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- PDB-7rks: Structure of the SARS-CoV receptor binding domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 7rks
TitleStructure of the SARS-CoV receptor binding domain in complex with the human neutralizing antibody Fab fragment, C118
Components
  • C118 Antibody Fab Heavy Chain
  • C118 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 / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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 / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.3Dec 29, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 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
H: C118 Antibody Fab Heavy Chain
I: C118 Antibody Fab Heavy Chain
L: C118 Antibody Fab Light Chain
M: C118 Antibody Fab Light Chain
R: Spike protein S1
S: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5878
Polymers141,5926
Non-polymers9952
Water00
1
H: C118 Antibody Fab Heavy Chain
L: C118 Antibody Fab Light Chain
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2204
Polymers70,7963
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: C118 Antibody Fab Heavy Chain
M: C118 Antibody Fab Light Chain
S: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3664
Polymers70,7963
Non-polymers5711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.923, 89.993, 93.865
Angle α, β, γ (deg.)90.000, 113.334, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "H"
d_2ens_1(chain "I" and (resid 1 through 126 or resid 135 through 214))
d_1ens_2chain "L"
d_2ens_2(chain "M" and ((resid 1 and (name N or name...
d_1ens_3(chain "R" and (resid 321 through 502 or resid 600))
d_2ens_3(chain "S" and (resid 321 through 502 or resid 538))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNLYSA1 - 220
d_21ens_1GLNPROB1 - 140
d_22ens_1THRLYSB142 - 221
d_11ens_2GLNTHRC1 - 214
d_21ens_2GLNTHRD1 - 214
d_11ens_3ASNGLUE1 - 182
d_21ens_3ASNGLUH1 - 182

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.99912321205, 0.039441154924, -0.0140428786682), (0.0386445963901, 0.997842422254, 0.0530763178854), (0.0161059713422, 0.0524870998311, -0.998491713555)71.454837768, -0.422184497905, -32.0201056644
2given(-0.99933278559, 0.0298245319911, 0.0210827165539), (0.0308546252566, 0.998254813553, 0.0503519544669), (-0.0195441998059, 0.050968858236, -0.998508988314)71.5397504514, 0.263484924633, -30.4190710453
3given(-0.997020849819, 0.0771263166684, 0.00097790806622), (0.0771016769865, 0.996900599928, -0.0156373037544), (-0.00218092477909, -0.0155153195263, -0.99987725168)70.5973578272, -0.567025533467, -30.8106529604

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Components

#1: Antibody C118 Antibody Fab Heavy Chain


Mass: 25700.611 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 C118 Antibody Fab Light Chain


Mass: 22736.170 Da / Num. of mol.: 2
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: 22359.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P59594
#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.: 1
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
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium fluoride, 20% PEG 3,350

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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: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→46.61 Å / Num. obs: 72486 / % possible obs: 95.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 59.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0622 / Rpim(I) all: 0.0396 / Net I/σ(I): 13.14
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 3085 / CC1/2: 0.918 / Rpim(I) all: 0.28 / % possible all: 79.5

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Processing

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

7k8m


Resolution: 2.7→46.61 Å / SU ML: 0.4387 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2467 3606 4.97 %
Rwork0.1946 68880 -
obs0.1972 72486 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.79 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9516 0 66 0 9582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00959839
X-RAY DIFFRACTIONf_angle_d1.16613413
X-RAY DIFFRACTIONf_chiral_restr0.06041486
X-RAY DIFFRACTIONf_plane_restr0.00971712
X-RAY DIFFRACTIONf_dihedral_angle_d13.16883484
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.08941338455
ens_2d_2MX-RAY DIFFRACTIONTorsion NCS1.52371244827
ens_3d_2SX-RAY DIFFRACTIONTorsion NCS0.811934711001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.48371010.40972007X-RAY DIFFRACTION70.79
2.74-2.770.37581120.37392269X-RAY DIFFRACTION81.15
2.77-2.810.42221310.34962387X-RAY DIFFRACTION85.53
2.81-2.860.40571420.31782596X-RAY DIFFRACTION94.19
2.86-2.90.41371470.28952771X-RAY DIFFRACTION98.02
2.9-2.950.33421520.27252715X-RAY DIFFRACTION97.98
2.95-30.2951410.26562747X-RAY DIFFRACTION97.44
3-3.050.3261310.24312693X-RAY DIFFRACTION97.41
3.05-3.110.29791550.25112768X-RAY DIFFRACTION97.05
3.11-3.180.32461410.23532661X-RAY DIFFRACTION97.02
3.18-3.240.28021440.23972738X-RAY DIFFRACTION96.42
3.24-3.320.27371390.23432639X-RAY DIFFRACTION94.33
3.32-3.40.31071380.2622697X-RAY DIFFRACTION96.13
3.4-3.50.2751440.2182698X-RAY DIFFRACTION97.6
3.5-3.60.27411480.22122751X-RAY DIFFRACTION97.87
3.6-3.710.36571320.20182742X-RAY DIFFRACTION97.49
3.71-3.850.24811390.20622667X-RAY DIFFRACTION97.03
3.85-40.24631340.18482727X-RAY DIFFRACTION96.36
4-4.180.20951350.18222619X-RAY DIFFRACTION93.9
4.18-4.40.21541360.15392757X-RAY DIFFRACTION97.64
4.4-4.680.1921440.13682738X-RAY DIFFRACTION97.63
4.68-5.040.17711470.13522688X-RAY DIFFRACTION97.19
5.04-5.550.19091300.15112687X-RAY DIFFRACTION95.3
5.55-6.350.1891480.15842720X-RAY DIFFRACTION97.85
6.35-7.990.19771550.17052710X-RAY DIFFRACTION96.69
7.99-46.610.19431400.14952688X-RAY DIFFRACTION96.06

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