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Open data
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Basic information
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Title | OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE | ||||||||||||
![]() | SARS-CoV2-beta Spike ectodomain with Omi-38 fab globally refined | ||||||||||||
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Function / homology | ![]() virion component / 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 ...virion component / 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 / 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 | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | Duyvesteyn HME / Ren J / Stuart DI | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees. Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / ...Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Donal Skelly / Thomas G Ritter / Ali Amini / Sagida Bibi / Sandra Adele / Sile Ann Johnson / Bede Constantinides / Hermione Webster / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / Derrick Crook / Andrew J Pollard / Teresa Lambe / Philip Goulder / / Neil G Paterson / Mark A Williams / David R Hall / Juthathip Mongkolsapaya / Elizabeth E Fry / Wanwisa Dejnirattisai / Jingshan Ren / David I Stuart / Gavin R Screaton / ![]() ![]() Abstract: Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA. ...Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern. | ||||||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 17.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.2 KB 23.2 KB | Display Display | ![]() |
Images | ![]() | 35.7 KB | ||
Others | ![]() ![]() | 262.6 MB 262.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 716.2 KB | Display | ![]() |
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Full document | ![]() | 715.8 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zrcMC ![]() 7zf3C ![]() 7zf4C ![]() 7zf5C ![]() 7zf6C ![]() 7zf7C ![]() 7zf8C ![]() 7zf9C ![]() 7zfaC ![]() 7zfbC ![]() 7zfcC ![]() 7zfdC ![]() 7zfeC ![]() 7zffC ![]() 7zr7C ![]() 7zr8C ![]() 7zr9C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | SARS-CoV2-beta Spike ectodomain with Omi-38 fab globally refined | ||||||||||||||||||||||||||||||||||||
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: SARS-CoV2-beta Spike ectodomain with Omi-38 fab globally refined...
File | emd_14910_half_map_1.map | ||||||||||||
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Annotation | SARS-CoV2-beta Spike ectodomain with Omi-38 fab globally refined half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV2-beta Spike ectodomain with Omi-38 fab globally refined...
File | emd_14910_half_map_2.map | ||||||||||||
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Annotation | SARS-CoV2-beta Spike ectodomain with Omi-38 fab globally refined half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Entire | Name: OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN |
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Components |
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-Supramolecule #1: OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Supramolecule | Name: OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Supramolecule | Name: SARS-COV-2 BETA SPIKE GLYCOPROTEIN / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #3: OMI-38 FAB
Supramolecule | Name: OMI-38 FAB / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Spike glycoprotein,Fibritin
Macromolecule | Name: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 141.993984 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MFVFLVLLPL VSSQCVNFTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFA NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String: MFVFLVLLPL VSSQCVNFTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFA NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRGLPQ GFSALEPLVD LPIGINITRF QT LHISYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIR GDEVR QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGV KGFN CYFPLQSYGF QPTYGVGYQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEH VNNSYECDIP IGAGICASYQ TQTNSPGSAS SVASQSIIAY TMSLGVENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLN RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KDFGGFNFS QILPDPSKPS KRSFIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGA ALQIPFAMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTA SALGKLQDVV NQNAQALNTL V KQLSSNFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHG SAWSHPQFEK GGGSGGGSGG SAWSH PQFE K |
-Macromolecule #2: Omi-38 Fab Heavy Chain
Macromolecule | Name: Omi-38 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.847407 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QVQLVESGAE VKKPGSSVKV SCKASGGNFN MYTISWVRQA PGRGLEWMGR FIPIANKANY AQNFPGRVTI TADKSTSTVY MELRSLTSD DTAVYYCARS GSYDAFDVWG QGTMVTVSS |
-Macromolecule #3: Omi-38 Fab Light Chain
Macromolecule | Name: Omi-38 Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.865176 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: AIRMTQSPST LSASVGDRVT ITCRASQTIN SWLAWYQQKP GKAPKLLIYD ASNLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYESYSPITF GQGTRLEIK |
-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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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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) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |