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- EMDB-72060: HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F... -

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Basic information

Entry
Database: EMDB / ID: EMD-72060
TitleHCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L Fabs
Map dataEM map for HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L Fabs
Sample
  • Complex: HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L 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_72060.png

Downloads & links

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Map

FileDownload / File: emd_72060.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 E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L 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-0.27422988 - 0.71453655
Average (Standard dev.)0.0012153039 (±0.018867554)
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_72060_additional_1.map
AnnotationSharpened map for HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L 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_72060_half_map_1.map
AnnotationHalf-map A for HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L 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_72060_half_map_2.map
AnnotationHalf-map B for HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L 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 E4K, E11K, A9K, E9L, E8K, B1K, E7K, F...

EntireName: HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L Fabs
Components
  • Complex: HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L Fabs
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
    • Protein or peptide: E10L Fab light chain
    • Protein or peptide: E10L Fab heavy chain
    • Protein or peptide: A9K Fab heavy chain
    • Protein or peptide: A9K Fab light chain
    • Protein or peptide: E8K Fab heavy chaun
    • Protein or peptide: E8K Fab light chain
    • Protein or peptide: F12L Fab heavy chain
    • Protein or peptide: F12L Fab light chain
    • Protein or peptide: E9L Fab light chain
    • Protein or peptide: E9L Fab heavy chaun
    • Protein or peptide: B1K Fab heavy chain
    • Protein or peptide: B1K Fab light chain
    • Protein or peptide: E4K Fab heavy chain
    • Protein or peptide: E4K Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F...

SupramoleculeName: HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L 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: E10L Fab light chain

MacromoleculeName: E10L Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.679746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASV SGSPGQSITI SCTGTSSDVG GYNHVSWYQE RPGKAPQLII YDVSYRPAGV SSRFSGSKSG NTASLIISWL QAEDEADYY CSSHTNNYGL VVFGGGTKVT VL

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Macromolecule #4: E10L Fab heavy chain

MacromoleculeName: E10L Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.452051 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGASVKV SCKASGYTFS NYYMHWVRQA PGEGLEWMGR VNPSGGASTY AQKLQGRVTM TRDTSTSTFY MHLSSLKSD DTAVYYCARG GGLRFGDLFY FQHWGQGTQV TVS

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Macromolecule #5: A9K Fab heavy chain

MacromoleculeName: A9K Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.993544 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFSFS AYAMHWVRQA PGRGLEWVAV IWFDGSKKVY ADSVKGRFTI SRDNSKNTLH LQMDSLRAE DTAVYYCSRE EYRSFNYWGQ GTLVTVS

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Macromolecule #6: A9K Fab light chain

MacromoleculeName: A9K Fab light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.597867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT IICRASRSIG TNLNWYQQRV GKAPNLLIYD ASRLHSGVPS RFSGSGTGTA FTLTISSLQP EDFATYYCQ QSYSTPRTFG PGTKVDSK

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Macromolecule #7: E8K Fab heavy chaun

MacromoleculeName: E8K Fab heavy chaun / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.369004 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLMQSPGE VKKPGASVKV SCRSFGYSFT FYGMNWLRQA PGQGLEWMGW ISTSNGGTNY AQKFQDRLTM TMDTSASTTY MELRSLRSD DTAVYYCARD FPRLYNYDNG NYRWFGSWGQ GTLVTVS

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Macromolecule #8: E8K Fab light chain

MacromoleculeName: E8K Fab light chain / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.477892 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPDS LGVSLGERAT ISCKSSQSVF FSANQKNYLA WYQQKLGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLT ISSLQVEDV AVYYCQQYYS TPFTFGPGTK VDLK

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Macromolecule #9: F12L Fab heavy chain

MacromoleculeName: F12L Fab heavy chain / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.956502 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSQTLSL TCSVSGGSIG GDKYYWTWIR QSPGKGLDWI GYTYFGGTTY YNPSLKSRIT ISEDMSKNQF SLKLNSVTA ADTAVYYCVA ATTTVRFDYW GQGMLVTVS

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Macromolecule #10: F12L Fab light chain

MacromoleculeName: F12L Fab light chain / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.438832 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QAVLTQPSSL STSPGASASL TCTLRSGINV HTYRIYWYQQ KPGSPPQYLL RYKSDSDNHQ GIGVPTRFSG SKDASANAGI LLISGLQSE DEADYYCMIW HNSAVVFGGG TRLTVL

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Macromolecule #11: E9L Fab light chain

MacromoleculeName: E9L Fab light chain / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.46159 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELTQPPSV SVSPGQAATI TCSGDKLGNK YVCWYQQKPG QSPALVIYQD TKRPSGIPER FSGSNSGNTA TLTISGTQAM DEADYYCQA WDSNTAYVFG TGTKVTVL

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Macromolecule #12: E9L Fab heavy chaun

MacromoleculeName: E9L Fab heavy chaun / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.016661 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVRPSETLSL TCNVLGGSIS TYHWSWIRQP AGKGLEWIGR MDSSGNTNYN PSLKSRVTMS VDTSKNQFSL KLRSVIAAD MATYYCARAT RNGWYVLDSW GQGILVTVS

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Macromolecule #13: B1K Fab heavy chain

MacromoleculeName: B1K Fab heavy chain / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.984405 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QGQLVQSGAE VKRPGASVKV SCKASGYTFN TFGITWVRQA PGQGLEWVGR INTYNGNTNY GQKFQGRITM TRDTSTGTAY MELRSLRSD DTAVYYCARD LTWGYCDYWG QGTLVTVS

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Macromolecule #14: B1K Fab light chain

MacromoleculeName: B1K Fab light chain / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.566924 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPST LSASVGDRVT ITCRASQSIG TSLAWYQQKP GKAPKLLLYM ASTLEAGVPS RFSGGGSGTD FALTISSLQP DDFATYYCQ HFDTYPYTFG RGTKVDIK

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Macromolecule #15: E4K Fab heavy chain

MacromoleculeName: E4K Fab heavy chain / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.517076 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVHLVQSGAE VKKPGASVKV SCKASGYTFS NYGISWVRQA PGQGLEWMGW ISGYNGNTNY AQKFKDRVIM STDPFTSTVY LEVRSLRSD DTAVYYCARE GSRPYYYRGM DVWGQGTTVT VS

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Macromolecule #16: E4K Fab light chain

MacromoleculeName: E4K Fab light chain / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.741196 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQFPAT LSLSPGERAT LFCRASQSIS SYVAWYQHKP GQAPRLLIYD TVSRATGVPA RFSGAGSGTD FTLSISSLES GDFGVYYCQ QRGMSLPWTF GQGTKVEIK

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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: 141765
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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