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- PDB-7m51: B6 Fab fragment bound to the OC43 spike stem helix peptide -

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Basic information

Entry
Database: PDB / ID: 7m51
TitleB6 Fab fragment bound to the OC43 spike stem helix peptide
Components
  • B6 antigen-binding (Fab) fragment heavy chain
  • B6 antigen-binding (Fab) fragment light chain
  • Spike glycoprotein stem helix peptide
KeywordsANTIVIRAL PROTEIN / IMMUNE SYSTEM / Broadly neutralizing antibody / Structural genomics / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


carbohydrate binding / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Human coronavirus OC43
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSauer, M.M. / Park, Y.J. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01GM120553 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural basis for broad coronavirus neutralization.
Authors: Maximilian M Sauer / M Alejandra Tortorici / Young-Jun Park / Alexandra C Walls / Leah Homad / Oliver J Acton / John E Bowen / Chunyan Wang / Xiaoli Xiong / Willem de van der Schueren / Joel ...Authors: Maximilian M Sauer / M Alejandra Tortorici / Young-Jun Park / Alexandra C Walls / Leah Homad / Oliver J Acton / John E Bowen / Chunyan Wang / Xiaoli Xiong / Willem de van der Schueren / Joel Quispe / Benjamin G Hoffstrom / Berend-Jan Bosch / Andrew T McGuire / David Veesler /
Abstract: Three highly pathogenic β-coronaviruses have crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. To evaluate the possibility of identifying ...Three highly pathogenic β-coronaviruses have crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. To evaluate the possibility of identifying antibodies with broad neutralizing activity, we isolated a monoclonal antibody, termed B6, that cross-reacts with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses. B6 broadly neutralizes entry of pseudotyped viruses from lineages A and C, but not from lineage B, and the latter includes SARS-CoV and SARS-CoV-2. Cryo-EM, X-ray crystallography and membrane fusion assays reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery. The data indicate that antibody binding sterically interferes with the spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages, along with a proof of concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-β-coronavirus vaccine.
History
DepositionMar 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein stem helix peptide
H: B6 antigen-binding (Fab) fragment heavy chain
L: B6 antigen-binding (Fab) fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6357
Polymers49,2673
Non-polymers3684
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-27 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.990, 60.493, 79.390
Angle α, β, γ (deg.)90.000, 94.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-581-

HOH

21H-653-

HOH

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Components

#1: Protein/peptide Spike glycoprotein stem helix peptide / S glycoprotein / E2 / Peplomer protein


Mass: 1917.035 Da / Num. of mol.: 1 / Fragment: residues 1232-1246 of the spike glycoprotein / Source method: obtained synthetically / Source: (synth.) Human coronavirus OC43 / References: UniProt: P36334
#2: Antibody B6 antigen-binding (Fab) fragment heavy chain


Mass: 23348.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody B6 antigen-binding (Fab) fragment light chain


Mass: 24001.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium Thiocyanate and 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.73→46.34 Å / Num. obs: 45379 / % possible obs: 98.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.051 / Rrim(I) all: 0.094 / Net I/σ(I): 7.3 / Num. measured all: 147068 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.73-1.762.61.013612823630.3440.731.2540.795.8
8.99-46.343.10.01710893490.9980.0120.0212998.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.03 Å46.34 Å
Translation6.03 Å46.34 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NB8

6nb8


Resolution: 1.8→43.57 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 2054 5.07 %
Rwork0.1821 38421 -
obs0.1846 40475 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.2 Å2 / Biso mean: 27.6512 Å2 / Biso min: 9.94 Å2
Refinement stepCycle: final / Resolution: 1.8→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 24 524 3948
Biso mean--36.91 34.85 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033686
X-RAY DIFFRACTIONf_angle_d0.695045
X-RAY DIFFRACTIONf_dihedral_angle_d12.5181343
X-RAY DIFFRACTIONf_chiral_restr0.044569
X-RAY DIFFRACTIONf_plane_restr0.004648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.34511190.2952504262397
1.84-1.890.33681310.2632525265698
1.89-1.940.28271430.23682490263399
1.94-20.27031490.21782572272199
2-2.060.26251380.207725422680100
2.06-2.130.29171450.198325782723100
2.13-2.220.27361470.187725642711100
2.22-2.320.25841210.19172565268699
2.32-2.440.26251370.199125652702100
2.44-2.60.28331340.201425592693100
2.6-2.80.271130.197425952708100
2.8-3.080.24631310.181726112742100
3.08-3.520.2111450.16532554269999
3.52-4.440.18451500.14142557270798
4.44-43.570.16281510.15662640279199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.00745.47361.85672.00350.29532.00380.2381-0.52860.93941.2795-0.29380.5503-0.3293-0.94390.06350.36150.06330.06450.3926-0.08420.345410.165411.706542.3898
22.1633-0.4380.29011.0318-0.27884.92350.0159-0.17880.04070.09690.04580.2168-0.0365-0.56-0.05960.14070.00810.02970.2024-0.00190.19026.65926.03524.3696
32.7632-2.9219-0.87227.1971.70321.53310.12530.16870.0271-0.1753-0.1214-0.145-0.0241-0.15680.00430.1145-0.0221-0.01280.13050.04410.140416.5547-3.3233-3.4399
43.2074-1.184-2.97591.31671.05687.1466-0.0199-0.29790.05550.11490.0339-0.0942-0.0540.3458-0.01910.1555-0.0242-0.00950.1631-0.01240.140928.30145.011529.1737
52.5235-1.2682.29151.2081-1.55975.31860.05330.2238-0.026-0.0849-0.0566-0.01340.06760.09610.00450.12050.00170.02930.0984-0.01280.149129.17624.092-9.2141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1232 through 1242 )A0
2X-RAY DIFFRACTION2chain 'H' and (resid 3 through 121 )H3 - 121
3X-RAY DIFFRACTION3chain 'H' and (resid 122 through 222 )H122 - 222
4X-RAY DIFFRACTION4chain 'L' and (resid 3 through 115 )L3 - 115
5X-RAY DIFFRACTION5chain 'L' and (resid 116 through 220 )L116 - 220

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