+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60100 | ||||||||||||
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Title | SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Spike protein / RBD / Antibody / Fab / Viral protein / VIRAL PROTEIN-IMMUNE SYSTEM 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | ||||||||||||
Authors | Yan Q / Gao X / Liu B / Hou R / He P / Li Z / Chen Q / Wang J / He J / Chen L ...Yan Q / Gao X / Liu B / Hou R / He P / Li Z / Chen Q / Wang J / He J / Chen L / Zhao J / Xiong X | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: To Be Published Title: Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants Authors: Yan Q / Gao X / Liu B / Hou R / He P / Ma Y / Zhang Y / Zhang Y / Li Z / Chen Q / Wang J / Huang X / Liang H / Zheng H / Yao Y / Chen X / Niu X / He J / Chen L / Zhao J / Xiong X | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60100.map.gz | 32.3 MB | EMDB map data format | |
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Header (meta data) | emd-60100-v30.xml emd-60100.xml | 20.7 KB 20.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_60100_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_60100.png | 63.9 KB | ||
Filedesc metadata | emd-60100.cif.gz | 7.1 KB | ||
Others | emd_60100_half_map_1.map.gz emd_60100_half_map_2.map.gz | 59.4 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60100 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60100 | HTTPS FTP |
-Validation report
Summary document | emd_60100_validation.pdf.gz | 787.9 KB | Display | EMDB validaton report |
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Full document | emd_60100_full_validation.pdf.gz | 787.5 KB | Display | |
Data in XML | emd_60100_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_60100_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60100 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60100 | HTTPS FTP |
-Related structure data
Related structure data | 8zheMC 8zhdC 8zhfC 8zhgC 8zhhC 8zhiC 8zhjC 8zhkC 8zhlC 8zhmC 8zhnC 8zhoC 8zhpC M: atomic model generated by this map C: citing same article (ref.) |
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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_60100.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3688 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_60100_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_60100_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs
Entire | Name: SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs
Supramolecule | Name: SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: SARS-CoV-2 spike trimer (6P)
Supramolecule | Name: SARS-CoV-2 spike trimer (6P) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: R1-26 Fab
Supramolecule | Name: R1-26 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Spike glycoprotein,Fibritin,Expression Tag
Macromolecule | Name: Spike glycoprotein,Fibritin,Expression Tag / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 141.253875 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV YSSANNCTFE Y VSQPFLMD ...String: VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV YSSANNCTFE Y VSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QTLLALHRSY LT PGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRVQPTESIV RFP NITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSFVIRGDE VRQI APGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPCNGVEG FNCYF PLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFLPFQQ FGRDIA DTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGSNVF QTRAGCL IG AEHVNNSYEC DIPIGAGICA SYQTQTNSPG SASSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTISV TTEILPVS M TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGFN FSQILPDPS KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GPALQIPFP MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STPSALGKLQ DVVNQNAQAL NTLVKQLSSN F GAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RVDFCGKGYH LM SFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNTFVSGNCD VVI GIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDLQELGKY EQGS GYIPE APRDGQAYVR KDGEWVLLST FLGRSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAWSHPQ FEK UniProtKB: Spike glycoprotein, Fibritin |
-Macromolecule #2: Heavy chain of R1-26 Fab
Macromolecule | Name: Heavy chain of R1-26 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.908293 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGWSLILLFL VAVATRVLSE VQLVESGGGL VQPGGSLRLS CAASGFTFSS YWMSWVRQAP GKGLEWVANI KQDGSEKYYV DSVKGRFTI SRDNAKNSLY LQMNSLRAED TAVYYCARGQ LGPWVGVDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG G TAALGCLV ...String: MGWSLILLFL VAVATRVLSE VQLVESGGGL VQPGGSLRLS CAASGFTFSS YWMSWVRQAP GKGLEWVANI KQDGSEKYYV DSVKGRFTI SRDNAKNSLY LQMNSLRAED TAVYYCARGQ LGPWVGVDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG G TAALGCLV KDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PK SCD |
-Macromolecule #3: Light chain of R1-26 Fab
Macromolecule | Name: Light chain of R1-26 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.558242 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGWSCIILFL VATATGVNFM LTQPHSVSES PGKTVTISCT GSSGSIASNY VQWYQQRPGS APTTVIYEDN QRPSGVPDRF SGSIDSSSN SASLTISGLK TEDEADYYCQ SYDSSNWVFG GGTQLTVLGT KLTVLGQPKA APSVTLFPPS SEELQANKAT L VCLISDFY ...String: MGWSCIILFL VATATGVNFM LTQPHSVSES PGKTVTISCT GSSGSIASNY VQWYQQRPGS APTTVIYEDN QRPSGVPDRF SGSIDSSSN SASLTISGLK TEDEADYYCQ SYDSSNWVFG GGTQLTVLGT KLTVLGQPKA APSVTLFPPS SEELQANKAT L VCLISDFY PGAVTVAWKA DSSPVKAGVE TTTPSKQSNN KYAASSYLSL TPEQWKSHRS YSCQVTHEGS TVEKTVAPTE CS |
-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: 30 / 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: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K |
-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: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |