+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32772 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 Omicron variant spike RBD in complex with Fab 9A8 | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | SARS-CoV-2 / Omicron / RBD-Fab complex / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex | |||||||||
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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: 4.3 Å | |||||||||
Authors | Wang X / Wang L | |||||||||
Funding support | 1 items
| |||||||||
Citation | Journal: Cell Discov / Year: 2022 Title: A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD. Authors: Shuo Liu / Zijing Jia / Jianhui Nie / Ziteng Liang / Jingshu Xie / Lei Wang / Li Zhang / Xiangxi Wang / Youchun Wang / Weijin Huang / | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_32772.map.gz | 7.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-32772-v30.xml emd-32772.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_32772.png | 40.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32772 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32772 | HTTPS FTP |
-Validation report
Summary document | emd_32772_validation.pdf.gz | 306.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_32772_full_validation.pdf.gz | 306.3 KB | Display | |
Data in XML | emd_32772_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_32772_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32772 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32772 | HTTPS FTP |
-Related structure data
Related structure data | 7wt9MC 7wt7C 7wt8C 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_32772.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : SARS-CoV-2 Omicron variant spike RBD in complex with Fab 9A8
Entire | Name: SARS-CoV-2 Omicron variant spike RBD in complex with Fab 9A8 |
---|---|
Components |
|
-Supramolecule #1: SARS-CoV-2 Omicron variant spike RBD in complex with Fab 9A8
Supramolecule | Name: SARS-CoV-2 Omicron variant spike RBD in complex with Fab 9A8 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: Fab 9A8
Supramolecule | Name: Fab 9A8 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: SARS-CoV-2 Omicron variant spike
Supramolecule | Name: SARS-CoV-2 Omicron variant spike / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
---|
-Macromolecule #1: Heavy chain of Fab 9A8
Macromolecule | Name: Heavy chain of Fab 9A8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.998468 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VQLVESGGGL VQPGGSLRLS CAASGIIVSS NYMSWVRQGP GKGLEWVSVI YSGGSTYYAD SVKARFTISR DNSKNTLYLQ MNSLRAEDT AVYYCAREVV GSNSNMDVWG QGTTVTVSSA STK |
-Macromolecule #2: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 141.391969 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DHKNNKSWME SEFRVYSSAN N CTFEYVSQ ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DHKNNKSWME SEFRVYSSAN N CTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPINIV REPEDLPQGF SALEPLVDLP IGINITRFQT LL ALHRSYL TPGDSSSGWT AGAAAYYVGY LQPRTFLLKY NENGTITDAV DCALDPLSET KCTLKSFTVE KGIYQTSNFR VQP TESIVR FPNITNLCPF DEVFNATRFA SVYAWNRKRI SNCVADYSVL YNLAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVI RGDEV RQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKVSG NYNYLYRLFR KSNLKPFERD ISTEIYQAGN KPCNG VAGF NCYFPLRSYS FRPTYGVGHQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL KGTGVLTESN KKFLPF QQF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVPVAIH ADQLTPTWRV YSTGSNV FQ TRAGCLIGAE YVNNSYECDI PIGAGICASY QTQTKSHRAA ASVASQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISV T TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL KRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKYFGGFNF SQILPDPSKP SKRSPIEDLL FNKVTLADAG FIKQYGDCLG DIAARDLICA QKFKGLTVLP PLLTDEMIAQ YTSALLAGTI TSGWTFGAG PALQIPFPMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLSST PSALGKLQDV VNHNAQALNT L VKQLSSKF GAISSVLNDI FSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DF CGKGYHL MSFPQSAPHG VVFLHVTYVP AQEKNFTTAP AICHDGKAHF PREGVFVSNG THWFVTQRNF YEPQIITTDN TFV SGNCDV VIGIVNNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQE LGKYE QYIKWPWYIW LGFIAGLIAI VMVTIMLCCM TSCCSCLKGC CSCGSCCKFD EDDSEPVLKG VKLHYT |
-Macromolecule #3: Light chain of Fab 9A8
Macromolecule | Name: Light chain of Fab 9A8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.816036 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCQASQDIN IYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTFTINSLQP EDIATYYCQ QYDNLPRTFG QGTKVEIK |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm |
-Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 380727 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |