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- PDB-7tow: Antibody DH1058 Fab fragment bound to SARS-CoV-2 fusion peptide -

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Basic information

Entry
Database: PDB / ID: 7tow
TitleAntibody DH1058 Fab fragment bound to SARS-CoV-2 fusion peptide
Components
  • DH1058 Fab Light chain
  • DH1058 Fab heavy chain
  • Spike protein S2
KeywordsIMMUNE SYSTEM/Viral Protein / Antibody / Fab fragment / IMMUNE SYSTEM / 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 / 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 / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
PHOSPHATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGobeil, S. / Acharya, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145687 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI165147 United States
CitationJournal: Mol Cell / Year: 2022
Title: Structural diversity of the SARS-CoV-2 Omicron spike.
Authors: Sophie M-C Gobeil / Rory Henderson / Victoria Stalls / Katarzyna Janowska / Xiao Huang / Aaron May / Micah Speakman / Esther Beaudoin / Kartik Manne / Dapeng Li / Rob Parks / Maggie Barr / ...Authors: Sophie M-C Gobeil / Rory Henderson / Victoria Stalls / Katarzyna Janowska / Xiao Huang / Aaron May / Micah Speakman / Esther Beaudoin / Kartik Manne / Dapeng Li / Rob Parks / Maggie Barr / Margaret Deyton / Mitchell Martin / Katayoun Mansouri / Robert J Edwards / Amanda Eaton / David C Montefiori / Gregory D Sempowski / Kevin O Saunders / Kevin Wiehe / Wilton Williams / Bette Korber / Barton F Haynes / Priyamvada Acharya /
Abstract: Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via ...Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor-binding domain (RBD) and neutralizing antibody epitope presentation, affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility.
History
DepositionJan 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: DH1058 Fab heavy chain
L: DH1058 Fab Light chain
A: DH1058 Fab heavy chain
B: DH1058 Fab Light chain
E: Spike protein S2
D: Spike protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,56011
Polymers104,2506
Non-polymers3105
Water14,286793
1
H: DH1058 Fab heavy chain
L: DH1058 Fab Light chain
E: Spike protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3006
Polymers52,1253
Non-polymers1753
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-64 kcal/mol
Surface area21090 Å2
MethodPISA
2
A: DH1058 Fab heavy chain
B: DH1058 Fab Light chain
D: Spike protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2605
Polymers52,1253
Non-polymers1352
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-52 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.916, 76.788, 119.786
Angle α, β, γ (deg.)90.000, 100.854, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein/peptide , 1 types, 2 molecules ED

#3: Protein/peptide Spike protein S2


Mass: 2900.286 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

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Antibody , 2 types, 4 molecules HALB

#1: Antibody DH1058 Fab heavy chain


Mass: 25669.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody DH1058 Fab Light chain


Mass: 23555.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 798 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 793 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3000, 100mM Tris base/HCl pH 7.0, 200mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→39.21 Å / Num. obs: 48438 / % possible obs: 92.9 % / Redundancy: 5.59 % / Biso Wilson estimate: 22.78 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rsym value: 0.075 / Net I/σ(I): 22.5
Reflection shellResolution: 2.15→2.23 Å / Mean I/σ(I) obs: 5.4 / Num. unique obs: 4817 / CC1/2: 0.96 / CC star: 0.99 / Rpim(I) all: 0.115

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGU

5ggu


Resolution: 2.15→39.21 Å / SU ML: 0.2643 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.1988
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2337 1998 4.12 %
Rwork0.1668 46440 -
obs0.1696 48438 92.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.25 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7181 0 13 793 7987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727392
X-RAY DIFFRACTIONf_angle_d0.943410038
X-RAY DIFFRACTIONf_chiral_restr0.05881112
X-RAY DIFFRACTIONf_plane_restr0.00841294
X-RAY DIFFRACTIONf_dihedral_angle_d15.20162666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.25041420.16763249X-RAY DIFFRACTION91.82
2.21-2.270.26771390.17323365X-RAY DIFFRACTION94.47
2.27-2.330.26041450.1793377X-RAY DIFFRACTION94.47
2.33-2.410.27481440.18663378X-RAY DIFFRACTION94.58
2.41-2.490.28131410.19063323X-RAY DIFFRACTION93.98
2.49-2.590.29871480.19983336X-RAY DIFFRACTION93.38
2.59-2.710.30861350.20573313X-RAY DIFFRACTION92.71
2.71-2.850.26461410.20243234X-RAY DIFFRACTION90.53
2.85-3.030.24931310.18572936X-RAY DIFFRACTION82.69
3.03-3.270.25491490.18273288X-RAY DIFFRACTION92.52
3.27-3.60.25831470.16513489X-RAY DIFFRACTION96.39
3.6-4.120.20171470.14483418X-RAY DIFFRACTION95.76
4.12-5.180.16661430.12193363X-RAY DIFFRACTION93.15
5.18-39.210.17021460.15183371X-RAY DIFFRACTION91.66

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