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- PDB-6nb8: Crystal structure of anti- SARS-CoV human neutralizing S230 antib... -

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Basic information

Entry
Database: PDB / ID: 6nb8
TitleCrystal structure of anti- SARS-CoV human neutralizing S230 antibody Fab fragment
Components
  • S230 antigen-binding (Fab) fragment, heavy chain
  • S230 antigen-binding (Fab) fragment, light chain
KeywordsIMMUNE SYSTEM / Fab / Coronavirus / SARS / Glycoprotein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsWalls, A.J. / Xiong, X. / Park, Y.J. / Tortorici, M.A. / Snijder, J. / Quispe, J. / Cameroni, E. / Gopal, R. / Dai, M. / Lanzavecchia, A. ...Walls, A.J. / Xiong, X. / Park, Y.J. / Tortorici, M.A. / Snijder, J. / Quispe, J. / Cameroni, E. / Gopal, R. / Dai, M. / Lanzavecchia, A. / Zambon, M. / Rey, F.A. / Corti, D. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 United States
CitationJournal: Cell / Year: 2019
Title: Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion.
Authors: Alexandra C Walls / Xiaoli Xiong / Young-Jun Park / M Alejandra Tortorici / Joost Snijder / Joel Quispe / Elisabetta Cameroni / Robin Gopal / Mian Dai / Antonio Lanzavecchia / Maria Zambon / ...Authors: Alexandra C Walls / Xiaoli Xiong / Young-Jun Park / M Alejandra Tortorici / Joost Snijder / Joel Quispe / Elisabetta Cameroni / Robin Gopal / Mian Dai / Antonio Lanzavecchia / Maria Zambon / Félix A Rey / Davide Corti / David Veesler /
Abstract: Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways ...Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways to combat these viruses. The trimeric spike transmembrane glycoprotein S mediates entry into host cells and is the major target of neutralizing antibodies. To understand the humoral immune response elicited upon natural infections with coronaviruses, we structurally characterized the SARS-CoV and MERS-CoV S glycoproteins in complex with neutralizing antibodies isolated from human survivors. Although the two antibodies studied blocked attachment to the host cell receptor, only the anti-SARS-CoV S antibody triggered fusogenic conformational changes via receptor functional mimicry. These results provide a structural framework for understanding coronavirus neutralization by human antibodies and shed light on activation of coronavirus membrane fusion, which takes place through a receptor-driven ratcheting mechanism.
History
DepositionDec 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
H: S230 antigen-binding (Fab) fragment, heavy chain
L: S230 antigen-binding (Fab) fragment, light chain


Theoretical massNumber of molelcules
Total (without water)48,9732
Polymers48,9732
Non-polymers00
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-26 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.823, 104.406, 108.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody S230 antigen-binding (Fab) fragment, heavy chain


Mass: 24882.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody S230 antigen-binding (Fab) fragment, light chain


Mass: 24089.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 3.5 M sodium formate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 23, 2018
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.499→75.302 Å / Num. obs: 69810 / % possible obs: 99.6 % / Redundancy: 6.1 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.065 / Rsym value: 0.059 / Net I/av σ(I): 9.6 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.5-1.584.40.6411.198720.3370.7290.64197.7
1.58-1.686.10.4651.795380.2030.5090.465100
1.68-1.796.50.2922.690280.1230.3180.292100
1.79-1.946.50.174.183670.0720.1850.1799.9
1.94-2.126.50.1036.177500.0450.1130.10399.9
2.12-2.376.60.0719.770620.030.0780.07199.9
2.37-2.746.50.05313.462370.0220.0570.053100
2.74-3.356.50.03916.153170.0170.0430.039100
3.35-4.745.90.02921.142040.0130.0320.02999.7
4.74-37.8236.20.02326.424350.010.0250.02399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.05 Å48.21 Å
Translation6.05 Å48.21 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0232refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C5V

6c5v


Resolution: 1.5→37.68 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.167 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16714 3514 5 %RANDOM
Rwork0.12851 ---
obs0.13055 66205 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.587 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2---1.29 Å20 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.5→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 0 468 3910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133864
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173398
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.6445313
X-RAY DIFFRACTIONr_angle_other_deg1.3881.5757968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3775525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55521.925187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75815627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8091525
X-RAY DIFFRACTIONr_chiral_restr0.0670.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024577
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02842
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8131.6781986
X-RAY DIFFRACTIONr_mcbond_other1.8071.6761985
X-RAY DIFFRACTIONr_mcangle_it2.3692.5242546
X-RAY DIFFRACTIONr_mcangle_other2.3712.5272547
X-RAY DIFFRACTIONr_scbond_it2.3341.981878
X-RAY DIFFRACTIONr_scbond_other2.3051.981878
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9292.8372767
X-RAY DIFFRACTIONr_long_range_B_refined4.01821.2674321
X-RAY DIFFRACTIONr_long_range_B_other3.59420.34199
X-RAY DIFFRACTIONr_rigid_bond_restr1.45137262
X-RAY DIFFRACTIONr_sphericity_free28.4095289
X-RAY DIFFRACTIONr_sphericity_bonded14.10857325
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 212 -
Rwork0.263 4667 -
obs--95.26 %
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)
10.02470.02520.00680.0307-0.00090.0150.001-0.00420.00220.0003-0.00260.0018-0.0012-0.00310.00150.01910.00080.00020.0175-0.0010.0003-15.5332-8.85333.7571
20.00090.00010.00060.00010.00050.0026-0.0023-0.00380.0003-0.0002-0.00030.00070.0015-0.00540.00260.02320.0003-0.00150.0234-0.00130.0035-14.122719.9773-10.6547
30.00990.00270.01530.03240.00080.0302-0.0009-0.00070.00210.0001-0.0008-0.0004-0.00090.00010.00170.0162-0.00040.00020.0173-0.00060.0009-15.1456-14.3646-17.9061
40.00030.00010.0001000.0001-0.00060.0023-0.00020.00040.0007-0.0001-0.00010.0013-0.00010.02130.0008-0.00120.0224-0.00160.0028-4.668821.4597-22.5339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 127
2X-RAY DIFFRACTION2H128 - 230
3X-RAY DIFFRACTION3L1 - 110
4X-RAY DIFFRACTION4L111 - 219

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