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- PDB-7jn5: Crystal structure of SARS-CoV receptor binding domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 7jn5
TitleCrystal structure of SARS-CoV receptor binding domain in complex with human antibody CR3022
Components
  • CR3022 heavy chain
  • CR3022 light chain
  • Spike glycoproteinSpike protein
KeywordsViral protein/IMMUNE SYSTEM / SARS / coronavirus / antibody / IMMUNE SYSTEM / 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 ...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 / membrane => GO:0016020 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion membrane / membrane / identical protein binding
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 (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
PHOSPHATE ION / Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human SARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 Å
AuthorsWu, N.C. / Yuan, M. / Zhu, X. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139445 United States
Bill & Melinda Gates FoundationOPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI44462 United States
CitationJournal: Plos Pathog. / Year: 2020
Title: A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody.
Authors: Wu, N.C. / Yuan, M. / Bangaru, S. / Huang, D. / Zhu, X. / Lee, C.D. / Turner, H.L. / Peng, L. / Yang, L. / Burton, D.R. / Nemazee, D. / Ward, A.B. / Wilson, I.A.
History
DepositionAug 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _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 / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CR3022 heavy chain
L: CR3022 light chain
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6476
Polymers73,9063
Non-polymers7413
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-38 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.736, 59.931, 51.721
Angle α, β, γ (deg.)90.000, 99.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules HF

#1: Protein CR3022 heavy chain


Mass: 23546.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 25982.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q19QX0, UniProt: P59594*PLUS

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Antibody , 1 types, 1 molecules L

#2: Antibody CR3022 light chain


Mass: 24376.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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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Non-polymers , 2 types, 31 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 2 M sodium chloride 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 21548 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.054 / Rrim(I) all: 0.107 / Χ2: 0.969 / Net I/σ(I): 6.7 / Num. measured all: 78204
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.763.20.86113830.7440.5481.0270.44697
2.76-2.833.20.62814290.8410.3980.7480.47495.3
2.83-2.913.70.64514250.8330.3810.7520.49398.6
2.91-2.993.80.4814370.9130.280.5570.51498.5
2.99-3.093.80.37214250.9410.2190.4330.57998.9
3.09-3.23.70.28314620.9660.1670.330.59198.1
3.2-3.333.70.20514310.9770.1220.240.65997.7
3.33-3.483.40.15313970.9810.0930.180.90596
3.48-3.663.80.1314470.9890.0760.1510.94698.2
3.66-3.893.80.09914450.9920.0570.1150.97398.2
3.89-4.193.80.08114360.9940.0470.0941.25598
4.19-4.623.50.06214250.9940.0370.0731.54895.4
4.62-5.283.80.05614610.9960.0320.0651.51798.6
5.28-6.653.70.05414480.9960.0310.0621.47496.5
6.65-503.60.04514970.9970.0270.0531.96697.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41, 2AJF

