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- PDB-8sic: Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) ... -

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Basic information

Entry
Database: PDB / ID: 8sic
TitleCrystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine
Components
  • (Cy137C02 Fab ...) x 2
  • Envelope glycoprotein gp350
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral protein / envelope glycoprotein / monoclonal antibody / antiviral / immune system / macaques / Epstein-Barr virus / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell membrane / virion membrane / membrane
Similarity search - Function
: / : / : / : / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal / Herpesvirus major outer envelope glycoprotein / Herpes virus envelope glycoprotein gp350, N-terminal A domain
Similarity search - Domain/homology
Envelope glycoprotein GP350
Similarity search - Component
Biological speciesMacaca fascicularis (crab-eating macaque)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsJoyce, M.G. / Jensen, J.L. / Chen, W.H. / Kanekiyo, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-07-2-0067 United States
CitationJournal: To Be Published
Title: Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine
Authors: Joyce, M.G. / Jensen, J.L. / Chen, W.H. / Kanekiyo, M.
History
DepositionApr 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cy137C02 Fab heavy chain
B: Cy137C02 Fab light chain
E: Envelope glycoprotein gp350
G: Envelope glycoprotein gp350
H: Cy137C02 Fab heavy chain
L: Cy137C02 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,90625
Polymers187,0146
Non-polymers3,89119
Water2,090116
1
A: Cy137C02 Fab heavy chain
B: Cy137C02 Fab light chain
E: Envelope glycoprotein gp350
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,34212
Polymers93,5073
Non-polymers1,8359
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Envelope glycoprotein gp350
H: Cy137C02 Fab heavy chain
L: Cy137C02 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,56313
Polymers93,5073
Non-polymers2,05610
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.047, 71.377, 395.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11G-620-

HOH

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Components

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody Cy137C02 Fab heavy chain


Mass: 23805.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody Cy137C02 Fab light chain


Mass: 22806.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 19 molecules EG

#3: Protein Envelope glycoprotein gp350 / Membrane antigen / MA


Mass: 46895.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: strain B95-8 / Gene: BLLF1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P03200
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
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, 118 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 8000, 0.22 M sodium acetate, 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.76→71.43 Å / Num. obs: 51461 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.5
Reflection shellResolution: 2.76→2.91 Å / Rmerge(I) obs: 1.213 / Mean I/σ(I) obs: 2 / Num. unique obs: 2338

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house structure of gp350 in a complex with a receptor fragment

