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- PDB-6c6y: Crystal structure of Middle-East Respiratory Syndrome (MERS) coro... -

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Basic information

Entry
Database: PDB / ID: 6c6y
TitleCrystal structure of Middle-East Respiratory Syndrome (MERS) coronavirus neutralizing antibody JC57-14 isolated from a vaccinated rhesus macaque in complex with MERS Receptor Binding Domain
Components
  • JC57-14 Heavy chain
  • JC57-14 Light chain
  • Spike glycoprotein
KeywordsIMMUNE SYSTEM / antibody / neutralizing / vaccine
Function / homology
Function and homology information


ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / : / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Single Sheet / Betacoronavirus spike glycoprotein S1, receptor binding / Alpha-Beta Plaits ...ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / : / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Single Sheet / Betacoronavirus spike glycoprotein S1, receptor binding / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemin-binding periplasmic protein
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Betacoronavirus England 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsJoyce, M.G. / Mascola, J.R. / Graham, B.S. / Kwong, P.D.
CitationJournal: J. Virol. / Year: 2018
Title: Importance of Neutralizing Monoclonal Antibodies Targeting Multiple Antigenic Sites on the Middle East Respiratory Syndrome Coronavirus Spike Glycoprotein To Avoid Neutralization Escape.
Authors: Wang, L. / Shi, W. / Chappell, J.D. / Joyce, M.G. / Zhang, Y. / Kanekiyo, M. / Becker, M.M. / van Doremalen, N. / Fischer, R. / Wang, N. / Corbett, K.S. / Choe, M. / Mason, R.D. / Van Galen, ...Authors: Wang, L. / Shi, W. / Chappell, J.D. / Joyce, M.G. / Zhang, Y. / Kanekiyo, M. / Becker, M.M. / van Doremalen, N. / Fischer, R. / Wang, N. / Corbett, K.S. / Choe, M. / Mason, R.D. / Van Galen, J.G. / Zhou, T. / Saunders, K.O. / Tatti, K.M. / Haynes, L.M. / Kwong, P.D. / Modjarrad, K. / Kong, W.P. / McLellan, J.S. / Denison, M.R. / Munster, V.J. / Mascola, J.R. / Graham, B.S.
History
DepositionJan 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 4, 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
A: JC57-14 Heavy chain
B: JC57-14 Light chain
H: JC57-14 Heavy chain
L: JC57-14 Light chain
R: Spike glycoprotein
S: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,3157
Polymers139,2196
Non-polymers961
Water00
1
A: JC57-14 Heavy chain
B: JC57-14 Light chain
S: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7064
Polymers69,6103
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: JC57-14 Heavy chain
L: JC57-14 Light chain
R: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)69,6103
Polymers69,6103
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.580, 148.070, 259.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN B AND (RESID 2 THROUGH 104 OR RESID 107...
211(CHAIN L AND (RESID 2 THROUGH 104 OR RESID 107...

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Components

#1: Antibody JC57-14 Heavy chain


Mass: 23074.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody JC57-14 Light chain


Mass: 23570.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 22963.977 Da / Num. of mol.: 2 / Fragment: Receptor Binding Domain residues 381-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betacoronavirus England 1 / Gene: S, 3 / Production host: Homo sapiens (human) / References: UniProt: K9N5Q8
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 90 mM CHES pH 9.5, 18% PEG 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 21926 / % possible obs: 91.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 9.96
Reflection shellResolution: 3.3→3.42 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPT

4zpt


Resolution: 3.32→42.44 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.62
RfactorNum. reflection% reflection
Rfree0.267 971 5.09 %
Rwork0.232 --
obs0.234 19078 80.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 87.41 Å2
Refinement stepCycle: LAST / Resolution: 3.32→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9698 0 5 0 9703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029948
X-RAY DIFFRACTIONf_angle_d0.57713576
X-RAY DIFFRACTIONf_dihedral_angle_d14.1865974
X-RAY DIFFRACTIONf_chiral_restr0.0421553
X-RAY DIFFRACTIONf_plane_restr0.0051727
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11B1839X-RAY DIFFRACTIONPOSITIONAL
12L1839X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3169-3.49170.37250.2995424X-RAY DIFFRACTION13
3.4917-3.71040.3136930.30071705X-RAY DIFFRACTION54
3.7104-3.99670.31431630.26513045X-RAY DIFFRACTION96
3.9967-4.39850.26941700.23143175X-RAY DIFFRACTION100
4.3985-5.03410.2421720.19623223X-RAY DIFFRACTION100
5.0341-6.3390.27611660.23553215X-RAY DIFFRACTION100
6.339-42.44630.2381820.22213320X-RAY DIFFRACTION99
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)
11.8884-0.51580.87621.78360.33760.6098-0.08440.09581.1563-0.16050.24430.3511-0.8001-0.91160.32320.95690.455-0.28550.85160.1411.007852.94223.6772212.7812
21.8495-0.49790.5541.7355-0.07510.8389-0.14520.08010.5485-0.338-0.01220.5497-0.1742-0.13710.09770.51810.3419-0.24291.06070.11180.779250.3548213.7911207.6672
31.14830.028-0.38810.24270.39660.8326-0.02950.11810.7194-0.05370.12580.2657-0.3492-0.48280.26150.75240.5772-0.19961.03840.09370.89350.3352219.9837214.9068
41.97281.7158-0.56781.5075-0.33421.82120.3162-0.35390.10830.42810.055-0.07060.0070.31360.15220.76780.29060.00130.539-0.20230.619560.059208.0626255.3165
51.8054-1.12760.52160.9431-0.53520.33540.04590.16720.3126-0.0381-0.13870.0675-0.357-0.3334-0.54931.03360.520.00220.8512-0.20580.713857.5292216.4454244.3632
61.0735-0.4203-0.58011.19170.5910.71450.2070.13570.1586-0.1107-0.0808-0.0935-0.2315-0.26830.77620.59960.4155-0.08450.7138-0.2940.57961.0329214.0484246.3771
71.8105-1.1453-1.02132.34130.71230.73690.24780.32280.1915-0.1941-0.23850.0632-0.3461-0.31680.04961.18780.476-0.01290.8974-0.34150.79255.6681222.3238250.0221
81.1051-0.3524-0.02731.1535-0.17841.6017-0.05380.0234-0.0042-0.09950.06130.21590.0973-0.2203-0.29680.28030.1075-0.18090.32290.14650.400167.1736198.7712216.2195
91.06360.7746-1.07521.5269-1.07392.3313-0.3706-0.01740.3235-0.12740.16730.09560.0724-0.2507-0.1880.32060.1838-0.10790.45250.03630.514568.8416205.1577208.1631
108.3749-0.02414.74052.5294-0.43196.3891-0.03710.09790.6652-0.04880.0213-0.232-0.3854-0.04980.09510.33130.0779-0.16190.3256-0.0690.412471.431206.5494217.183
110.67030.2627-0.47591.5778-0.99210.78180.07870.40210.0178-0.13450.23430.4050.3598-0.41430.07170.3670.0976-0.04060.37960.00420.267964.4884202.3805219.0933
126.0084-1.3707-1.86112.1576-0.23135.2543-0.1423-0.71420.39260.90130.00231.3875-0.8047-0.849-0.22670.87830.26310.1470.8954-0.30321.081355.2084205.2406250.7586
