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- PDB-6nb5: Crystal structure of anti- MERS-CoV human neutralizing LCA60 anti... -

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Basic information

Entry
Database: PDB / ID: 6nb5
TitleCrystal structure of anti- MERS-CoV human neutralizing LCA60 antibody Fab fragment
Components
  • LCA60 antigen-binding (Fab) fragment, heavy chain
  • LCA60 antigen-binding (Fab) fragment, light chain
KeywordsIMMUNE SYSTEM / Fab / Coronavirus / MERS-CoV / 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: 3 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: LCA60 antigen-binding (Fab) fragment, heavy chain
L: LCA60 antigen-binding (Fab) fragment, light chain
I: LCA60 antigen-binding (Fab) fragment, heavy chain
M: LCA60 antigen-binding (Fab) fragment, light chain


Theoretical massNumber of molelcules
Total (without water)94,1254
Polymers94,1254
Non-polymers00
Water0
1
H: LCA60 antigen-binding (Fab) fragment, heavy chain
L: LCA60 antigen-binding (Fab) fragment, light chain


Theoretical massNumber of molelcules
Total (without water)47,0622
Polymers47,0622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-21 kcal/mol
Surface area19390 Å2
MethodPISA
2
I: LCA60 antigen-binding (Fab) fragment, heavy chain
M: LCA60 antigen-binding (Fab) fragment, light chain


Theoretical massNumber of molelcules
Total (without water)47,0622
Polymers47,0622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-21 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.725, 69.575, 93.838
Angle α, β, γ (deg.)90.00, 107.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody LCA60 antigen-binding (Fab) fragment, heavy chain


Mass: 24516.527 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 LCA60 antigen-binding (Fab) fragment, light chain


Mass: 22545.926 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 30 % (v/v) Jeffamine ED-2001 pH 7.0 and 0.1 M HEPES pH 7.0

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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: Jun 27, 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: 3→39.18 Å / Num. obs: 17505 / % possible obs: 99.6 % / Redundancy: 3.1 % / CC1/2: 0.927 / Rmerge(I) obs: 0.293 / Rpim(I) all: 0.197 / Rrim(I) all: 0.354 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3-3.183.11.00228070.4760.6751.21399.7
9-39.152.90.0536740.9960.0370.06597.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.55 Å39.15 Å
Translation6.55 Å39.15 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C5V

6c5v


Resolution: 3→39.18 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.828 / SU B: 36.119 / SU ML: 0.6 / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2827 873 5 %RANDOM
Rwork0.22802 ---
obs0.2307 16620 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.337 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å22.29 Å2
2---4.05 Å20 Å2
3---1.85 Å2
Refinement stepCycle: 1 / Resolution: 3→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 0 0 0 6395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136550
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175922
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.6448921
X-RAY DIFFRACTIONr_angle_other_deg1.3221.57113842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34522.78241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.843151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4111522
X-RAY DIFFRACTIONr_chiral_restr0.0520.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027288
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021286
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_it3.5545.433441
X-RAY DIFFRACTIONr_mcbond_other3.5535.4293440
X-RAY DIFFRACTIONr_mcangle_it6.0428.1324289
X-RAY DIFFRACTIONr_mcangle_other6.0428.1334290
X-RAY DIFFRACTIONr_scbond_it3.0675.5493109
X-RAY DIFFRACTIONr_scbond_other3.0665.553110
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2228.1964633
X-RAY DIFFRACTIONr_long_range_B_refined8.80862.6916717
X-RAY DIFFRACTIONr_long_range_B_other8.80962.6776716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 68 -
Rwork0.342 1202 -
obs--99.69 %

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