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Yorodumi- EMDB-41156: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41156 | |||||||||
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Title | HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Virus / glycoprotein / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information host cell endosome membrane / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Human betaherpesvirus 5 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Goldsmith JG / McLellan JS | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: HCMV neutralization by broad antibody targeting Authors: Zehner M / Goldsmith JG / McLellan JS / Klein F | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41156.map.gz | 131.7 MB | EMDB map data format | |
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Header (meta data) | emd-41156-v30.xml emd-41156.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_41156.png | 47.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41156 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41156 | HTTPS FTP |
-Validation report
Summary document | emd_41156_validation.pdf.gz | 340.4 KB | Display | EMDB validaton report |
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Full document | emd_41156_full_validation.pdf.gz | 339.9 KB | Display | |
Data in XML | emd_41156_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_41156_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41156 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41156 | HTTPS FTP |
-Related structure data
Related structure data | 8tcoMC 8teaC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41156.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Entire | Name: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab |
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Components |
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-Supramolecule #1: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab
Supramolecule | Name: HCMV Trimer in complex with CS2it1p2_F7K Fab and CS4tt1p1_E3K Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Human betaherpesvirus 5 |
-Macromolecule #1: Envelope glycoprotein H
Macromolecule | Name: Envelope glycoprotein H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Molecular weight | Theoretical: 84.538617 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Envelope glycoprotein L
Macromolecule | Name: Envelope glycoprotein L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Molecular weight | Theoretical: 29.877336 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: Envelope glycoprotein O
Macromolecule | Name: Envelope glycoprotein O / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Molecular weight | Theoretical: 54.299551 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: CS4tt1p1_E3K Fab light chain
Macromolecule | Name: CS4tt1p1_E3K Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.793338 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #5: CS4tt1p1_E3K Fab heavy chain
Macromolecule | Name: CS4tt1p1_E3K Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.053139 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #6: CS2it1p2_F7K Fab heavy chain
Macromolecule | Name: CS2it1p2_F7K Fab heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.41534 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #7: CS2it1p2_F7K Fab light chain
Macromolecule | Name: CS2it1p2_F7K Fab light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.607836 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 7 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 376687 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |