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- EMDB-41179: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-41179
TitleHCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Map dataComposite map for HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Sample
  • Complex: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
    • Protein or peptide: Envelope protein UL128
    • Protein or peptide: Envelope glycoprotein UL130
    • Protein or peptide: UL131A
    • Protein or peptide: CS3pt1p4_C1L Fab light chain
    • Protein or peptide: CS2pt1p2_A10L Fab heavy chain
    • Protein or peptide: CS3pt1p4_C1L Fab heavy chain
    • Protein or peptide: CS2pt1p2_A10L Fab light chain
KeywordsVirus / glycoprotein / antibody / VIRAL PROTEIN
Function / homologyHerpesvirus UL130, cytomegalovirus / HCMV glycoprotein pUL130 / viral envelope / Envelope glycoprotein UL130 / UL128 / UL131A
Function and homology information
Biological speciesHuman betaherpesvirus 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGoldsmith JG / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HCMV neutralization by broad antibody targeting
Authors: Zehner M / Goldsmith JG / McLellan JS / Klein F
History
DepositionJul 5, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41179.png

Downloads & links

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Map

FileDownload / File: emd_41179.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map for HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Voxel sizeX=Y=Z: 0.94 Å
Density
Contour LevelBy AUTHOR: 23.0
Minimum - Maximum-6.6431904 - 244.089580000000012
Average (Standard dev.)0.002870319 (±1.1350448)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Sample components

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Entire : HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab

EntireName: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
Components
  • Complex: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
    • Protein or peptide: Envelope protein UL128
    • Protein or peptide: Envelope glycoprotein UL130
    • Protein or peptide: UL131A
    • Protein or peptide: CS3pt1p4_C1L Fab light chain
    • Protein or peptide: CS2pt1p2_A10L Fab heavy chain
    • Protein or peptide: CS3pt1p4_C1L Fab heavy chain
    • Protein or peptide: CS2pt1p2_A10L Fab light chain

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Supramolecule #1: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab

SupramoleculeName: HCMV Pentamer in complex with CS2pt1p2_A10L Fab and CS3pt1p4_C1L Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #7, #5-#6, #4
Source (natural)Organism: Human betaherpesvirus 5

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Macromolecule #1: Envelope protein UL128

MacromoleculeName: Envelope protein UL128 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 18.940904 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEWSWVFLFF LSVTTGVHSE ECCEFINVNH PPERCYDFKM CNRFTVALRC PDGEVCYSPE KTAEIRGIVT TMTHSLTRQV VHNKLTSCN YNPLYLEADG RIRCGKVNDK AQYLLGAAGS VPYRWINLEY DKITRIVGLD QYLESVKKHK RLDVCRAKMG Y MLQ

UniProtKB: UL128

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Macromolecule #2: Envelope glycoprotein UL130

MacromoleculeName: Envelope glycoprotein UL130 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 24.018285 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEWSWVFLFF LSVTTGVHSS PWSTLTANQN PSPPWSKLTY SKPHDAATFY CPFLYPSPPR SPLQFSGFQQ VSTGPECRNE TLYLLYNRE GQTLVERSST WVKKVIWYLS GRNQTILQRM PQTASKPSDG NVQISVEDAK IFGAHMVPKQ TKLLRFVVND G TRYQMCVM ...String:
MEWSWVFLFF LSVTTGVHSS PWSTLTANQN PSPPWSKLTY SKPHDAATFY CPFLYPSPPR SPLQFSGFQQ VSTGPECRNE TLYLLYNRE GQTLVERSST WVKKVIWYLS GRNQTILQRM PQTASKPSDG NVQISVEDAK IFGAHMVPKQ TKLLRFVVND G TRYQMCVM KLESWAHVFR DYSVSFQVRL TFTEANNQTY TFCTHPNLIV

UniProtKB: Envelope glycoprotein UL130

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Macromolecule #3: UL131A

MacromoleculeName: UL131A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 15.262057 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEWSWVFLFF LSVTTGVHSQ CQRETAEKND YYRVPHYWDA CSRALPDQTR YKYVEQLVDL TLNYHYDASH GLDNFDVLKR INVTEVSLL ISDFRRQNRR GGTNKRTTFN AAGSLAPHAR SLEFSVRLFA N

UniProtKB: UL131A

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Macromolecule #4: CS2pt1p2_A10L Fab light chain

MacromoleculeName: CS2pt1p2_A10L Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.850111 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPPSA SGTPGQRVTI SCSGSSSNIG SNTVHWYQQL PGTAPKLLIY SNNQRPSGVP DRFSGSRSGT SASLAISGLR SEDEADYYC AAWDDSLNGR VFGTGTKVTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSALTQPPSA SGTPGQRVTI SCSGSSSNIG SNTVHWYQQL PGTAPKLLIY SNNQRPSGVP DRFSGSRSGT SASLAISGLR SEDEADYYC AAWDDSLNGR VFGTGTKVTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #5: CS2pt1p2_A10L Fab heavy chain

MacromoleculeName: CS2pt1p2_A10L Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.916252 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEFGLSWVFL VALIKGVQCQ VHLEESGGGL VKPGGSLRLS CVASGFSFSD YYMSWIRQAP GKGLEWLSYI SPSGSPTSNA DSMKGRFTI SRDNARSSLY LQVHSLRVED TAVYYCARDN TVFGVVTTPM DHWGQGTLVT VSSASTKGPS VFPLAPSSKS T SGGTAALG ...String:
MEFGLSWVFL VALIKGVQCQ VHLEESGGGL VKPGGSLRLS CVASGFSFSD YYMSWIRQAP GKGLEWLSYI SPSGSPTSNA DSMKGRFTI SRDNARSSLY LQVHSLRVED TAVYYCARDN TVFGVVTTPM DHWGQGTLVT VSSASTKGPS VFPLAPSSKS T SGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RV EPK

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Macromolecule #6: CS3pt1p4_C1L Fab heavy chain

MacromoleculeName: CS3pt1p4_C1L Fab heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.630592 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGGTFT DYALSWVRQA PGQGLEWMGG IIPVLGTPHY AQKFEDRVTI IADESTGTVF MALSSLRSD DTGMYYCARG VTHPYYYYAM DVWGQGTTIT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGGTFT DYALSWVRQA PGQGLEWMGG IIPVLGTPHY AQKFEDRVTI IADESTGTVF MALSSLRSD DTGMYYCARG VTHPYYYYAM DVWGQGTTIT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPK

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Macromolecule #7: CS3pt1p4_C1L Fab light chain

MacromoleculeName: CS3pt1p4_C1L Fab light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.239676 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPASV SGSPGQSISI SCTGTSSDVG AYDYVSWYQQ HPGKAPRLII YDVNKRPSGV PYRFSGSKSG TAASLTISGL QSEDEAVYY CGSYTSSSAF FYVFGTGTMV TVLRQPKANP TVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADSS P VKAGVETT ...String:
QSALTQPASV SGSPGQSISI SCTGTSSDVG AYDYVSWYQQ HPGKAPRLII YDVNKRPSGV PYRFSGSKSG TAASLTISGL QSEDEAVYY CGSYTSSSAF FYVFGTGTMV TVLRQPKANP TVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADSS P VKAGVETT TPSKQSNNKY AASSYLSLTP EQWKSHRSYS CQVTHEGSTV EKTVAPTECS

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71677
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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