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- PDB-7si2: Crystal structure of neutralizing antibody 10-28 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7si2
TitleCrystal structure of neutralizing antibody 10-28 in complex with SARS-CoV-2 spike receptor binding domain (RBD)
Components
  • 10-28 Heavy Chain
  • 10-28 Light Chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / SARS-CoV-2 / Viral protein / Spike glycoprotein / Receptor Binding Protein / RBD / Neutralizing antibody / 10-28 / Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / 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 / symbiont entry into host cell / 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 / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsReddem, E.R. / Shapiro, L.
Funding support China, 1items
OrganizationGrant numberCountry
Jack Ma Foundation China
CitationJournal: Sci Transl Med / Year: 2022
Title: An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses.
Authors: Lihong Liu / Sho Iketani / Yicheng Guo / Eswar R Reddem / Ryan G Casner / Manoj S Nair / Jian Yu / Jasper F-W Chan / Maple Wang / Gabriele Cerutti / Zhiteng Li / Nicholas C Morano / Candace ...Authors: Lihong Liu / Sho Iketani / Yicheng Guo / Eswar R Reddem / Ryan G Casner / Manoj S Nair / Jian Yu / Jasper F-W Chan / Maple Wang / Gabriele Cerutti / Zhiteng Li / Nicholas C Morano / Candace D Castagna / Laura Corredor / Hin Chu / Shuofeng Yuan / Vincent Kwok-Man Poon / Chris Chun-Sing Chan / Zhiwei Chen / Yang Luo / Marcus Cunningham / Alejandro Chavez / Michael T Yin / David S Perlin / Moriya Tsuji / Kwok-Yung Yuen / Peter D Kwong / Zizhang Sheng / Yaoxing Huang / Lawrence Shapiro / David D Ho /
Abstract: The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related ...The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.
History
DepositionOct 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 6, 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
D: 10-28 Light Chain
E: 10-28 Heavy Chain
F: 10-28 Light Chain
G: 10-28 Heavy Chain
H: 10-28 Heavy Chain
L: 10-28 Light Chain
A: Spike protein S1
B: Spike protein S1
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,70512
Polymers222,4329
Non-polymers1,2733
Water00
1
D: 10-28 Light Chain
E: 10-28 Heavy Chain
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5684
Polymers74,1443
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-26 kcal/mol
Surface area28300 Å2
MethodPISA
2
F: 10-28 Light Chain
G: 10-28 Heavy Chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5684
Polymers74,1443
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-24 kcal/mol
Surface area28600 Å2
MethodPISA
3
H: 10-28 Heavy Chain
L: 10-28 Light Chain
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5684
Polymers74,1443
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-26 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.785, 226.677, 186.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
12chain D
22chain F
32(chain L and (resid 1 through 194 or (resid 195...
13chain E
23chain G
33chain H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUPROPROchain AAG335 - 52717 - 209
211LEULEUPROPROchain BBH335 - 52717 - 209
311LEULEUPROPROchain CCI335 - 52717 - 209
112ASPASPGLUGLUchain DDA1 - 2141 - 214
212ASPASPGLUGLUchain FFC1 - 2141 - 214
312ASPASPALAALA(chain L and (resid 1 through 194 or (resid 195...LF1 - 1941 - 194
322CYSCYSCYSCYS(chain L and (resid 1 through 194 or (resid 195...LF195195
332ASPASPGLUGLU(chain L and (resid 1 through 194 or (resid 195...LF1 - 2141 - 214
342ASPASPGLUGLU(chain L and (resid 1 through 194 or (resid 195...LF1 - 2141 - 214
113GLNGLNSERSERchain EEB1 - 2221 - 222
213GLNGLNSERSERchain GGD1 - 2221 - 222
313GLNGLNSERSERchain HHE1 - 2221 - 222

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody 10-28 Light Chain


Mass: 23384.875 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 10-28 Heavy Chain


Mass: 24186.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Spike protein S1


Mass: 26572.881 Da / Num. of mol.: 3 / Fragment: receptor-binding domain (UNP reisdues 319-537)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
Has ligand of interestY
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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG3350, 30% PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.03→186.25 Å / Num. obs: 51186 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.17 / Rrim(I) all: 0.35 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.03-3.12141.643810.3610.90.9100
3.2-811.50.0858170.9970.0260.08999.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIXphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7L5B

7l5b


Resolution: 3.2→108.64 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 2361 5.55 %
Rwork0.1984 40188 -
obs0.2019 42549 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.79 Å2 / Biso mean: 77.8011 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.2→108.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14301 0 84 0 14385
Biso mean--107.05 --
Num. residues----1860
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1737X-RAY DIFFRACTION9.755TORSIONAL
12B1737X-RAY DIFFRACTION9.755TORSIONAL
13C1737X-RAY DIFFRACTION9.755TORSIONAL
21D1917X-RAY DIFFRACTION9.755TORSIONAL
22F1917X-RAY DIFFRACTION9.755TORSIONAL
23L1917X-RAY DIFFRACTION9.755TORSIONAL
31E1944X-RAY DIFFRACTION9.755TORSIONAL
32G1944X-RAY DIFFRACTION9.755TORSIONAL
33H1944X-RAY DIFFRACTION9.755TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.270.40861460.33152249239596
3.27-3.340.35071240.30242289241395
3.34-3.410.32471450.26962258240396
3.41-3.50.31391440.26172289243396
3.5-3.590.31321350.24562304243996
3.59-3.70.33081070.24612326243396
3.7-3.820.31391530.23662333248698
3.82-3.960.31471380.23322340247898
3.96-4.110.31531280.20812365249398
4.11-4.30.28121440.18222375251999
4.3-4.530.22791330.16322382251599
4.53-4.810.20611680.15422363253199
4.81-5.180.22151480.16392411255999
5.18-5.70.21741490.160524042553100
5.7-6.530.24471360.173224532589100
6.53-8.230.2271400.184224602600100
8.23-108.640.20171230.17612587271099
Refinement TLS params.Method: refined / Origin x: -48.6177 Å / Origin y: -53.7965 Å / Origin z: 5.6181 Å
111213212223313233
T0.5995 Å2-0.0186 Å2-0.0711 Å2-0.6342 Å20.031 Å2--0.5862 Å2
L0.2184 °20.1014 °2-0.0192 °2-0.3713 °20.1687 °2--0.0999 °2
S-0.0157 Å °0.0435 Å °-0.0357 Å °0.0104 Å °0.0204 Å °-0.006 Å °-0.0093 Å °-0.0157 Å °-0.0114 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allD1 - 214
2X-RAY DIFFRACTION1allE1 - 222
3X-RAY DIFFRACTION1allF1 - 214
4X-RAY DIFFRACTION1allG1 - 222
5X-RAY DIFFRACTION1allH1 - 222
6X-RAY DIFFRACTION1allL1 - 214
7X-RAY DIFFRACTION1allA335 - 527
8X-RAY DIFFRACTION1allA528 - 529
9X-RAY DIFFRACTION1allB335 - 527
10X-RAY DIFFRACTION1allB528 - 529
11X-RAY DIFFRACTION1allC335 - 527
12X-RAY DIFFRACTION1allC528 - 529

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