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- PDB-7lq7: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7lq7
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV503 and COVA1-16
Components
  • COVA1-16 heavy chain
  • COVA1-16 light chain
  • CV503 heavy chain
  • CV503 light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM / antibody / coronavirus / Fab / spike / COVID-19 / RBD / receptor binding domain
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 / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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 / 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-2 / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsYuan, M. / Zhu, X. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: Sci Transl Med / Year: 2021
Title: Bispecific antibodies targeting distinct regions of the spike protein potently neutralize SARS-CoV-2 variants of concern.
Authors: Cho, H. / Gonzales-Wartz, K.K. / Huang, D. / Yuan, M. / Peterson, M. / Liang, J. / Beutler, N. / Torres, J.L. / Cong, Y. / Postnikova, E. / Bangaru, S. / Talana, C.A. / Shi, W. / Yang, E.S. ...Authors: Cho, H. / Gonzales-Wartz, K.K. / Huang, D. / Yuan, M. / Peterson, M. / Liang, J. / Beutler, N. / Torres, J.L. / Cong, Y. / Postnikova, E. / Bangaru, S. / Talana, C.A. / Shi, W. / Yang, E.S. / Zhang, Y. / Leung, K. / Wang, L. / Peng, L. / Skinner, J. / Li, S. / Wu, N.C. / Liu, H. / Dacon, C. / Moyer, T. / Cohen, M. / Zhao, M. / Lee, F.E. / Weinberg, R.S. / Douagi, I. / Gross, R. / Schmaljohn, C. / Pegu, A. / Mascola, J.R. / Holbrook, M. / Nemazee, D. / Rogers, T.F. / Ward, A.B. / Wilson, I.A. / Crompton, P.D. / Tan, J.
History
DepositionFeb 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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

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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: CV503 heavy chain
D: CV503 light chain
E: Spike protein S1
F: CV503 heavy chain
G: CV503 light chain
L: CV503 light chain
T: COVA1-16 heavy chain
U: COVA1-16 light chain
P: COVA1-16 heavy chain
y: COVA1-16 heavy chain
H: CV503 heavy chain
Q: COVA1-16 light chain
z: COVA1-16 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,30118
Polymers353,63715
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35090 Å2
ΔGint-172 kcal/mol
Surface area136750 Å2
Unit cell
Length a, b, c (Å)172.218, 122.742, 175.459
Angle α, β, γ (deg.)90.000, 118.220, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13B
23E
14C
24F
15C
25T
16C
26P
17C
27y
18C
28H
19D
29G
110D
210L
111F
211T
112F
212P
113F
213y
114F
214H
115G
215L
116T
216P
117T
217y
118T
218H
119U
219Q
120U
220z
121P
221y
122P
222H
123y
223H
124Q
224z

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPROPROAA333 - 5271 - 195
21THRTHRPROPROBB333 - 5271 - 195
12THRTHRPROPROAA333 - 5271 - 195
22THRTHRPROPROEE333 - 5271 - 195
13THRTHRPROPROBB333 - 5271 - 195
23THRTHRPROPROEE333 - 5271 - 195
14GLNGLNCYSCYSCC1 - 2161 - 224
24GLNGLNCYSCYSFF1 - 2161 - 224
15GLNGLNCYSCYSCC1 - 2161 - 224
25GLNGLNCYSCYSTI1 - 2161 - 232
16GLNGLNCYSCYSCC1 - 2161 - 224
26GLNGLNCYSCYSPK1 - 2161 - 232
17GLNGLNCYSCYSCC1 - 2161 - 224
27GLNGLNCYSCYSyL1 - 2161 - 232
18GLNGLNLYSLYSCC1 - 2141 - 222
28GLNGLNLYSLYSHM1 - 2141 - 222
19SERSERGLUGLUDD2 - 2102 - 214
29SERSERGLUGLUGG2 - 2102 - 214
110SERSERTHRTHRDD2 - 2092 - 213
210SERSERTHRTHRLH2 - 2092 - 213
111GLNGLNCYSCYSFF1 - 2161 - 224
211GLNGLNCYSCYSTI1 - 2161 - 232
112GLNGLNCYSCYSFF1 - 2161 - 224
212GLNGLNCYSCYSPK1 - 2161 - 232
113GLNGLNCYSCYSFF1 - 2161 - 224
213GLNGLNCYSCYSyL1 - 2161 - 232
114GLNGLNSERSERFF1 - 2151 - 223
214GLNGLNSERSERHM1 - 2151 - 223
115SERSERTHRTHRGG2 - 2092 - 213
215SERSERTHRTHRLH2 - 2092 - 213
116GLNGLNCYSCYSTI1 - 2161 - 232
216GLNGLNCYSCYSPK1 - 2161 - 232
117GLNGLNCYSCYSTI1 - 2161 - 232
217GLNGLNCYSCYSyL1 - 2161 - 232
118GLNGLNSERSERTI1 - 2151 - 231
218GLNGLNSERSERHM1 - 2151 - 223
119ASPASPGLUGLUUJ1 - 2131 - 213
219ASPASPGLUGLUQN1 - 2131 - 213
120ASPASPGLUGLUUJ1 - 2131 - 213
220ASPASPGLUGLUzO1 - 2131 - 213
121GLNGLNCYSCYSPK1 - 2161 - 232
221GLNGLNCYSCYSyL1 - 2161 - 232
122GLNGLNSERSERPK1 - 2151 - 231
222GLNGLNSERSERHM1 - 2151 - 223
123GLNGLNSERSERyL1 - 2151 - 231
223GLNGLNSERSERHM1 - 2151 - 223
124ASPASPGLUGLUQN1 - 2131 - 213
224ASPASPGLUGLUzO1 - 2131 - 213

