[English] 日本語
Yorodumi- EMDB-36423: Structure of XBB spike protein (S) dimer-trimer in complex with b... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36423 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of XBB spike protein (S) dimer-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution. | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Antibody / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | Hao A / Mao Q / Chen Z / Huang J / Sun L | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: To Be Published Title: Structure of XBB spike protein (S) dimer-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution. Authors: Hao A / Mao Q / Chen Z / Huang J / Sun L | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_36423.map.gz | 337.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-36423-v30.xml emd-36423.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_36423.png | 53.2 KB | ||
Filedesc metadata | emd-36423.cif.gz | 6.3 KB | ||
Others | emd_36423_half_map_1.map.gz emd_36423_half_map_2.map.gz | 338.1 MB 338.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36423 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36423 | HTTPS FTP |
-Validation report
Summary document | emd_36423_validation.pdf.gz | 689.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_36423_full_validation.pdf.gz | 688.9 KB | Display | |
Data in XML | emd_36423_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_36423_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36423 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36423 | HTTPS FTP |
-Related structure data
Related structure data | 8jmmMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_36423.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.19 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_36423_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_36423_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : XBB spike protein (S) in complex with bispecific antibody G7-Fc
Entire | Name: XBB spike protein (S) in complex with bispecific antibody G7-Fc |
---|---|
Components |
|
-Supramolecule #1: XBB spike protein (S) in complex with bispecific antibody G7-Fc
Supramolecule | Name: XBB spike protein (S) in complex with bispecific antibody G7-Fc type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Details: XBB / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 143.147531 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MPMGSLQPLA TLYLLGMLVA SVLAQCVNLI TRTQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYQKNNKSW M ESEFRVYS ...String: MPMGSLQPLA TLYLLGMLVA SVLAQCVNLI TRTQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYQKNNKSW M ESEFRVYS SANNCTFEYV SQPFLMDLEG KEGNFKNLRE FVFKNIDGYF KIYSKHTPIN LERDLPQGFS ALEPLVDLPI GI NITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIY QTSNFR VQPTESIVRF PNITNLCPFH EVFNATTFAS VYAWNRKRIS NCVADYSVIY NFAPFFAFKC YGVSPTKLND LCFT NVYAD SFVIRGNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKPSGN YNYLYRLFRK SKLKPFERDI STEIY QAGN KPCNGVAGSN CYSPLQSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLT ESN KKFLPFQQFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTW RV YSTGSNVFQT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHGSAS SVASQSIIAY TMSLGAENSV AYSNNSIA I PTNFTISVTT EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPP IKYFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTI TSGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV N HNAQALNT LVKQLSSKFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CV LGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQ IITTDN TFVSGNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNL NESLI DLQELGKYEQ GSGYIPEAPR DGQAYVRKDG EWVFLSTFLS GLEVLFQGPG GWSHPQFEKG GGSGGGSGGS AWSHP QFEK GGSHHHHHHH H UniProtKB: Spike glycoprotein |
-Macromolecule #2: 7F3 Fv
Macromolecule | Name: 7F3 Fv / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 27.871873 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRSNWPQYTF GQGTKLEIKG GGGSGGGGSG GGGSEVQLVE SGGGLVKPGR SLRLSCTASG FTFGDYAMSW F RQAPGKGL ...String: EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRSNWPQYTF GQGTKLEIKG GGGSGGGGSG GGGSEVQLVE SGGGLVKPGR SLRLSCTASG FTFGDYAMSW F RQAPGKGL EWVGFIRSKA YGGTTEYAAS VKGRFTISRD DSKSIAYLQM NSLKTEDTAV YYCTRDRYAR YDILTGLSPA GA DYFYYAM DVWGQGTTVT VSS |
-Macromolecule #3: GW01 Fv
Macromolecule | Name: GW01 Fv / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.330619 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QSVLTQPPSA SGTPGQRVTI SCSGSSSNIG SNTVNWYQQL PGTAPKLLIY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC AAWDDSLNWV FGGGTKLTVL GGGGSGGGGS GGGGSEVQLV ESGGGVVQPG GSLRLSCAAS GFRFDDHAMH W VRQAPGKG ...String: QSVLTQPPSA SGTPGQRVTI SCSGSSSNIG SNTVNWYQQL PGTAPKLLIY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC AAWDDSLNWV FGGGTKLTVL GGGGSGGGGS GGGGSEVQLV ESGGGVVQPG GSLRLSCAAS GFRFDDHAMH W VRQAPGKG LEWVSVISGD GGSTYYADSV KGRFSISRDD SKNSLYLQMN SLRTEDTALY YCAKDRSYGP PDVFNYEYGM DV WGQGTTV TVSSGS |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 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: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 539055 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |