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- PDB-7m52: B6 Fab fragment bound to the HKU4 spike stem helix peptide -

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Basic information

Entry
Database: PDB / ID: 7m52
TitleB6 Fab fragment bound to the HKU4 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 / Center for Structural Genomics of Infectious Diseases / CSGID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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, HKU4-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-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, HKU4-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-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)
Bat coronavirus HKU4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 1.2Jun 30, 2021Group: Other / Structure summary / Category: audit_author / pdbx_SG_project / struct_keywords
Item: _audit_author.name / _pdbx_SG_project.full_name_of_center ..._audit_author.name / _pdbx_SG_project.full_name_of_center / _pdbx_SG_project.initial_of_center / _struct_keywords.text
Revision 1.3Oct 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 1.4Oct 23, 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)49,4766
Polymers49,2003
Non-polymers2763
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-28 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.590, 60.600, 79.765
Angle α, β, γ (deg.)90.000, 93.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-590-

HOH

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Components

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


Mass: 1849.986 Da / Num. of mol.: 1 / Fragment: Residues 1231-1245 of the spike glycoprotein / Source method: obtained synthetically / Source: (synth.) Bat coronavirus HKU4 / References: UniProt: A3EX94
#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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.6 M Sodium Chloride, 0.1 M MES-NaOH, and 20% (w/v) PEG 4000

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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 PILATUS3 R CdTe 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: 1.42→46.69 Å / Num. obs: 80866 / % possible obs: 96.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 7.8 / Num. measured all: 277580
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
1.42-1.443.31.4081275038210.3380.8981.6750.692.9
7.78-46.693.10.02516735430.9980.0160.0328.598.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.04 Å46.69 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: 6NB8

6nb8


Resolution: 1.5→46.69 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 3574 5.18 %
Rwork0.1642 65478 -
obs0.166 69052 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.26 Å2 / Biso mean: 26.7009 Å2 / Biso min: 8.75 Å2
Refinement stepCycle: final / Resolution: 1.5→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 24 518 3931
Biso mean--24.61 35.53 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153752
X-RAY DIFFRACTIONf_angle_d1.5025178
X-RAY DIFFRACTIONf_dihedral_angle_d14.2011399
X-RAY DIFFRACTIONf_chiral_restr0.089598
X-RAY DIFFRACTIONf_plane_restr0.014665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.520.27551300.26182425255593
1.52-1.540.28611510.26362433258495
1.54-1.560.2651330.24442486261995
1.56-1.590.30121440.22822437258195
1.59-1.610.21951180.22412486260496
1.61-1.640.23361320.21652485261795
1.64-1.670.24711170.2122497261497
1.67-1.70.26141070.22232526263396
1.7-1.730.26831230.2152486260996
1.73-1.760.2391310.2032481261297
1.76-1.80.23271570.18622497265496
1.8-1.840.20131450.18192483262896
1.84-1.890.20471360.16282529266597
1.89-1.940.21091570.15892452260997
1.94-20.16931300.15352571270197
2-2.060.18731380.16212515265397
2.06-2.140.21531440.15732530267497
2.14-2.220.19291220.16082562268498
2.22-2.320.19011240.16992549267397
2.32-2.450.22541350.16582540267598
2.45-2.60.22631490.16692536268599
2.6-2.80.20541360.16712585272198
2.8-3.080.18631420.16552568271098
3.08-3.530.18071480.14842589273799
3.53-4.440.16321590.12732573273299
4.44-46.690.16731660.1452657282399
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)
11.4284-0.1159-2.06411.07610.51634.68920.0169-0.4160.19080.3240.0610.0074-0.2747-0.0071-0.22150.44370.38750.11631.1182-0.13180.099910.562711.160542.4064
21.7526-0.45470.18970.7542-0.03922.7049-0.0847-0.6141-0.20220.13550.17990.2912-0.0016-0.6057-0.05480.15280.02230.04220.35470.05930.22077.89656.240424.4613
31.2762-1.7259-0.38465.41031.48111.24980.06430.10590.0219-0.1477-0.1239-0.0561-0.0552-0.14550.06230.10580.002-0.01630.0870.01230.139716.5367-3.1394-3.0989
41.7879-0.413-0.80550.99270.42294.7708-0.1456-0.45260.03870.18340.141-0.0613-0.06490.01670.00670.14920.0242-0.01170.21130.00660.123529.21234.657429.403
52.3504-0.84961.51580.6528-0.87133.27590.150.3282-0.0157-0.1301-0.09810.00780.05480.1277-0.04820.13180.0264-0.00290.0915-0.00730.11829.43914.0261-9.1534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1231 through 1241 )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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