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- PDB-7lk9: Crystal structure of SARS-CoV-2 RBD-targeting antibody COV107-23 ... -

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Basic information

Entry
Database: PDB / ID: 7lk9
TitleCrystal structure of SARS-CoV-2 RBD-targeting antibody COV107-23 HC + COVD21-C8 LC
Components
  • COV107-23 heavy chain
  • COVD21-C8 light chain
KeywordsIMMUNE SYSTEM / coronavirus / COVID-19 / SARS-CoV-2 / antibody / Fab / receptor binding domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsYuan, M. / Zhu, X. / Wilson, I.A. / Wu, N.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R00 AI139445 United States
Citation
Journal: Nat Commun / Year: 2021
Title: Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain.
Authors: Tan, T.J.C. / Yuan, M. / Kuzelka, K. / Padron, G.C. / Beal, J.R. / Chen, X. / Wang, Y. / Rivera-Cardona, J. / Zhu, X. / Stadtmueller, B.M. / Brooke, C.B. / Wilson, I.A. / Wu, N.C.
#1: Journal: Biorxiv / Year: 2021
Title: Sequence signatures of two IGHV3-53/3-66 public clonotypes to SARS-CoV-2 receptor binding domain.
Authors: Tan, T.J.C. / Yuan, M. / Kuzelka, K. / Padron, G.C. / Beal, J.R. / Chen, X. / Wang, Y. / Rivera-Cardona, J. / Zhu, X. / Stadtmueller, B.M. / Brooke, C.B. / Wilson, I.A. / Wu, N.C.
History
DepositionFeb 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: COV107-23 heavy chain
L: COVD21-C8 light chain
A: COV107-23 heavy chain
B: COVD21-C8 light chain
C: COV107-23 heavy chain
D: COVD21-C8 light chain
M: COV107-23 heavy chain
N: COVD21-C8 light chain


Theoretical massNumber of molelcules
Total (without water)186,7768
Polymers186,7768
Non-polymers00
Water00
1
H: COV107-23 heavy chain
L: COVD21-C8 light chain


Theoretical massNumber of molelcules
Total (without water)46,6942
Polymers46,6942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-21 kcal/mol
Surface area19400 Å2
MethodPISA
2
A: COV107-23 heavy chain
B: COVD21-C8 light chain


Theoretical massNumber of molelcules
Total (without water)46,6942
Polymers46,6942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-19 kcal/mol
Surface area19400 Å2
MethodPISA
3
C: COV107-23 heavy chain
D: COVD21-C8 light chain


Theoretical massNumber of molelcules
Total (without water)46,6942
Polymers46,6942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-21 kcal/mol
Surface area19380 Å2
MethodPISA
4
M: COV107-23 heavy chain
N: COVD21-C8 light chain


Theoretical massNumber of molelcules
Total (without water)46,6942
Polymers46,6942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-21 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.297, 78.383, 91.626
Angle α, β, γ (deg.)100.120, 112.090, 92.800
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain H
41chain M
12(chain B and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))
22(chain D and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))
32(chain L and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))
42chain N

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
111GLUGLUSERSERchain AAC1 - 2151 - 219
211GLUGLUSERSERchain CCE1 - 2151 - 219
311GLUGLUSERSERchain HHA1 - 2151 - 219
411GLUGLUSERSERchain MMG1 - 2151 - 219
112GLUGLUSERSER(chain B and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))BD1 - 71 - 7
122THRTHRPROPRO(chain B and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))BD10 - 1510 - 15
132ALAALAGLUGLU(chain B and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))BD19 - 21319 - 214
212GLUGLUSERSER(chain D and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))DF1 - 71 - 7
222THRTHRPROPRO(chain D and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))DF10 - 1510 - 15
232ALAALAGLUGLU(chain D and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))DF19 - 21319 - 214
312GLUGLUSERSER(chain L and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))LB1 - 71 - 7
322THRTHRPROPRO(chain L and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))LB10 - 1510 - 15
332ALAALAGLUGLU(chain L and (resid 1 through 7 or resid 10 through 15 or resid 19 through 213))LB19 - 21319 - 214
412GLUGLUGLUGLUchain NNH1 - 2131 - 214

NCS ensembles :
ID
1
2

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Components

#1: Antibody
COV107-23 heavy chain


Mass: 23188.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
COVD21-C8 light chain


Mass: 23505.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M of sodium citrate pH 4, 1 M lithium chloride, and 20% (w/v) polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 24563 / % possible obs: 88 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.299 / Rpim(I) all: 0.188 / Rrim(I) all: 0.354 / Χ2: 0.649 / Net I/σ(I): 2.1 / Num. measured all: 79514
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.42.60.70919700.7270.4640.8510.4983.4
3.4-3.512.80.60519960.7820.3980.7280.65286.6
3.51-3.632.90.58120790.7890.3780.6960.57789.5
3.63-3.7830.52520380.8170.3370.6260.62488.4
3.78-3.953.10.52620970.820.3390.6280.63689.4
3.95-4.163.20.40320770.890.2540.4780.59289.4
4.16-4.423.30.28919880.9410.1810.3420.61485.5
4.42-4.763.20.24718430.9550.1560.2930.72179.7
4.76-5.243.50.24820870.9590.1530.2920.62888.4
5.24-5.993.70.2721600.960.1620.3160.55895
5.99-7.553.70.25321850.9580.1510.2950.5293.7
7.55-503.70.08920430.9920.0540.1041.10287.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XC2

6xc2


Resolution: 3.4→40.19 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3115 1087 4.85 %
Rwork0.2759 21308 -
obs0.2776 22395 88.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.17 Å2 / Biso mean: 62.1955 Å2 / Biso min: 35.17 Å2
Refinement stepCycle: final / Resolution: 3.4→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12881 0 0 0 12881
Num. residues----1707
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2568X-RAY DIFFRACTION6.831TORSIONAL
12C2568X-RAY DIFFRACTION6.831TORSIONAL
13H2568X-RAY DIFFRACTION6.831TORSIONAL
14M2568X-RAY DIFFRACTION6.831TORSIONAL
21B2507X-RAY DIFFRACTION6.831TORSIONAL
22D2507X-RAY DIFFRACTION6.831TORSIONAL
23L2507X-RAY DIFFRACTION6.831TORSIONAL
24N2507X-RAY DIFFRACTION6.831TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4001-3.55470.39871320.3569260587
3.5547-3.7420.37651320.3457269889
3.742-3.97630.35751380.325267689
3.9763-4.28290.3381300.2914267889
4.2829-4.71340.30191380.2581245782
4.7134-5.3940.28961400.2457265488
5.394-6.79050.30381480.2628284494
6.7905-40.190.22331290.2057269689

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