Resolution: 2.76→71.38 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2949 2611 5.07 %
Rwork0.2455 --
obs0.248 51461 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.76→71.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12965 0 141 116 13222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413435
X-RAY DIFFRACTIONf_angle_d0.65918353
X-RAY DIFFRACTIONf_dihedral_angle_d7.7481897
X-RAY DIFFRACTIONf_chiral_restr0.052148
X-RAY DIFFRACTIONf_plane_restr0.0052338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.810.44411400.44132338X-RAY DIFFRACTION95
2.81-2.860.43941470.41642560X-RAY DIFFRACTION100
2.86-2.920.43171350.40632515X-RAY DIFFRACTION100
2.92-2.980.39281340.37112540X-RAY DIFFRACTION100
2.98-3.050.39531190.34552538X-RAY DIFFRACTION100
3.05-3.130.38561490.33272538X-RAY DIFFRACTION100
3.13-3.210.32851360.29942534X-RAY DIFFRACTION100
3.21-3.310.37421570.29592559X-RAY DIFFRACTION100
3.31-3.410.38011510.28772521X-RAY DIFFRACTION100
3.41-3.540.39561440.3132545X-RAY DIFFRACTION100
3.54-3.680.37181300.3142572X-RAY DIFFRACTION100
3.68-3.840.33491220.26852585X-RAY DIFFRACTION100
3.84-4.050.3111310.23752574X-RAY DIFFRACTION100
4.05-4.30.26041340.21532607X-RAY DIFFRACTION100
4.3-4.630.25491290.19542576X-RAY DIFFRACTION100
4.63-5.10.23141350.17972624X-RAY DIFFRACTION100
5.1-5.840.26221350.21262645X-RAY DIFFRACTION100
5.84-7.350.26571350.22782651X-RAY DIFFRACTION100
7.35-71.380.21271480.19212828X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.4617-0.29450.41044.0865-0.24273.8517-0.1299-0.1407-0.02880.2303-0.0267-0.00160.37330.33380.19380.84820.259-0.05150.5158-0.07250.441392.261103.496500.578
20.04611.01270.06591.01510.18046.4307-0.17710.00360.04260.3752-0.2295-0.03830.3058-0.28580.28480.78580.2263-0.0770.4698-0.05860.530292.517110.782508.08
32.0335-5.2436.15727.466-4.06493.7848-1.5461-2.81310.95113.97161.67361.09790.1619-0.90670.20071.81160.17960.15550.97190.00161.225782.961127.997538.873
43.6559-2.4238-3.13153.9612-1.1747.32590.33090.7097-0.8570.0458-0.03890.67280.7798-1.799-0.42021.98610.4375-0.1197-1.01270.1270.575587.329114.48525.026
56.98561.7894-0.23312.39281.43733.9217-0.0972-0.1510.98110.2076-0.08980.4127-0.2473-0.51910.32031.23860.259-0.02040.52530.00090.546986.706119.221529.196
64.5237-2.4505-0.81941.40520.86412.7959-0.3361-0.496-0.8701-0.29620.53780.75621.0739-0.28940.18621.7108-0.0020.04060.5207-0.04130.851184.603110.853533.231
71.32310.1186-2.00185.41622.11687.2394-0.09680.14550.2922-0.39690.16410.0872-0.28040.1156-0.05910.91720.1618-0.16630.4971-0.00350.46994.644126.154494.454
81.49461.1846-1.46911.71311.01995.07410.2229-0.16660.06330.46390.04410.3465-0.6224-0.7132-0.05490.8367-0.0321-0.1830.459-0.05610.618393.799126.679529.917
92.7370.3823-0.24339.02261.4625.97220.96420.13160.784-0.3628-0.7808-0.4709-0.2010.6381-0.17590.7150.00960.10660.473-0.03540.585999.547132.873530.189
102.0058-1.67540.52815.6893-0.07886.54470.1712-0.36020.0789-0.13740.1265-0.47080.17650.1637-0.1870.7789-0.0269-0.01530.3887-0.03350.647498.153128.714533.646
110.9723-1.6793-0.84352.79482.31915.3306-0.1250.1267-0.0668-0.09580.0437-0.0709-0.44720.11040.08930.5515-0.1543-0.00180.6378-0.03140.570887.776114.265453.507
123.3806-3.01261.35914.0053-3.54984.4518-0.0884-0.65190.632-0.50360.5744-1.4208-0.67830.8616-0.16220.619-0.16660.13691.0556-0.25440.6756100.017114.488455.365
132.0847-0.31511.71093.32420.44914.469-0.1237-0.00690.3023-0.06350.3143-0.1072-0.794-0.0675-0.20630.6194-0.1558-0.02680.6492-0.05480.551389.252116.221461.835
144.67090.8061.45455.91191.73445.98-0.4594-0.3245-0.54231.05460.49860.52430.7699-0.57790.00431.04210.02860.13790.79660.03330.540187.58891.704476.411
154.09972.0573-0.75944.81130.45881.2508-0.38180.0777-0.35660.95860.2891-0.10460.75840.0769-0.06590.88730.00570.05590.6761-0.08330.490988.61994.426472.292
16-0.0716-0.37731.36593.64053.07935.8411-0.08830.103-0.0601-0.59060.13790.0871-0.1261-0.2423-0.06110.6951-0.15750.0610.84460.01380.504186.052100.607430.149
17-0.37010.38770.41733.08621.29894.4356-0.16320.0384-0.1280.05510.24870.06050.53730.2308-0.15020.28030.01140.04920.8419-0.04760.739584.41861.771415.616
183.7424-0.5670.97722.5539-0.48085.45070.165-0.3421-0.3653-0.0704-0.0721-0.35910.86080.677-0.23180.41770.12590.1220.7572-0.04470.681293.18560.828410.865
190.04320.18580.3550.1740.19958.3155-0.07410.1074-0.2027-0.03550.13420.04110.6757-0.125-0.16960.38260.02740.03780.7927-0.12170.74784.50761.188405.773