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24

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Components

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Protein , 2 types, 6 molecules ABECFH

#1: Protein Spike protein S1


Mass: 23104.867 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Protein CV503 heavy chain


Mass: 23544.420 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)

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Antibody , 3 types, 9 molecules DGLTPyUQz

#3: Antibody CV503 light chain


Mass: 22713.990 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#4: Antibody COVA1-16 heavy chain


Mass: 25100.061 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#5: Antibody COVA1-16 light chain


Mass: 23415.799 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)

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Sugars , 1 types, 3 molecules

#6: 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.: 3 / 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

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Details

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: 4.62 Å3/Da / Density % sol: 73.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate pH 4.2, 1 M lithium chloride, and 9% (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: 3.4→50 Å / Num. obs: 87462 / % possible obs: 98.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.043 / Rrim(I) all: 0.111 / Χ2: 0.611 / Net I/σ(I): 5.7 / Num. measured all: 589794
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.486.81.58258350.5360.6491.7120.41799.8
3.48-3.576.81.20758590.6340.4951.3060.41799.7
3.57-3.666.80.92758190.7150.3811.0040.42899.4
3.66-3.776.80.7157950.8260.2920.7690.42398.8
3.77-3.896.50.5158180.8930.2150.5550.43698.3
3.89-4.0360.34356040.930.1520.3760.4696.1
4.03-4.196.80.24658560.9740.1010.2660.4998.9
4.19-4.387.20.16658820.9880.0660.1790.53599.7
4.38-4.617.10.12258310.9930.0490.1320.61199.6
4.61-4.96.90.09858770.9950.040.1060.64999.5
4.9-5.286.70.08658690.9950.0360.0940.67399.6
5.28-5.816.40.07957340.9950.0330.0860.70497.3
5.81-6.656.60.06958320.9970.0290.0750.73998.2
6.65-8.377.20.04959400.9990.020.0530.89199.7
8.37-506.50.03559110.9990.0150.0381.28297.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JMW

7jmw


Resolution: 3.4→41.29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 27.734 / SU ML: 0.406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 2000 2.3 %RANDOM
Rwork0.1974 ---
obs0.1983 85417 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 314.66 Å2 / Biso mean: 131.837 Å2 / Biso min: 64.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å2-0.95 Å2
2---2.76 Å2-0 Å2
3---1.42 Å2
Refinement stepCycle: final / Resolution: 3.4→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24270 0 42 0 24312
Biso mean--191.35 --
Num. residues----3216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01224941
X-RAY DIFFRACTIONr_angle_refined_deg11.64234003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37553192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21323.0931080
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.192153771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2951592
X-RAY DIFFRACTIONr_chiral_restr0.0670.23302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219097
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A59710.08
12B59710.08
21A59970.08
22E59970.08
31B60070.06
32E60070.06
41C60880.07
42F60880.07
51C49010.2
52T49010.2
61C50600.2
62P50600.2
71C48960.2
72y48960.2
81C61920.08
82H61920.08
91D57640.11
92G57640.11
101D58240.1
102L58240.1
111F49040.2
112T49040.2
121F49710.19
122P49710.19
131F48920.2
132y48920.2
141F61320.06
142H61320.06
151G58830.1
152L58830.1
161T63950.08
162P63950.08
171T64190.08
172y64190.08
181T48980.2
182H48980.2
191U64000.07
192Q64000.07
201U63720.08
202z63720.08
211P64230.08
212y64230.08
221P50730.2
222H50730.2
231y48900.2
232H48900.2
241Q64300.07
242z64300.07
LS refinement shellResolution: 3.401→3.489 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 149 -
Rwork0.342 6121 -
all-6270 -
obs--95.94 %

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