133.5015-1.8126-2.25751.6381-0.55645.77110.07340.272-0.1440.0028-0.20961.5359-0.5806-1.3454-0.10660.67150.1559-0.0210.7053-0.36621.152256.7021199.7928242.193
142.849-0.46353.51741.1769-0.34544.3896-0.6033-1.1189-0.46950.99890.19481.4614-0.1611-1.22330.84820.90880.2460.47420.7642-0.04271.548651.3591194.8134253.1185
155.6561-2.14310.99642.49941.90693.269-0.119-1.1186-0.11260.86140.23451.01790.3092-0.2980.19030.94050.04330.31920.3883-0.06810.715860.0717194.1605252.3175
163.6239-0.1218-0.45845.28580.32282.7492-0.17020.7932-0.0753-0.2122-0.24380.4238-0.0302-0.90670.04750.40920.22760.0770.5420.00210.340343.616163.7152251.3395
170.72610.7929-0.53721.1007-1.1061.3802-0.29360.6382-0.1198-0.11410.5890.0817-0.0751-0.93330.08760.31950.1287-0.01870.7624-0.08980.302847.6124165.8273238.0174
185.7649-0.01662.49314.4094-1.53193.1123-0.35640.8055-1.833-1.37970.50.28210.952-0.5893-0.16440.9648-0.29330.22460.9757-0.30411.427655.0652165.8093217.3051
193.0191-1.4073-1.60193.9061-0.38483.29860.27530.07340.37980.2001-0.2175-0.2499-0.5650.20080.10830.4754-0.0690.04330.27210.09520.377367.5022177.4697249.2402
202.68740.5437-0.08612.0603-0.88543.5110.42030.08290.00270.0048-0.4347-0.2902-0.34480.16050.33340.42440.02680.0380.17530.05240.248165.6398170.0343256.3356
210.97130.6819-0.0970.815-0.86343.8576-0.1144-0.03580.21570.1103-0.0237-0.11590.19320.59130.28060.45920.12410.04370.24970.01160.375865.6183172.4974246.4275
223.06910.73241.41090.17880.28161.6866-0.15380.4953-0.1197-0.3057-0.02610.60290.1953-0.4284-0.41570.7922-0.1696-0.42210.5573-0.11120.752354.6147178.0655210.2965
231.4950.92750.44291.10650.49312.09660.17920.0745-0.0074-0.3136-0.15890.6598-0.06350.1084-0.63550.5667-0.0591-0.21780.2794-0.12810.461757.4498178.548218.2436
242.6859-1.6325-0.63752.27380.65431.4228-0.3725-0.34140.02790.18880.21840.0925-0.2863-0.72690.1120.6046-0.0330.0550.5834-0.16590.18662.7241185.3065225.662
255.5753-1.8282-0.17255.3838-0.8583.7739-0.0402-0.13-0.91780.10580.10220.97480.1109-1.18020.16350.6346-0.17030.32680.7524-0.18690.612257.0194180.5891222.837
263.3141-1.3244-0.52412.18190.40932.83140.06110.43620.0509-0.7932-0.20641.0903-0.3935-0.86510.92510.7356-0.2135-0.36341.13020.00750.639755.5371189.4918213.4672
273.34220.744-1.11172.4031-0.04350.389-0.21311.0825-0.2061-1.0498-0.16740.40280.1186-0.2026-0.53510.78840.0616-0.0460.5719-0.03510.203264.5041187.0813214.0575
281.228-0.89660.94710.7606-0.37681.724-0.1298-0.19130.6877-0.0271-0.0835-0.4341-0.97030.6349-4.10611.0097-0.59860.27860.6896-0.33270.646261.4794182.7535282.9763
299.2786-0.5435-1.66430.2274-0.14240.5928-0.0734-0.09982.01770.18180.1374-0.5302-1.8970.97690.24481.8141-1.03030.05222.6995-0.29941.252473.1342180.7254294.615
302.17330.2384-0.37851.92721.19023.25410.1581-0.4684-0.04440.0654-0.1519-0.0217-0.00690.3728-0.18650.4509-0.14740.1030.21-0.11460.181857.7086165.8393278.5781
310.2382-0.26990.19922.61921.01320.83080.3395-0.01051.3369-1.0975-0.0251-1.384-1.53941.3162-0.49421.9149-0.09450.85052.3893-0.3922.535278.3067185.7749287.875
325.37090.8456-1.58045.6959-3.63497.27740.0173-0.8575-1.1696-0.616-0.2389-0.25611.63680.0336-0.98730.8482-0.2047-0.33530.86420.39160.718462.5729190.994187.8065
