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

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Basic information

Entry
Database: PDB / ID: 7lka
TitleCrystal structure of SARS-CoV-2 RBD-targeting antibody COV107-23
Components
  • COV107-23 heavy chain
  • COV107-23 light chain
KeywordsIMMUNE SYSTEM / coronavirus / COVID-19 / SARS-CoV-2 / antibody / Fab / receptor binding domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 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 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 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 / pdbx_initial_refinement_model
Revision 1.4Oct 30, 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
H: COV107-23 heavy chain
L: COV107-23 light chain
A: COV107-23 heavy chain
B: COV107-23 light chain
C: COV107-23 heavy chain
D: COV107-23 light chain
E: COV107-23 heavy chain
F: COV107-23 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,4959
Polymers186,4368
Non-polymers591
Water20,3391129
1
H: COV107-23 heavy chain
L: COV107-23 light chain


Theoretical massNumber of molelcules
Total (without water)46,6092
Polymers46,6092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-25 kcal/mol
Surface area18940 Å2
MethodPISA
2
A: COV107-23 heavy chain
B: COV107-23 light chain


Theoretical massNumber of molelcules
Total (without water)46,6092
Polymers46,6092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-26 kcal/mol
Surface area19030 Å2
MethodPISA
3
C: COV107-23 heavy chain
D: COV107-23 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6683
Polymers46,6092
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-29 kcal/mol
Surface area19400 Å2
MethodPISA
4
E: COV107-23 heavy chain
F: COV107-23 light chain


Theoretical massNumber of molelcules
Total (without water)46,6092
Polymers46,6092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-25 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.421, 74.797, 172.676
Angle α, β, γ (deg.)90.000, 99.410, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11H-308-

HOH

21H-437-

HOH

31A-415-

HOH

41A-421-

HOH

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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
COV107-23 light chain


Mass: 23419.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.085 M of sodium citrate - citric acid pH 5.6, 0.17 M ammonium acetate, 15% (v/v) glycerol, 25.5% (w/v) polyethylene glycol 4000

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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: 1.98→50 Å / Num. obs: 130797 / % possible obs: 94.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.057 / Rrim(I) all: 0.151 / Χ2: 0.745 / Net I/σ(I): 4.4 / Num. measured all: 882641
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.015.51.46864960.6630.6431.6080.41894.5
2.01-2.055.91.27264960.7530.5441.3880.40394.6
2.05-2.096.21.16165070.7780.4911.2640.42493.4
2.09-2.136.20.97561350.8330.411.060.41889.4
2.13-2.186.60.83756600.8780.3440.9070.42682.2
2.18-2.236.90.76865970.8920.3110.830.42595.9
2.23-2.297.10.70367320.9280.2810.7580.44397.2
2.29-2.357.10.59967330.9430.2390.6460.47597.3
2.35-2.427.10.4967190.9660.1950.5280.44696.8
2.42-2.4970.40967030.9690.1650.4420.46397.4
2.49-2.586.90.34767290.9750.1410.3750.597.2
2.58-2.696.90.2867170.9830.1140.3030.51997
2.69-2.816.70.21566650.9870.0880.2330.56296.5
2.81-2.966.70.16864800.9910.0690.1820.67993.2
2.96-3.146.50.12857380.9940.0530.1390.88582.7
3.14-3.397.20.10367410.9960.0410.1111.0896.7
3.39-3.737.30.08368580.9970.0330.091.37698.5
3.73-4.267.10.06968320.9980.0280.0741.53898.2
4.26-5.376.80.05367390.9980.0220.0581.5395.6
5.37-506.90.05265200.9980.0210.0571.5391

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6xc2

6xc2


Resolution: 1.981→31.005 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 6632 5.09 %
Rwork0.2151 123785 -
obs0.2176 130417 93.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.46 Å2 / Biso mean: 38.1706 Å2 / Biso min: 11.43 Å2
Refinement stepCycle: final / Resolution: 1.981→31.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12918 0 4 1129 14051
Biso mean--39.4 41.18 -
Num. residues----1718
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9811-2.00360.3871990.3415381588
2.0036-2.02720.35092180.3045419595
2.0272-2.05190.352210.2952406193
2.0519-2.07790.34672170.2946410893
2.0779-2.10520.34612140.2843399092
2.1052-2.13410.32852340.2739387889
2.1341-2.16450.33931750.2676350580
2.1645-2.19680.31182200.2654387688
2.1968-2.23120.34062180.2667421997
2.2312-2.26770.31182330.2655432797
2.2677-2.30680.33962350.2618414097
2.3068-2.34880.32242410.2551429397
2.3488-2.39390.29492230.2392422397
2.3939-2.44280.29982620.2351420297
2.4428-2.49580.28622170.2302431597
2.4958-2.55390.33392490.2363422697
2.5539-2.61770.30942130.2331426797
2.6177-2.68850.28391880.239430497
2.6885-2.76750.34172120.2345424897
2.7675-2.85680.32022440.2336415895
2.8568-2.95880.31752170.2333410193
2.9588-3.07720.28552070.2222369784
3.0772-3.21710.26581910.2241385587
3.2171-3.38650.26272470.213429197
3.3865-3.59840.25912380.1948432598
3.5984-3.87570.2141910.1941437198
3.8757-4.26490.23472260.1737435198
4.2649-4.880.18582670.1543424697
4.88-6.14040.18591940.1768393287
6.1404-31.0050.18372210.1759426693

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