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- EMDB-46759: Cryo-EM structure of neutralizing human antibody D48 in complex w... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of neutralizing human antibody D48 in complex with HSV-1 glycoprotein B trimer gB-Ecto.516P.531E.DS | |||||||||
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![]() | immune complex / neutralization / herpes fusogen / VIRAL PROTEIN | |||||||||
Function / homology | ![]() host cell endosome / host cell Golgi apparatus / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Roark RS / Shapiro L / Kwong PD | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Prefusion structure and neutralization of HSV-1 glycoprotein B Authors: Roark RS / Shapiro L / Kwong PD | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 203.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.3 KB 17.3 KB | Display Display | ![]() |
Images | ![]() | 91.5 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 200 MB 200 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 910 KB | Display | ![]() |
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Full document | ![]() | 909.5 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9dd7MC ![]() 9dd6C ![]() 9dd8C ![]() 9ddaC ![]() 9ddcC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_46759_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_46759_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : D48 Fab in complex with HSV-1 gB trimer
Entire | Name: D48 Fab in complex with HSV-1 gB trimer |
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Components |
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-Supramolecule #1: D48 Fab in complex with HSV-1 gB trimer
Supramolecule | Name: D48 Fab in complex with HSV-1 gB trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Glycoprotein B
Macromolecule | Name: Glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 90.326195 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MHQGAPSWGR RWFVVWALLG LTLGVLVASA APSSPGTPGV AAATQAANGG PATPAPPALG AAPTGDPKPK KNKKPKNPTP PRPAGDNAT VAAGHATLRE HLRDIKAENT DANFYVCPPP TGATVVQFEQ PRRCPTRPEG QNYTEGIAVV FKENIAPYKF K ATMYYKDV ...String: MHQGAPSWGR RWFVVWALLG LTLGVLVASA APSSPGTPGV AAATQAANGG PATPAPPALG AAPTGDPKPK KNKKPKNPTP PRPAGDNAT VAAGHATLRE HLRDIKAENT DANFYVCPPP TGATVVQFEQ PRRCPTRPEG QNYTEGIAVV FKENIAPYKF K ATMYYKDV TVSQVWFGHR YSQFMGIFED RAPVPFEEVI DKINAKGVCR STAKYVRNNL ETTAFHRDDH ETDMELKPAN AC TRTSRGW HTTDLKYNPS RVEAFHRYGT TVNCIVEEVD ARSVYPYDEF VLATGDFVYM SPFYGYREGS HTEHTSYAAD RFK QVDGFY ARDLTTKARA TAPTTRNLLT TPKFTVAWDW VPKRPSVCTM TKWQEVDEML RSEYGGSFRF SSDAISTTFT TNLT EYPLS RVDLGDCIGK DARDAMDRIF ARRYNATHIK VGQPQYYLAN GGFLIAYQPL LSNTLAELYV REHLREQSRK PPNPT PPPP GASANASVER IKTTSSIEFA RLQFTYNHIQ RPVNDMLGRV AIAWCEEQNH ELTLWNEARK LNPNAIASVT VGRRVS ARM LGDVMAVSTC VPVAADNVIV QNSMRISSRP GACYSRPLVS FRYCDQGPLV EGQLGENNEL RLTRDAIEPC TVGHRRY FT FGGGYVYFEE YAYSHQLSRA DITTVSTFID LNITMLEDHE FVPLEVYTRH EIKDSGLLDY TEVQRRNQLH DLRFADID T VIHADANGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGRSL EVLFQGPGHH HHHHHHSAWS HPQFEKGGGS GGGGSGGSA WSHPQFEK UniProtKB: Glycoprotein B |
-Macromolecule #2: D48 heavy chain
Macromolecule | Name: D48 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.317124 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: VQLVETGGGV VRPGRSLRLS CTTSGFSFSG SAMHWVRQAP GKGLEWVAVI SHDGNIIQYH DSVKGRFTIS RDNSKNVLLL QMNSLRVDD TAMYYCARDV WLLPATISYA FDFWGQGTMV T |
-Macromolecule #3: D48 light chain
Macromolecule | Name: D48 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.716142 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: VIWMTQSPPS LSASIGDTVT ITCRASQGIS NSIAWYQRRP GKAPELLVYA AYRLQSGVPS RLSGSGSGAE YTLTIKNMQP EDFATYYCQ QYYDNPLTFG GGTKVEIK |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |