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- PDB-7rku: Structure of the SARS-CoV-2 receptor binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7rku
TitleStructure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C022
Components
  • C022 Antibody Fab Heavy Chain
  • C022 Antibody Fab Light Chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / Surface protein / Fab / coronavirus / fusion protein / binding domain / VIRAL PROTEIN / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 ...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 / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJette, C.A. / Bjorkman, P.J. / Barnes, C.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI138938-S1 United States
CitationJournal: Cell Rep / Year: 2021
Title: Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies.
Authors: Claudia A Jette / Alexander A Cohen / Priyanthi N P Gnanapragasam / Frauke Muecksch / Yu E Lee / Kathryn E Huey-Tubman / Fabian Schmidt / Theodora Hatziioannou / Paul D Bieniasz / Michel C ...Authors: Claudia A Jette / Alexander A Cohen / Priyanthi N P Gnanapragasam / Frauke Muecksch / Yu E Lee / Kathryn E Huey-Tubman / Fabian Schmidt / Theodora Hatziioannou / Paul D Bieniasz / Michel C Nussenzweig / Anthony P West / Jennifer R Keeffe / Pamela J Bjorkman / Christopher O Barnes /
Abstract: Many anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) neutralizing antibodies target the angiotensin-converting enzyme 2 (ACE2) binding site on viral spike receptor-binding ...Many anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) neutralizing antibodies target the angiotensin-converting enzyme 2 (ACE2) binding site on viral spike receptor-binding domains (RBDs). Potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly emergent zoonotic sarbecoviruses and variants, but they usually show only weak neutralization potencies. Here, we characterize two class 4 anti-RBD antibodies derived from coronavirus disease 2019 (COVID-19) donors that exhibit breadth and potent neutralization of zoonotic coronaviruses and SARS-CoV-2 variants. C118-RBD and C022-RBD structures reveal orientations that extend from the cryptic epitope to occlude ACE2 binding and CDRH3-RBD main-chain H-bond interactions that extend an RBD β sheet, thus reducing sensitivity to RBD side-chain changes. A C118-spike trimer structure reveals rotated RBDs that allow access to the cryptic epitope and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 13, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: 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
A: Spike protein S1
B: Spike protein S1
C: Spike protein S1
D: Spike protein S1
E: C022 Antibody Fab Heavy Chain
F: C022 Antibody Fab Light Chain
G: C022 Antibody Fab Heavy Chain
H: C022 Antibody Fab Heavy Chain
I: C022 Antibody Fab Light Chain
J: C022 Antibody Fab Heavy Chain
K: C022 Antibody Fab Light Chain
L: C022 Antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,99216
Polymers294,37612
Non-polymers1,6164
Water00
1
A: Spike protein S1
G: C022 Antibody Fab Heavy Chain
I: C022 Antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1814
Polymers73,5943
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
J: C022 Antibody Fab Heavy Chain
K: C022 Antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1814
Polymers73,5943
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Spike protein S1
H: C022 Antibody Fab Heavy Chain
L: C022 Antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8154
Polymers73,5943
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Spike protein S1
E: C022 Antibody Fab Heavy Chain
F: C022 Antibody Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8154
Polymers73,5943
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.385, 178.385, 247.318
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 334 through 527)
d_2ens_1(chain "B" and resid 334 through 527)
d_3ens_1(chain "C" and resid 334 through 527)
d_4ens_1(chain "D" and resid 334 through 527)
d_1ens_2(chain "E" and (resid 1 through 20 or (resid 21...
d_2ens_2(chain "G" and (resid 1 through 20 or (resid 21...
d_3ens_2(chain "H" and (resid 1 through 126 or resid 133 through 229))
d_4ens_2(chain "J" and (resid 1 through 20 or (resid 21...
d_1ens_3(chain "F" and (resid 1 through 9 or (resid 10...
d_2ens_3(chain "I" and (resid 1 through 9 or (resid 10...
d_3ens_3(chain "K" and (resid 1 through 146 or resid 148 through 177 or resid 179 through 197))
d_4ens_3(chain "L" and (resid 1 through 9 or (resid 10...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNPROA2 - 195
d_21ens_1ASNPROE2 - 195
d_31ens_1ASNPROI1 - 194
d_41ens_1ASNPROK1 - 194
d_11ens_2GLNPROM1 - 142
d_12ens_2GLYPROM149 - 229
d_21ens_2GLNPROO1 - 223
d_31ens_2GLNPROP1 - 142
d_32ens_2GLYPROP149 - 229
d_41ens_2GLNPROJ1 - 142
d_42ens_2GLYPROJ144 - 224
d_11ens_3ASPSERN1 - 162
d_12ens_3THRALAN164 - 193
d_13ens_3GLUGLUN195 - 213
d_21ens_3ASPSERI1 - 162
d_22ens_3THRALAI164 - 193
d_23ens_3GLUGLUI195 - 213
d_31ens_3ASPSERK1 - 162
d_32ens_3THRALAK164 - 193
d_33ens_3GLUGLUK195 - 213
d_41ens_3ASPSERL1 - 162
d_42ens_3THRALAL164 - 193
d_43ens_3GLUGLUL195 - 213

NCS ensembles :
ID
ens_1
ens_2
ens_3

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Components

#1: Protein
Spike protein S1


Mass: 24004.926 Da / Num. of mol.: 4 / Fragment: Receptor Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody
C022 Antibody Fab Heavy Chain


Mass: 25978.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody
C022 Antibody Fab Light Chain


Mass: 23610.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.05M ammonium sulfate, 0.05M BIS-Tris, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→44.6 Å / Num. obs: 73262 / % possible obs: 99.5 % / Redundancy: 10.3 % / Biso Wilson estimate: 125.06 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.87
Reflection shellResolution: 3.2→3.32 Å / Num. unique obs: 7338 / CC1/2: 0.277 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Coot0.8.9.1model building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K8M

7k8m


Resolution: 3.2→44.6 Å / SU ML: 0.511 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2311 3595 4.93 %
Rwork0.1876 69365 -
obs0.1898 72960 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.39 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19668 0 106 0 19774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01120324
X-RAY DIFFRACTIONf_angle_d1.282227686
X-RAY DIFFRACTIONf_chiral_restr0.06493067
X-RAY DIFFRACTIONf_plane_restr0.00963533
X-RAY DIFFRACTIONf_dihedral_angle_d14.50377240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.410639754073
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.929440084188
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.976753780576
ens_2d_2MX-RAY DIFFRACTIONTorsion NCS4.5671602254
ens_2d_3MX-RAY DIFFRACTIONTorsion NCS0.437744752325
ens_2d_4MX-RAY DIFFRACTIONTorsion NCS4.58605167867
ens_3d_2NX-RAY DIFFRACTIONTorsion NCS4.10929182106
ens_3d_3NX-RAY DIFFRACTIONTorsion NCS4.1040228587
ens_3d_4NX-RAY DIFFRACTIONTorsion NCS0.47729285631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.240.36891220.36212534X-RAY DIFFRACTION93.55
3.24-3.290.34941180.32362631X-RAY DIFFRACTION98.85
3.29-3.330.36171340.33952644X-RAY DIFFRACTION99.32
3.33-3.380.3641100.33592694X-RAY DIFFRACTION99.89
3.38-3.440.38891830.31122664X-RAY DIFFRACTION99.93
3.44-3.490.36491170.29592677X-RAY DIFFRACTION100
3.49-3.550.31161300.28052699X-RAY DIFFRACTION99.93
3.55-3.620.35981390.25242644X-RAY DIFFRACTION100
3.62-3.690.3151270.23732687X-RAY DIFFRACTION99.96
3.69-3.760.29271530.24472673X-RAY DIFFRACTION99.96
3.76-3.840.25311390.23112645X-RAY DIFFRACTION99.93
3.84-3.930.28771400.22132681X-RAY DIFFRACTION99.96
3.93-4.030.24671330.20882685X-RAY DIFFRACTION100
4.03-4.140.23881230.2192700X-RAY DIFFRACTION100
4.14-4.260.27021470.18472664X-RAY DIFFRACTION100
4.26-4.40.21991430.16692649X-RAY DIFFRACTION99.96
4.4-4.560.18721240.15062707X-RAY DIFFRACTION100
4.56-4.740.1651520.14442647X-RAY DIFFRACTION99.96
4.74-4.950.16251450.15332710X-RAY DIFFRACTION100
4.95-5.220.22591330.16042650X-RAY DIFFRACTION99.96
5.22-5.540.19761530.16432687X-RAY DIFFRACTION100
5.54-5.970.21991420.16142680X-RAY DIFFRACTION100
5.97-6.570.24471780.18742644X-RAY DIFFRACTION100
6.57-7.510.25871260.18092706X-RAY DIFFRACTION99.96
7.52-9.450.18771400.1512698X-RAY DIFFRACTION99.96
9.45-44.60.19291440.16272665X-RAY DIFFRACTION98.05

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