSGASVRV SCKTSGYMFN GYFLHWVRQA PGQGLEWMGW INPYNGATRL SQKFRGRVTL TRDTAISTAY LELTGLTYG DTAVYYCARP MTGFLVRGVM WGGFGPWGQG TLVTVS

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Macromolecule #5: Immunoglobulin heavy variable 1-46

MacromoleculeName: Immunoglobulin heavy variable 1-46 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.243856 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGASMKV SCKASGYTFT NYYLHWVRQA PGQGLEWMGL IDPSGGNTNY AQKFQGRVTM TRDRSTSTVY MELSSLRPE DTTVYYCARG GYNSRLRLDS WGQGTLVTVS

UniProtKB: Immunoglobulin heavy variable 1-46

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Macromolecule #6: Immunoglobulin kappa variable 3-20

MacromoleculeName: Immunoglobulin kappa variable 3-20 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.560817 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK SGQAPRLLIY GASSRATGIP DRFSGSASGT DFTLTISRLE PEDFALYYC QQYGSSPLTF GGGTKVEIK

UniProtKB: Immunoglobulin kappa variable 3-20

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Macromolecule #7: A12K Fab heavy chain

MacromoleculeName: A12K Fab heavy chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.971682 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGGG LVKPGGSLRL SCAASGFTFT DYYMSWIRQS PGKGLEWISY ISSSGSYTFY PDSVKGRFTV SRDNTKNSLF LQMDRLRVE DTAVYYCARS PMKRLDFWGQ GVLVTVS

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Macromolecule #8: Immunoglobulin heavy variable 4-34

MacromoleculeName: Immunoglobulin heavy variable 4-34 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.668204 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQQWGAG LLKPWETLSL TCAVYGGSIN EYYWSWIRQP PGGGLEWIGE INHSGSTNYN PSLKSRITTS VDTSKNQFSL RLSSVTVAD TAVYYCARGH RKGARISGRN WFDPWGQGSL VTVS

UniProtKB: Immunoglobulin heavy variable 4-34

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Macromolecule #9: A12K Fab light chain

MacromoleculeName: A12K Fab light chain / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.702073 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVMTQSPAT LSLSPGERAT LSCRASQSVG STLAWYQQKP GQAPRLLIFG TSTRATGVPT RFSGSGSGTE FTLIISSLRS EDSGLYFCQ HYESWPPWTF GQGTKVEVK

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Macromolecule #10: Immunoglobulin kappa variable 1-39

MacromoleculeName: Immunoglobulin kappa variable 1-39 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.678971 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASQSIS TYLNWYRQKP GKAPSLLIYA ISSLQTGVPS RFSGSGSGTD FTLTINNLQP EDFATYYCQ QSFSTPRTFG QGTKVEIK

UniProtKB: Immunoglobulin kappa variable 1-39

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Macromolecule #11: Immunoglobulin heavy variable 4-39

MacromoleculeName: Immunoglobulin heavy variable 4-39 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.333833 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGASIS SSGYYWGWIR QSPGKGLEWI GTIYYSGSTY YNPSLKSRVT ISVDTSNNQF SMKLSSVTA ADTAVYYCVR RVTYTKTWAF DYWGQGTLVT VS

UniProtKB: Immunoglobulin heavy variable 4-39

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Macromolecule #12: B5L Fab light chain

MacromoleculeName: B5L Fab light chain / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.503529 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASV SGSPGQSITI SCSGTSSNVG GYNYVSWYQQ HPGKAPKLII YDVTNRPAGV SSRFSGSKSG NTASLTISWL QAEDEADYY CSSFASGDTR VFGTGTKVTV L

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Macromolecule #13: C5K Fab light chain

MacromoleculeName: C5K Fab light chain / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.82417 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQYPST LSASVGDRVT ITCRARQSIG SWLAWYQQKP GKAPKLLIYK ASNLENGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYDSYYSFGQ GTKLEMK

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Macromolecule #14: Immunoglobulin heavy variable 1-46

MacromoleculeName: Immunoglobulin heavy variable 1-46 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.339016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGASVKV SCKASGDTLR RYYIHWVRQA PGQGLEWMGI INPSGGSTTY AQKFQGRVSM TRDTSTSTVY MELRSLRSD DTAVYYCARG GPTVVVVAAT PFDDWGQGTL VTVS

UniProtKB: Immunoglobulin heavy variable 1-46

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Macromolecule #15: C4K Fab heavy chain

MacromoleculeName: C4K Fab heavy chain / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.167801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVQSGGG LVRPGRSLTL SCVGSGVNIE NFAMHWVRQV PGKGLEWVSS ISWNSATTAY ADSVKGRFRI SRDNDKNSLY LHMTSLRIE DTALYYCAKE VSVITEWRGL DVWGQGTTVS

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Macromolecule #16: C4K Fab light chain

MacromoleculeName: C4K Fab light chain / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.697043 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVLTQSPAT LSLSPGERAT LSCRASQSVA DYLAWYQHKP GQVPRLLIYA ASKRAAGVPS RFSGGGSGTD FSLIINSLEP EDFATYYCQ ERSNWPRGTF GGGTKVEIR

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Macromolecule #17: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 17 / Number of copies: 3 / 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

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

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

8tco

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 92567
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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