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- PDB-7m55: B6 Fab fragment bound to the MERS-CoV spike stem helix peptide -

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Basic information

Entry
Database: PDB / ID: 7m55
TitleB6 Fab fragment bound to the MERS-CoV spike stem helix peptide
Components
  • B6 antigen binding fragment (Fab) heavy chain
  • B6 antigen binding fragment (Fab) light chain
  • Spike glycoprotein stem helix peptide
KeywordsANTIVIRAL PROTEIN / IMMUNE SYSTEM / Broadly neutralizing antibody / Structural genomics / SSGCID / Center for Structural Genomics of Infectious Diseases / CSGID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to 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, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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
Biological speciesMus musculus (house mouse)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 / Structure summary / Category: audit_author / 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

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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 fragment (Fab) heavy chain
L: B6 antigen binding fragment (Fab) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4616
Polymers49,1853
Non-polymers2763
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-27 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.589, 60.444, 79.710
Angle α, β, γ (deg.)90.000, 93.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-418-

HOH

21H-584-

HOH

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Components

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


Mass: 1834.909 Da / Num. of mol.: 1 / Fragment: residues 1230-1244 of the spike glycoprotein / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome-related coronavirus
References: UniProt: K9N5Q8
#2: Antibody B6 antigen binding fragment (Fab) 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 fragment (Fab) 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Magnesium Chloride 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: 1.4→43.49 Å / Num. obs: 86876 / % possible obs: 99.44 % / Redundancy: 1.9 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 12.71
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.51 / Num. unique obs: 8539 / CC1/2: 0.767 / CC star: 0.932 / % possible all: 98.26

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NB8

6nb8


Resolution: 1.4→43.49 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1996 4304 4.95 %
Rwork0.1732 82562 -
obs0.1745 86866 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.91 Å2 / Biso mean: 27.2984 Å2 / Biso min: 8.13 Å2
Refinement stepCycle: final / Resolution: 1.4→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 18 562 3962
Biso mean--21.02 35.64 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093703
X-RAY DIFFRACTIONf_angle_d1.0865091
X-RAY DIFFRACTIONf_dihedral_angle_d13.0691370
X-RAY DIFFRACTIONf_chiral_restr0.095583
X-RAY DIFFRACTIONf_plane_restr0.008656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.30411420.28082700284298
1.42-1.430.27951330.272706283998
1.43-1.450.26541370.25242718285599
1.45-1.470.30031480.24372732288099
1.47-1.490.24331370.2392685282299
1.49-1.510.22881560.229528022958100
1.51-1.530.27211610.226426682829100
1.53-1.550.26181460.220827912937100
1.55-1.580.22951350.212627452880100
1.58-1.60.22421450.210327472892100
1.6-1.630.23621360.204827712907100
1.63-1.660.23711490.203427152864100
1.66-1.690.28271440.202527982942100
1.69-1.730.22831480.196427342882100
1.73-1.760.22651310.199927172848100
1.76-1.80.22761560.193627832939100
1.8-1.850.2261410.187427622903100
1.85-1.90.23151400.181327422882100
1.9-1.960.20141370.178527712908100
1.96-2.020.19781550.175227412896100
2.02-2.090.18611400.177127552895100
2.09-2.170.16341370.171627662903100
2.17-2.270.21421460.176727672913100
2.27-2.390.20791490.172627562905100
2.39-2.540.19141580.17092744290299
2.54-2.740.18731470.16912755290299
2.74-3.020.21551390.16512785292499
3.02-3.450.16621290.15382787291699
3.45-4.350.16071320.13232784291699
4.35-43.490.17071500.1482835298599
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)
10.9498-0.416-1.34641.24311.18673.62110.0852-0.19530.14410.13640.04620.0122-0.2293-0.0079-0.12810.39510.30490.08481.0718-0.1110.16211.063311.253442.5683
20.942-0.11760.26640.2948-0.08451.3376-0.0957-1.0599-0.20040.08590.23910.2616-0.0553-0.7716-0.15550.14850.03640.03960.58540.12010.23578.15016.198824.4906
31.1176-1.1883-0.21534.58871.21211.03310.06090.1130.0381-0.0986-0.1269-0.09-0.0205-0.11830.05890.10930.0047-0.01740.06530.0120.153916.6699-3.3624-3.2643
41.2951-0.1239-0.79080.56920.42314.8304-0.1213-0.579-0.0170.15120.1314-0.0075-0.0974-0.1770.00860.15360.0502-0.01520.3070.01610.138729.17934.68629.5319
52.6384-0.85941.47680.7657-0.9063.24450.13510.3809-0.0025-0.1042-0.10310.01110.04730.1339-0.03370.12130.0262-0.00730.088-0.00630.130729.42964.0077-9.2925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1230 through 1240 )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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