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- PDB-7kn4: Crystal structure of SARS-CoV-2 spike protein receptor-binding do... -

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Basic information

Entry
Database: PDB / ID: 7kn4
TitleCrystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-E6 Fab
Components
  • S-E6 Fab heavy chain
  • S-E6 Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Antibody / Spike / Coronavirus / COVID-19 / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex / phage display / pre-pandemic
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 / symbiont-mediated-mediated suppression 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 / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLiu, H. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: Adv Sci / Year: 2022
Title: Neutralizing Antibodies to SARS-CoV-2 Selected from a Human Antibody Library Constructed Decades Ago.
Authors: Qiang, M. / Ma, P. / Li, Y. / Liu, H. / Harding, A. / Min, C. / Wang, F. / Liu, L. / Yuan, M. / Ji, Q. / Tao, P. / Shi, X. / Li, Z. / Li, T. / Wang, X. / Zhang, Y. / Wu, N.C. / Lee, C.D. / ...Authors: Qiang, M. / Ma, P. / Li, Y. / Liu, H. / Harding, A. / Min, C. / Wang, F. / Liu, L. / Yuan, M. / Ji, Q. / Tao, P. / Shi, X. / Li, Z. / Li, T. / Wang, X. / Zhang, Y. / Wu, N.C. / Lee, C.D. / Zhu, X. / Gilbert-Jaramillo, J. / Zhang, C. / Saxena, A. / Huang, X. / Wang, H. / James, W. / Dwek, R.A. / Wilson, I.A. / Yang, G. / Lerner, R.A.
History
DepositionNov 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 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
Revision 1.2Jan 12, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
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 6, 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
A: Spike protein S1
B: Spike protein S1
H: S-E6 Fab heavy chain
L: S-E6 Fab light chain
M: S-E6 Fab heavy chain
N: S-E6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4758
Polymers145,0326
Non-polymers4422
Water00
1
A: Spike protein S1
H: S-E6 Fab heavy chain
L: S-E6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7374
Polymers72,5163
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-28 kcal/mol
Surface area26710 Å2
MethodPISA
2
B: Spike protein S1
M: S-E6 Fab heavy chain
N: S-E6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7374
Polymers72,5163
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-31 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.106, 70.234, 91.889
Angle α, β, γ (deg.)90.000, 108.470, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 334 through 339 or (resid 340...
21(chain B and (resid 334 through 369 or (resid 370...
12(chain H and (resid 1 through 18 or (resid 19...
22(chain M and (resid 1 through 4 or (resid 5...
13(chain L and (resid 2 through 12 or (resid 13...
23(chain N and (resid 2 through 93 or (resid 94...

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
111ASNASNGLYGLY(chain A and (resid 334 through 339 or (resid 340...AA334 - 33916 - 21
121GLUGLUVALVAL(chain A and (resid 334 through 339 or (resid 340...AA340 - 34122 - 23
131ASNASNLYSLYS(chain A and (resid 334 through 339 or (resid 340...AA334 - 52816 - 210
141ASNASNLYSLYS(chain A and (resid 334 through 339 or (resid 340...AA334 - 52816 - 210
151ASNASNLYSLYS(chain A and (resid 334 through 339 or (resid 340...AA334 - 52816 - 210
161ASNASNLYSLYS(chain A and (resid 334 through 339 or (resid 340...AA334 - 52816 - 210
211ASNASNTYRTYR(chain B and (resid 334 through 369 or (resid 370...BB334 - 36916 - 51
221ASNASNSERSER(chain B and (resid 334 through 369 or (resid 370...BB370 - 37152 - 53
231ASNASNGLYGLY(chain B and (resid 334 through 369 or (resid 370...BB334 - 52616 - 208
241ASNASNGLYGLY(chain B and (resid 334 through 369 or (resid 370...BB334 - 52616 - 208
251ASNASNGLYGLY(chain B and (resid 334 through 369 or (resid 370...BB334 - 52616 - 208
261ASNASNGLYGLY(chain B and (resid 334 through 369 or (resid 370...BB334 - 52616 - 208
112GLNGLNLEULEU(chain H and (resid 1 through 18 or (resid 19...HC1 - 181 - 18
122SERSERSERSER(chain H and (resid 1 through 18 or (resid 19...HC1919
132GLNGLNLYSLYS(chain H and (resid 1 through 18 or (resid 19...HC1 - 2141 - 221
142GLNGLNLYSLYS(chain H and (resid 1 through 18 or (resid 19...HC1 - 2141 - 221
152GLNGLNLYSLYS(chain H and (resid 1 through 18 or (resid 19...HC1 - 2141 - 221
162GLNGLNLYSLYS(chain H and (resid 1 through 18 or (resid 19...HC1 - 2141 - 221
212GLNGLNLEULEU(chain M and (resid 1 through 4 or (resid 5...ME1 - 41 - 4
222ARGARGARGARG(chain M and (resid 1 through 4 or (resid 5...ME55
232GLNGLNLYSLYS(chain M and (resid 1 through 4 or (resid 5...ME1 - 2141 - 221
113ALAALASERSER(chain L and (resid 2 through 12 or (resid 13...LD2 - 122 - 11
123SERSERSERSER(chain L and (resid 2 through 12 or (resid 13...LD1312
133ALAALAPROPRO(chain L and (resid 2 through 12 or (resid 13...LD2 - 2092 - 212
143ALAALAPROPRO(chain L and (resid 2 through 12 or (resid 13...LD2 - 2092 - 212
153ALAALAPROPRO(chain L and (resid 2 through 12 or (resid 13...LD2 - 2092 - 212
213ALAALAASPASP(chain N and (resid 2 through 93 or (resid 94...NF2 - 932 - 94
223SERSERSERSER(chain N and (resid 2 through 93 or (resid 94...NF9495
233ALAALAPROPRO(chain N and (resid 2 through 93 or (resid 94...NF2 - 2092 - 212
243ALAALAPROPRO(chain N and (resid 2 through 93 or (resid 94...NF2 - 2092 - 212
253ALAALAPROPRO(chain N and (resid 2 through 93 or (resid 94...NF2 - 2092 - 212
263ALAALAPROPRO(chain N and (resid 2 through 93 or (resid 94...NF2 - 2092 - 212