331.91190.2552-3.25351.1117-1.4756.5446-0.4823-0.8295-1.1780.1411-0.2534-0.09320.91850.25930.93350.9772-0.4269-0.06740.80580.30940.674656.7306190.6627175.6239
340.04590.0060.01142.353-2.78913.32810.27061.7039-0.7679-1.59710.26930.76812.4729-0.20660.19181.84820.1718-0.02921.58740.28491.1772.1617185.1149172.9845
351.8984-0.57060.77430.9748-0.45021.6014-0.1639-0.04960.51670.22690.12950.0664-0.1195-0.81950.35940.4729-0.1206-0.17570.81450.32920.306463.5416208.4291185.0665
362.46380.891-1.38181.93130.54741.45651.8045-2.27031.14580.8674-1.09741.44981.137-1.0101-0.48422.1807-0.93960.20981.84390.55532.882774.593180.3227180.873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 38 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 39 THROUGH 62 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 63 THROUGH 118 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 119 THROUGH 133 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 134 THROUGH 156 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 157 THROUGH 199 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 200 THROUGH 213 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 1 THROUGH 18 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 19 THROUGH 75 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 76 THROUGH 90 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 91 THROUGH 113 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 114 THROUGH 139 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 140 THROUGH 186 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 187 THROUGH 197 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 198 THROUGH 214 )
16X-RAY DIFFRACTION16CHAIN 'H' AND (RESID 1 THROUGH 71 )
17X-RAY DIFFRACTION17CHAIN 'H' AND (RESID 72 THROUGH 142 )
18X-RAY DIFFRACTION18CHAIN 'H' AND (RESID 143 THROUGH 213 )
19X-RAY DIFFRACTION19CHAIN 'L' AND (RESID 1 THROUGH 18 )
20X-RAY DIFFRACTION20CHAIN 'L' AND (RESID 19 THROUGH 75 )
21X-RAY DIFFRACTION21CHAIN 'L' AND (RESID 76 THROUGH 113 )
22X-RAY DIFFRACTION22CHAIN 'L' AND (RESID 114 THROUGH 126 )
23X-RAY DIFFRACTION23CHAIN 'L' AND (RESID 127 THROUGH 139 )
24X-RAY DIFFRACTION24CHAIN 'L' AND (RESID 140 THROUGH 150 )
25X-RAY DIFFRACTION25CHAIN 'L' AND (RESID 151 THROUGH 186 )
26X-RAY DIFFRACTION26CHAIN 'L' AND (RESID 187 THROUGH 197 )
27X-RAY DIFFRACTION27CHAIN 'L' AND (RESID 198 THROUGH 214 )
28X-RAY DIFFRACTION28CHAIN 'R' AND (RESID 381 THROUGH 425 )
29X-RAY DIFFRACTION29CHAIN 'R' AND (RESID 426 THROUGH 439 )
30X-RAY DIFFRACTION30CHAIN 'R' AND (RESID 440 THROUGH 576 )
31X-RAY DIFFRACTION31CHAIN 'R' AND (RESID 577 THROUGH 588 )
32X-RAY DIFFRACTION32CHAIN 'S' AND (RESID 381 THROUGH 410 )
33X-RAY DIFFRACTION33CHAIN 'S' AND (RESID 411 THROUGH 426 )
34X-RAY DIFFRACTION34CHAIN 'S' AND (RESID 427 THROUGH 439 )
35X-RAY DIFFRACTION35CHAIN 'S' AND (RESID 440 THROUGH 576 )
36X-RAY DIFFRACTION36CHAIN 'S' AND (RESID 577 THROUGH 588 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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