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- PDB-7rnj: S2P6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem hel... -

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Basic information

Entry
Database: PDB / ID: 7rnj
TitleS2P6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
Components
  • Monoclonal antibody S2P6 Fab heavy chain
  • Monoclonal antibody S2P6 Fab light chain
  • Spike glycoprotein stem helix peptide
KeywordsANTIVIRAL PROTEIN / IMMUNE SYSTEM / COVID-19 / SARS-CoV-2 / neutralizing monoclonal antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsSnell, G. / Czudnochowski, N. / Croll, T.I. / Nix, J.C. / Corti, D. / Cameroni, E. / Pinto, D. / Beltramello, M. / Sauer, M.M. / Veesler, D.
CitationJournal: Science / Year: 2021
Title: Broad betacoronavirus neutralization by a stem helix-specific human antibody.
Authors: Dora Pinto / Maximilian M Sauer / Nadine Czudnochowski / Jun Siong Low / M Alejandra Tortorici / Michael P Housley / Julia Noack / Alexandra C Walls / John E Bowen / Barbara Guarino / Laura ...Authors: Dora Pinto / Maximilian M Sauer / Nadine Czudnochowski / Jun Siong Low / M Alejandra Tortorici / Michael P Housley / Julia Noack / Alexandra C Walls / John E Bowen / Barbara Guarino / Laura E Rosen / Julia di Iulio / Josipa Jerak / Hannah Kaiser / Saiful Islam / Stefano Jaconi / Nicole Sprugasci / Katja Culap / Rana Abdelnabi / Caroline Foo / Lotte Coelmont / Istvan Bartha / Siro Bianchi / Chiara Silacci-Fregni / Jessica Bassi / Roberta Marzi / Eneida Vetti / Antonino Cassotta / Alessandro Ceschi / Paolo Ferrari / Pietro E Cippà / Olivier Giannini / Samuele Ceruti / Christian Garzoni / Agostino Riva / Fabio Benigni / Elisabetta Cameroni / Luca Piccoli / Matteo S Pizzuto / Megan Smithey / David Hong / Amalio Telenti / Florian A Lempp / Johan Neyts / Colin Havenar-Daughton / Antonio Lanzavecchia / Federica Sallusto / Gyorgy Snell / Herbert W Virgin / Martina Beltramello / Davide Corti / David Veesler /
Abstract: The spillovers of betacoronaviruses in humans and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight the need for broad coronavirus countermeasures. We ...The spillovers of betacoronaviruses in humans and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight the need for broad coronavirus countermeasures. We describe five monoclonal antibodies (mAbs) cross-reacting with the stem helix of multiple betacoronavirus spike glycoproteins isolated from COVID-19 convalescent individuals. Using structural and functional studies, we show that the mAb with the greatest breadth (S2P6) neutralizes pseudotyped viruses from three different subgenera through the inhibition of membrane fusion, and we delineate the molecular basis for its cross-reactivity. S2P6 reduces viral burden in hamsters challenged with SARS-CoV-2 through viral neutralization and Fc-mediated effector functions. Stem helix antibodies are rare, oftentimes of narrow specificity, and can acquire neutralization breadth through somatic mutations. These data provide a framework for structure-guided design of pan-betacoronavirus vaccines eliciting broad protection.
History
DepositionJul 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Monoclonal antibody S2P6 Fab light chain
H: Monoclonal antibody S2P6 Fab heavy chain
B: Spike glycoprotein stem helix peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4397
Polymers49,0553
Non-polymers3844
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.642, 92.642, 223.408
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11L-413-

HOH

21H-415-

HOH

31B-1205-

HOH

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Components

#1: Antibody Monoclonal antibody S2P6 Fab light chain


Mass: 23776.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Monoclonal antibody S2P6 Fab heavy chain


Mass: 23474.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Spike glycoprotein stem helix peptide


Mass: 1803.964 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate pH 4.6, 25% (v/v) PEG Smear Broad

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.67→46.32 Å / Num. obs: 16691 / % possible obs: 99 % / Redundancy: 8 % / Biso Wilson estimate: 67.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.075 / Rrim(I) all: 0.217 / Net I/σ(I): 8.9 / Num. measured all: 133307
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
2.67-2.88.43.7141814321570.2671.3363.9520.699.7
8.86-46.326.50.03434945410.9980.0140.03741.696.1

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model of S2P6 Fab

Resolution: 2.67→45.84 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2736 782 4.77 %
Rwork0.2349 15610 -
obs0.2368 16392 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196 Å2 / Biso mean: 87.4783 Å2 / Biso min: 37.49 Å2
Refinement stepCycle: final / Resolution: 2.67→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 20 69 3113
Biso mean--82.75 65.29 -
Num. residues----422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023125
X-RAY DIFFRACTIONf_angle_d0.5274264
X-RAY DIFFRACTIONf_dihedral_angle_d9.9441044
X-RAY DIFFRACTIONf_chiral_restr0.044471
X-RAY DIFFRACTIONf_plane_restr0.005557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.840.38291160.32942319243590
2.84-3.060.361230.31722609273299
3.06-3.360.38651390.27482560269998
3.37-3.850.31291310.230626442775100
3.85-4.850.22041390.19822655279499
4.85-45.840.23651340.22252823295798
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)
17.0159-1.6494-3.18358.0928-1.79432.28390.7243-1.7911.79780.9695-0.11320.7761-1.8074-1.0357-0.56210.76590.04160.24460.8556-0.19480.7009-37.49460.907329.9411
23.4844-0.2178-0.76344.1286-0.27261.41550.0410.1395-0.0025-0.7121-0.0175-0.11720.0127-0.0088-0.01560.5996-0.0351-0.02670.555-0.06840.3154-24.422658.268.5067
34.97632.02410.39259.0037-0.63362.19380.09040.6052-1.0792-0.4567-0.62371.13860.2895-0.50980.56380.91150.26770.04950.9124-0.40931.1044-16.764429.1453-13.3838
44.67441.5197-0.19986.8822.34572.95550.089-0.1814-0.33380.1617-0.18390.16170.1761-0.25980.08450.5606-0.0872-0.05860.57280.00820.3125-35.574243.39820.5716
51.8950.5597-2.40782.88130.73063.8186-0.8012-0.9036-1.58960.7528-0.09030.68540.96050.55080.77051.09860.2610.22430.6040.24431.728-19.547524.72363.3744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1146 through 1159)B1146 - 1159
2X-RAY DIFFRACTION2chain 'L' and (resid 1 through 110)L1 - 110
3X-RAY DIFFRACTION3chain 'L' and (resid 111 through 215)L111 - 215
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 118)H1 - 118
5X-RAY DIFFRACTION5chain 'H' and (resid 119 through 213)H119 - 213

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