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Yorodumi- EMDB-29950: SARS-Cov2 S protein structure in complex with neutralizing monocl... -
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-Basic information
Entry | Database: EMDB / ID: EMD-29950 | |||||||||
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Title | SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10 | |||||||||
Map data | Composite map of antibody 002-S21B10 bound to SARS-CoV-2 spike glycoprotein trimer. | |||||||||
Sample |
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Keywords | antibody / spike / SARS-CoV-2 / viral protein-immune system complex / 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 / 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 / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Patel A / Ortlund EA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Elucidating the mechanism of SARS-CoV-2 Omicron variant escape from a RBD class-3 human antibody Authors: Patel A / Kumar S / Lai L / Chakravarthy C / Valanparambil R / Keen M / Laughlin ZT / Frank F / Cheedarla N / Verkerke HP / Neish AS / Roback JD / Davis CW / Wrammert J / Ahmed R / Suthar MS ...Authors: Patel A / Kumar S / Lai L / Chakravarthy C / Valanparambil R / Keen M / Laughlin ZT / Frank F / Cheedarla N / Verkerke HP / Neish AS / Roback JD / Davis CW / Wrammert J / Ahmed R / Suthar MS / Murali-Krishna K / Chandele A / Ortlund EA | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29950.map.gz | 255.1 MB | EMDB map data format | |
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Header (meta data) | emd-29950-v30.xml emd-29950.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_29950.png | 117.5 KB | ||
Filedesc metadata | emd-29950.cif.gz | 7.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29950 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29950 | HTTPS FTP |
-Related structure data
Related structure data | 8gdrMC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29950.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map of antibody 002-S21B10 bound to SARS-CoV-2 spike glycoprotein trimer. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.0582 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Antibody 002-S21B10 bound to spike glycoprotein trimer
Entire | Name: Antibody 002-S21B10 bound to spike glycoprotein trimer |
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Components |
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-Supramolecule #1: Antibody 002-S21B10 bound to spike glycoprotein trimer
Supramolecule | Name: Antibody 002-S21B10 bound to spike glycoprotein trimer type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3 |
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-Supramolecule #2: Antibody 002-S21B10
Supramolecule | Name: Antibody 002-S21B10 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Spike glycoprotein trimer
Supramolecule | Name: Spike glycoprotein trimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 128.766031 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQCVNLTTR TQLPPAYTNS FTRGVYYPDK VFRSSVLHST QDLFLPFFSN VTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF L GVYYHKNN ...String: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQCVNLTTR TQLPPAYTNS FTRGVYYPDK VFRSSVLHST QDLFLPFFSN VTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF L GVYYHKNN KSWMESEFRV YSSANNCTFE YVSQPFLMDL EGKQGNFKNL REFVFKNIDG YFKIYSKHTP INLVRDLPQG FS ALEPLVD LPIGINITRF QTLLALHRSY LTPGDSSSGW TAGAAAYYVG YLQPRTFLLK YNENGTITDA VDCALDPLSE TKC TLKSFT VEKGIYQTSN FRVQPTESIV RFPNITNLCP FGEVFNATRF ASVYAWNRKR ISNCVADYSV LYNSASFSTF KCYG VSPTK LNDLCFTNVY ADSFVIRGDE VRQIAPGQTG KIADYNYKLP DDFTGCVIAW NSNNLDSKVG GNYNYLYRLF RKSNL KPFE RDISTEIYQA GSTPCNGVEG FNCYFPLQSY GFQPTNGVGY QPYRVVVLSF ELLHAPATVC GPKKSTNLVK NKCVNF NFN GLTGTGVLTE SNKKFLPFQQ FGRDIADTTD AVRDPQTLEI LDITPCSFGG VSVITPGTNT SNQVAVLYQD VNCTEVP VA IHADQLTPTW RVYSTGSNVF QTRAGCLIGA EHVNNSYECD IPIGAGICAS YQTQTNSPSG AGSVASQSII AYTMSLGA E NSVAYSNNSI AIPTNFTISV TTEILPVSMT KTSVDCTMYI CGDSTECSNL LLQYGSFCTQ LNRALTGIAV EQDKNTQEV FAQVKQIYKT PPIKDFGGFN FSQILPDPSK PSKRSPIEDL LFNKVTLADA GFIKQYGDCL GDIAARDLIC AQKFNGLTVL PPLLTDEMI AQYTSALLAG TITSGWTFGA GPALQIPFPM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS T PSALGKLQ DVVNQNAQAL NTLVKQLSSN FGAISSVLND ILSRLDPPEA EVQIDRLITG RLQSLQTYVT QQLIRAAEIR AS ANLAATK MSECVLGQSK RVDFCGKGYH LMSFPQSAPH GVVFLHVTYV PAQEKNFTTA PAICHDGKAH FPREGVFVSN GTH WFVTQR NFYEPQIITT DNTFVSGNCD VVIGIVNNTV YDPLQPELDS FK UniProtKB: Spike glycoprotein |
-Macromolecule #2: Monoclonal antibody 002-S21B10 heavy chain variable domain
Macromolecule | Name: Monoclonal antibody 002-S21B10 heavy chain variable domain type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.113283 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QITLKESGPT LVKSTQTLTL TCTFSGFSLS TYGVGVGWIR QPPGKALEWL ALIYWDDDKR YTPSLKSRLT ITKDTSKNQV VLTMTNMDP LDTATYYCAQ HTVPTIFDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String: QITLKESGPT LVKSTQTLTL TCTFSGFSLS TYGVGVGWIR QPPGKALEWL ALIYWDDDKR YTPSLKSRLT ITKDTSKNQV VLTMTNMDP LDTATYYCAQ HTVPTIFDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVE PKSCDK |
-Macromolecule #3: Monoclonal antibody 002-S21B10 light chain variable domain
Macromolecule | Name: Monoclonal antibody 002-S21B10 light chain variable domain type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.86132 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QSALTQPASV SGSPEQSITI SCSGTSRDIG GYNYVAWYQH HPGKAPKLMI YEVSNRPSGV SNRFSGSKSG NMASLTISGL QAEDKADYY CTSYTTGSTV VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String: QSALTQPASV SGSPEQSITI SCSGTSRDIG GYNYVAWYQH HPGKAPKLMI YEVSNRPSGV SNRFSGSKSG NMASLTISGL QAEDKADYY CTSYTTGSTV VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 28 / 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
Concentration | 0.7 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Slit width: 20 eV |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9054 / Average electron dose: 54.37 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1021598 |
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Startup model | Type of model: OTHER |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Number classes: 4 / Avg.num./class: 255399 / Software - Name: cryoSPARC (ver. 3.3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 326424 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 100.25 / Target criteria: Correlation coefficient |
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Output model | PDB-8gdr: |