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- EMDB-41156: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-41156
TitleHCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Map data
Sample
  • Complex: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
    • Protein or peptide: Envelope glycoprotein O
    • Protein or peptide: CS4tt1p1_E3K Fab light chain
    • Protein or peptide: CS4tt1p1_E3K Fab heavy chain
    • Protein or peptide: CS2it1p2_F7K Fab heavy chain
    • Protein or peptide: CS2it1p2_F7K Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVirus / glycoprotein / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. / 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 / Envelope glycoprotein O / Envelope glycoprotein L
Similarity search - Component
Biological speciesHuman betaherpesvirus 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGoldsmith JA / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Immunity / Year: 2023
Title: Single-cell analysis of memory B cells from top neutralizers reveals multiple sites of vulnerability within HCMV Trimer and Pentamer.
Authors: Matthias Zehner / Mira Alt / Artem Ashurov / Jory A Goldsmith / Rebecca Spies / Nina Weiler / Justin Lerma / Lutz Gieselmann / Dagmar Stöhr / Henning Gruell / Eric P Schultz / Christoph ...Authors: Matthias Zehner / Mira Alt / Artem Ashurov / Jory A Goldsmith / Rebecca Spies / Nina Weiler / Justin Lerma / Lutz Gieselmann / Dagmar Stöhr / Henning Gruell / Eric P Schultz / Christoph Kreer / Linda Schlachter / Hanna Janicki / Kerstin Laib Sampaio / Cora Stegmann / Michelle D Nemetchek / Sabrina Dähling / Leon Ullrich / Ulf Dittmer / Oliver Witzke / Manuel Koch / Brent J Ryckman / Ramin Lotfi / Jason S McLellan / Adalbert Krawczyk / Christian Sinzger / Florian Klein /
Abstract: Human cytomegalovirus (HCMV) can cause severe diseases in fetuses, newborns, and immunocompromised individuals. Currently, no vaccines are approved, and treatment options are limited. Here, we ...Human cytomegalovirus (HCMV) can cause severe diseases in fetuses, newborns, and immunocompromised individuals. Currently, no vaccines are approved, and treatment options are limited. Here, we analyzed the human B cell response of four HCMV top neutralizers from a cohort of 9,000 individuals. By single-cell analyses of memory B cells targeting the pentameric and trimeric HCMV surface complexes, we identified vulnerable sites on the shared gH/gL subunits as well as complex-specific subunits UL and gO. Using high-resolution cryogenic electron microscopy, we revealed the structural basis of the neutralization mechanisms of antibodies targeting various binding sites. Moreover, we identified highly potent antibodies that neutralized a broad spectrum of HCMV strains, including primary clinical isolates, that outperform known antibodies used in clinical trials. Our study provides a deep understanding of the mechanisms of HCMV neutralization and identifies promising antibody candidates to prevent and treat HCMV infection.
History
DepositionJul 2, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41156.png

Downloads & links

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Map

FileDownload / File: emd_41156.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 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: 7.36
Minimum - Maximum-2.5929074 - 130.070879999999988
Average (Standard dev.)0.008308865 (±1.1802899)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 338.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab

EntireName: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Components
  • Complex: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
    • Protein or peptide: Envelope glycoprotein O
    • Protein or peptide: CS4tt1p1_E3K Fab light chain
    • Protein or peptide: CS4tt1p1_E3K Fab heavy chain
    • Protein or peptide: CS2it1p2_F7K Fab heavy chain
    • Protein or peptide: CS2it1p2_F7K Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab

SupramoleculeName: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
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: Envelope glycoprotein O

MacromoleculeName: Envelope glycoprotein O / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 54.299551 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGRKEMMVRD VPKMVFLISI SFLLVSFINC KVMSKALYNR PWRGLVLSKI GKYKLDQLKL EILRQLETTI STKYNVSKQP VKNLTMNMT EFPQYYILAG PIQNYSITYL WFDFYSTQLR KPAKYVYSQY NHTAKTITFR PPPCGTVPSM TCLSEMLNVS K RNDTGEQG ...String:
MGRKEMMVRD VPKMVFLISI SFLLVSFINC KVMSKALYNR PWRGLVLSKI GKYKLDQLKL EILRQLETTI STKYNVSKQP VKNLTMNMT EFPQYYILAG PIQNYSITYL WFDFYSTQLR KPAKYVYSQY NHTAKTITFR PPPCGTVPSM TCLSEMLNVS K RNDTGEQG CGNFTTFNPM FFNVPRWNTK LYVGPTKVNV DSQTIYFLGL TALLLRYAQR NCTHSFYLVN AMSRNLFRVP KY INGTKLK NTMRKLKRKQ APVKEQFEKK AKKTQSTTTP YFSYTTSAAL NVTTNVTYSI TTAARRVSTS TIAYRPDSSF MKS IMATQL RDLATWVYTT LRYRQNPFCE PSRNRTAVSE FMKNTHVLIR NETPYTIYGT LDMSSLYYNE TMFVENKTAS DSNK TTPTS PSMGFQRTFI DPLWDYLDSL LFLDEIRNFS LRSPTYVNLT PPEHRRAVNL STLNSLWWWL Q

UniProtKB: Envelope glycoprotein O

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Macromolecule #4: CS4tt1p1_E3K Fab light chain

MacromoleculeName: CS4tt1p1_E3K Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.793338 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQLTQSPSS LSASVGDRVT ITCRASQNIY NWLAWYQQKP GQAPKLLIFD ASTLEGGVPS RFGGSGSGTD FTLTISNLRP EDFATYFCQ HYYNYPPWTF GQGTKVTFRR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQLTQSPSS LSASVGDRVT ITCRASQNIY NWLAWYQQKP GQAPKLLIFD ASTLEGGVPS RFGGSGSGTD FTLTISNLRP EDFATYFCQ HYYNYPPWTF GQGTKVTFRR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #5: CS4tt1p1_E3K Fab heavy chain

MacromoleculeName: CS4tt1p1_E3K Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.053139 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVRLVESGGG FVQTGGSLRL SCAASGYTFD QYSMHWVRQV PGKGLQFVST ISSNGGSRYY ADSVKGRFVV SRDEEKEVLY LQMGRLRTD DTGIYFCARA KKIFGGIIPP SGMDVWGRGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
EVRLVESGGG FVQTGGSLRL SCAASGYTFD QYSMHWVRQV PGKGLQFVST ISSNGGSRYY ADSVKGRFVV SRDEEKEVLY LQMGRLRTD DTGIYFCARA KKIFGGIIPP SGMDVWGRGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPK

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Macromolecule #6: CS2it1p2_F7K Fab heavy chain

MacromoleculeName: CS2it1p2_F7K Fab heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.41534 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVRV SCKVSGYTLT DLSIHWVRQA PGKGLEWMGG FDPEHGEIMY AQKFQGRVTV TEDTSTHTTY MEVNSLRSE DTAVYYCATD SSIAMTGTYF SDLFALDVWG QGTTVIVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QVQLVQSGAE VKKPGASVRV SCKVSGYTLT DLSIHWVRQA PGKGLEWMGG FDPEHGEIMY AQKFQGRVTV TEDTSTHTTY MEVNSLRSE DTAVYYCATD SSIAMTGTYF SDLFALDVWG QGTTVIVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP K

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Macromolecule #7: CS2it1p2_F7K Fab light chain

MacromoleculeName: CS2it1p2_F7K Fab light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.607836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRLPAQLLGL LLLWLRGARC DIQMTQSPSS LSASVGDRVT ITCRASQTIN TNLNWYQQKP GKAPRLLIFG TFSLKSGVPS RFSGGGSGT DFTLTISSLQ PEDFAAYFCQ QSHSPPHTFG QGTKLELKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW ...String:
MRLPAQLLGL LLLWLRGARC DIQMTQSPSS LSASVGDRVT ITCRASQTIN TNLNWYQQKP GKAPRLLIFG TFSLKSGVPS RFSGGGSGT DFTLTISSLQ PEDFAAYFCQ QSHSPPHTFG QGTKLELKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 7 / 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: 49.0 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7lbe

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 376687
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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