204.4678-2.61470.59334.9350.88533.2967-0.2254-0.01820.32-0.57070.21730.3751-0.7222-0.2065-0.01340.5725-0.0635-0.01550.6953-0.01890.521583.97286.953395.761
211.65031.2925-1.2763.0181-0.84364.8112-0.06390.15980.0433-0.5080.8411-0.458-0.78421.1124-0.58330.3607-0.18110.16310.7278-0.14940.601990.38379.268400.052
220.43531.1446-1.04084.86940.86375.3382-0.03820.0941-0.02150.31560.2266-0.0544-0.13920.1069-0.11360.3190.10410.02540.64960.01580.489484.11474.653441.785
23-0.0161-0.0577-1.5412-0.0130.94367.27080.2142-0.29730.09120.0881-0.26670.2316-0.3549-0.39750.09730.4031-0.1320.01090.7938-0.0260.703486.60871.071366.435
247.01816.3008-5.60276.4187-6.27516.3653-1.79942.8731-0.8013-4.21870.4419-0.47541.2572-0.02920.8391.1218-0.03480.16021.1352-0.15781.010676.50451.138329.492
259.04651.82110.65258.7071.45187.63050.00720.02890.16970.1155-0.21890.76390.1379-0.10160.22210.32780.01430.020.34390.08410.527678.64262.548339.434
266.02970.10932.19549.46731.49867.74450.49590.1012-0.4805-0.69390.1296-0.37551.51970.1129-0.26741.1454-0.0141-0.00720.68840.11260.712392.07243.574370.898
273.2959-1.4441.60381.8274-1.01558.92860.0618-0.2240.47450.0785-0.22240.02610.68680.18840.17040.5216-0.18620.04370.6511-0.05840.540687.70854.559375.906
280.5609-1.59710.02633.90670.4983.82930.1733-0.2055-0.16340.1717-0.15810.21631.1547-0.7774-0.02040.8229-0.43130.04890.8278-0.05120.673986.77250.384374.771
292.3450.6421-0.04431.48422.27683.95270.2626-0.1945-0.08470.4817-0.23560.24940.6496-0.33280.10740.4455-0.01560.0790.3451-0.09730.535184.87949.021340.993
303.6817-3.18042.27876.09260.6613.57010.29240.0068-0.07450.7225-0.327-0.12110.40780.24-0.060.393-0.0728-0.05870.419-0.09220.576587.79250.9338.784
312.44611.588-3.5186.982-3.71472.0078-0.79590.2194-0.1247-0.3116-0.7466-3.20540.8262.63221.06220.60810.19550.02460.6295-0.01130.835196.81446.881331.093
326.1922-0.603-6.48488.8451.88336.82910.545-0.75671.37820.87560.6327-1.9281-0.26321.3796-1.19940.5043-0.0873-0.04780.69020.01321.022695.01353.02341.434
333.3051-0.1401-1.50478.8766-1.70414.73620.05240.07260.4983-0.4353-0.322-0.66330.56030.60330.10640.4567-0.0185-0.06550.4007-0.04070.62390.06649.136335.283
345.2953.2415-2.62546.1938-4.00342.6869-0.23321.0141-0.4385-1.65850.7507-1.27661.0056-2.0998-0.50560.7030.06060.00421.0091-0.03980.7886.13348.225324.121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:83 )A1 - 83
2X-RAY DIFFRACTION2( CHAIN A AND RESID 84:126 )A84 - 126
3X-RAY DIFFRACTION3( CHAIN A AND RESID 127:141 )A127 - 141
4X-RAY DIFFRACTION4( CHAIN A AND RESID 142:161 )A142 - 161
5X-RAY DIFFRACTION5( CHAIN A AND RESID 162:200 )A162 - 200
6X-RAY DIFFRACTION6( CHAIN A AND RESID 201:215 )A201 - 215
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:102 )B1 - 102
8X-RAY DIFFRACTION8( CHAIN B AND RESID 103:134 )B103 - 134
9X-RAY DIFFRACTION9( CHAIN B AND RESID 135:155 )B135 - 155
10X-RAY DIFFRACTION10( CHAIN B AND RESID 156:210 )B156 - 210
11X-RAY DIFFRACTION11( CHAIN E AND RESID 6:68 )E6 - 68
12X-RAY DIFFRACTION12( CHAIN E AND RESID 69:88 )E69 - 88
13X-RAY DIFFRACTION13( CHAIN E AND RESID 89:162 )E89 - 162
14X-RAY DIFFRACTION14( CHAIN E AND RESID 163:223 )E163 - 223
15X-RAY DIFFRACTION15( CHAIN E AND RESID 224:305 )E224 - 305
16X-RAY DIFFRACTION16( CHAIN E AND RESID 306:429 )E306 - 429
17X-RAY DIFFRACTION17( CHAIN G AND RESID 7:64 )G7 - 64
18X-RAY DIFFRACTION18( CHAIN G AND RESID 65:117 )G65 - 117
19X-RAY DIFFRACTION19( CHAIN G AND RESID 118:166 )G118 - 166
20X-RAY DIFFRACTION20( CHAIN G AND RESID 167:267 )G167 - 267
21X-RAY DIFFRACTION21( CHAIN G AND RESID 268:317 )G268 - 317
22X-RAY DIFFRACTION22( CHAIN G AND RESID 318:428 )G318 - 428
23X-RAY DIFFRACTION23( CHAIN H AND RESID 1:126 )H1 - 126
24X-RAY DIFFRACTION24( CHAIN H AND RESID 127:141 )H127 - 141
25X-RAY DIFFRACTION25( CHAIN H AND RESID 142:214 )H142 - 214
26X-RAY DIFFRACTION26( CHAIN L AND RESID 1:23 )L1 - 23
27X-RAY DIFFRACTION27( CHAIN L AND RESID 24:50 )L24 - 50
28X-RAY DIFFRACTION28( CHAIN L AND RESID 51:102 )L51 - 102
29X-RAY DIFFRACTION29( CHAIN L AND RESID 103:126 )L103 - 126
30X-RAY DIFFRACTION30( CHAIN L AND RESID 127:144 )L127 - 144
31X-RAY DIFFRACTION31( CHAIN L AND RESID 145:155 )L145 - 155
32X-RAY DIFFRACTION32( CHAIN L AND RESID 156:165 )L156 - 165
33X-RAY DIFFRACTION33( CHAIN L AND RESID 166:202 )L166 - 202
34X-RAY DIFFRACTION34( CHAIN L AND RESID 203:210 )L203 - 210

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