6w41

2ajf


Resolution: 2.705→44.987 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2721 1011 4.7 %
Rwork0.2111 20489 -
obs0.2139 21500 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.69 Å2 / Biso mean: 79.8061 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.705→44.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 47 30 4871
Biso mean--38.83 59.84 -
Num. residues----620
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7051-2.84770.34851330.3194278493
2.8477-3.02610.34731550.2908294598
3.0261-3.25970.39561390.2642292498
3.2597-3.58760.27211210.2377293697
3.5876-4.10640.27891570.209294198
4.1064-5.17240.22111560.1659295097
5.1724-44.9870.24741500.1912300997
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.96120.440.0647.0612-3.6783.22840.9553-0.3815-1.9079-1.0558-0.04051.29451.93950.718-1.00261.17490.1259-0.51971.50680.17741.327410.121-44.5514-3.514
24.9805-0.05312.16821.2867-0.38364.25080.62070.2601-0.4377-0.81410.1780.79761.33820.1207-0.55361.0568-0.0482-0.62741.25750.15861.39245.2108-33.4989-9.4762
32.67040.9855-3.96064.20150.78597.23150.5589-1.4409-1.59650.4476-0.22591.11081.3293-0.2311-0.1831.2593-0.2267-0.21681.28270.45251.369413.0441-43.11284.9287
45.78754.6065-0.59226.4511.85383.5811-0.64320.381-1.5091-0.66490.43820.77920.9492-0.67080.12431.19430.1838-0.52061.1362-0.1171.302323.4474-41.9359-6.2435
52.774-2.32153.64154.0026-2.47295.19760.0918-0.3279-0.5368-0.1390.38890.61480.1356-0.4752-0.68860.6807-0.1151-0.31741.07340.12810.874916.0115-29.8671-1.5771
66.5358-4.23391.63857.8028-2.98673.64830.3769-1.0667-1.0294-0.25890.62820.6878-0.1856-0.3549-0.58880.6603-0.0029-0.35831.0065-0.00340.845313.6064-26.4745-2.833
75.2678-2.58371.12194.2786-1.72593.26010.2602-0.1295-1.0545-0.98840.22931.36060.0081-0.4211-0.71980.98940.1023-0.57270.96770.06911.064.7224-21.5859-14.0959
83.9808-1.14320.79132.0694-1.81681.81770.59950.8816-0.7064-1.2141-0.21041.17650.0643-1.1323-0.69821.2796-0.0948-0.31951.42840.0911.2944-4.2964-11.2595-25.9417
95.9017-1.69543.29766.0259-2.75662.50080.54741.4795-0.3165-2.1424-0.11310.2090.9120.4205-0.43131.4680.1263-0.43041.0898-0.14440.932213.911-30.5652-19.3008
102.6541.7761.51411.75071.32331.07030.32970.4393-0.67220.18950.10032.1513-0.4027-0.8570.48360.88510.32630.03811.7104-0.09791.52678.6603-37.282712.7185
110.96180.0175-0.6170.4390.30940.66510.07170.6181-0.3091-0.0036-0.7095-0.25460.32620.467-0.09540.61720.1720.04221.24740.19340.533447.7892-29.27310.4801
120.8041-0.3089-0.26680.6687-0.50670.62440.05220.68040.2368-0.0372-0.1799-0.0321-0.0637-0.02420.00170.54490.0782-0.03460.82950.07980.493936.4874-26.08021.0716
130.4891-0.3924-0.18610.43930.26641.0641-0.274-0.03780.6108-0.0759-0.5177-0.0443-0.19120.082-0.58020.44360.0051-0.04890.87990.23490.626540.8213-24.21865.4202
144.4425-1.2082.84652.5324-0.35252.2086-0.27280.4163-0.6190.36960.1682-1.9111-0.11040.3639-0.75410.25490.1301-0.19130.32210.03670.288862.8098-30.885515.797
151.0796-0.17390.81771.7435-1.03113.1008-0.0420.04260.0868-0.09050.03390.1056-0.1693-0.0755-0.12080.4440.0038-0.10460.20610.04770.799763.4344-33.754219.7448
162.0263-1.71410.74138.5604-5.57235.45330.28120.3294-0.1803-0.1574-0.1603-0.42820.22980.5312-0.0830.4927-0.0316-0.05670.391-0.09090.802868.651-37.382718.9282
170.23930.0544-0.02980.12130.09050.1839-0.4501-0.89350.71150.10270.1847-0.1666-0.7806-0.52950.02080.73940.3416-0.13841.071-0.12940.692131.174-20.899125.8248
180.33270.18240.46811.11230.54020.5233-0.2907-0.54430.14730.13330.3265-0.17820.1778-0.77890.01530.35320.11360.02520.79230.03410.398531.0058-28.55421.3258
191.47880.2312-0.64473.50721.04770.7109-0.56680.005-1.2637-0.13621.4505-3.13740.10170.93351.04990.38060.2575-0.4826-1.09621.1986-0.297359.7642-32.931236.3451
202.55830.9277-3.85422.8665-1.52586.8154-0.33980.1343-0.53190.0162-0.1703-0.8491-0.21890.21510.34410.5672-0.0282-0.16870.3287-0.01860.791868.9493-29.455529.2607
216.83591.38660.30341.7277-0.94273.0004-0.332-0.37380.0590.64870.1659-0.7602-0.38010.22520.17280.64450.0754-0.2980.2967-0.0470.778765.7558-25.619832.8739
222.07911.1615-2.62471.3277-1.06655.7450.8918-0.5149-0.07790.7283-0.6807-0.8859-0.69450.64930.36450.71640.0209-0.44150.6442-0.00351.215376.357-28.267937.2404
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain F and resid 323:331)F323 - 331
2X-RAY DIFFRACTION2(chain F and resid 332:343)F332 - 343
3X-RAY DIFFRACTION3(chain F and resid 344:356)F344 - 356
4X-RAY DIFFRACTION4(chain F and resid 357:362)F357 - 362
5X-RAY DIFFRACTION5(chain F and resid 363:407)F363 - 407
6X-RAY DIFFRACTION6(chain F and resid 408:423)F408 - 423
7X-RAY DIFFRACTION7(chain F and resid 424:464)F424 - 464
8X-RAY DIFFRACTION8(chain F and resid 465:475)F465 - 475
9X-RAY DIFFRACTION9(chain F and resid 476:499)F476 - 499
10X-RAY DIFFRACTION10(chain F and resid 500:513)F500 - 513
11X-RAY DIFFRACTION11(chain H and resid 1:22)H1 - 22
12X-RAY DIFFRACTION12(chain H and resid 23:81)H23 - 81
13X-RAY DIFFRACTION13(chain H and resid 82:101)H82 - 101
14X-RAY DIFFRACTION14(chain H and resid 102:132)H102 - 132
15X-RAY DIFFRACTION15(chain H and resid 133:169)H133 - 169
16X-RAY DIFFRACTION16(chain H and resid 170:215)H170 - 215
17X-RAY DIFFRACTION17(chain L and resid 1:27D)L1 - 27
18X-RAY DIFFRACTION18(chain L and resid 27E:104)L27
19X-RAY DIFFRACTION19(chain L and resid 105:120)L105 - 120
20X-RAY DIFFRACTION20(chain L and resid 121:144)L121 - 144
21X-RAY DIFFRACTION21(chain L and resid 145:182)L145 - 182
22X-RAY DIFFRACTION22(chain L and resid 183:214)L183 - 214

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