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Spike protein S1


Mass: 26095.348 Da / Num. of mol.: 2
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: Antibody S-E6 Fab heavy chain


Mass: 23482.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody S-E6 Fab light chain


Mass: 22938.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#4: 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 / Feature type: SUBJECT OF INVESTIGATION
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 interestY
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: 51.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% isopropanol, 20% PEG 4000, 0.1 M citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03373 Å / Relative weight: 1
ReflectionResolution: 2.697→50 Å / Num. obs: 37826 / % possible obs: 93.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.055 / Rrim(I) all: 0.108 / Χ2: 0.883 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.752.60.5616470.720.380.6810.88782.8
2.75-2.82.90.50117660.8220.3230.60.88487.5
2.8-2.853.10.44618140.8370.2790.5290.8791.4
2.85-2.913.30.38919230.8720.2370.4580.90294.1
2.91-2.973.50.34418950.8950.2080.4040.91595.2
2.97-3.043.50.29719700.9170.1770.3470.90296.8
3.04-3.123.50.25419370.940.1540.2990.92296.9
3.12-3.23.40.20619650.9530.1260.2430.95896.9
3.2-3.33.70.17519650.9680.1030.2040.91197.5
3.3-3.43.70.1519460.970.0880.1750.94996.9
3.4-3.524.10.13119510.980.0730.1510.96896.8
3.52-3.6640.11419640.980.0640.1310.96596.4
3.66-3.833.90.09619210.9870.0550.1110.93795.2
3.83-4.033.70.08419210.9840.050.0980.92894.6
4.03-4.293.50.07318520.9890.0450.0860.92292
4.29-4.623.10.05918060.9890.0380.0710.82588.1
4.62-5.083.10.05718190.990.0370.0680.82689.1
5.08-5.813.80.05718770.9930.0330.0660.77192.2
5.81-7.323.90.05619250.9910.0320.0640.71193.5
7.32-503.50.04619620.9920.0280.0540.67892.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JMW

7jmw


Resolution: 2.7→49.382 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.291 1791 5.06 %
Rwork0.2408 33627 -
obs0.2433 35418 87.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.63 Å2 / Biso mean: 47.9311 Å2 / Biso min: 16.3 Å2
Refinement stepCycle: final / Resolution: 2.7→49.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8927 0 28 0 8955
Biso mean--104.21 --
Num. residues----1231
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1058X-RAY DIFFRACTION4.924TORSIONAL
12B1058X-RAY DIFFRACTION4.924TORSIONAL
21H1282X-RAY DIFFRACTION4.924TORSIONAL
22M1282X-RAY DIFFRACTION4.924TORSIONAL
31L1266X-RAY DIFFRACTION4.924TORSIONAL
32N1266X-RAY DIFFRACTION4.924TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.76990.4803810.383159454
2.7699-2.85140.408970.3299201668
2.8514-2.94350.33921280.3138237180
2.9435-3.04860.35281320.2995261488
3.0486-3.17070.32811390.3064273193
3.1707-3.3150.32591530.2765281296
3.315-3.48970.31811540.2638288597
3.4897-3.70830.29611570.2434283896
3.7083-3.99450.27571570.2286280695
3.9945-4.39620.26891600.1998271392
4.3962-5.03180.22961460.1879262288
5.0318-6.33750.26291490.2118277292
6.3375-49.3820.26951380.2175285392
Refinement TLS params.Method: refined / Origin x: 20.0066 Å / Origin y: -19.3408 Å / Origin z: 32.3249 Å
111213212223313233
T0.2712 Å20.0244 Å2-0.0575 Å2-0.1927 Å2-0.0181 Å2--0.2381 Å2
L0.6936 °20.2067 °2-0.1887 °2-0.2327 °2-0.0869 °2--0.1374 °2
S0.0448 Å °-0.0221 Å °0.087 Å °0.0358 Å °-0.0034 Å °0.1029 Å °-0.0415 Å °-0.0591 Å °-0.0415 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA334 - 528
2X-RAY DIFFRACTION1allA1501
3X-RAY DIFFRACTION1allB334 - 526
4X-RAY DIFFRACTION1allB1501
5X-RAY DIFFRACTION1allH1 - 214
6X-RAY DIFFRACTION1allL2 - 209
7X-RAY DIFFRACTION1allM1 - 214
8X-RAY DIFFRACTION1allN2 - 209

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