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- PDB-6tou: Rabies virus glycoprotein PH domain in complex with the scFv frag... -

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Basic information

Entry
Database: PDB / ID: 6tou
TitleRabies virus glycoprotein PH domain in complex with the scFv fragment of broadly neutralizing human antibody RVC20
Components
  • Glycoprotein,Glycoprotein
  • Single-chain FvSingle-chain variable fragment
KeywordsVIRAL PROTEIN / glycoprotein / antibody
Function / homologyRhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / membrane => GO:0016020 / viral envelope / virion membrane / Glycoprotein
Function and homology information
Biological speciesRabies lyssavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.587 Å
AuthorsHellert, J. / Rey, F.A.
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the prefusion-locking broadly neutralizing antibody RVC20 bound to the rabies virus glycoprotein.
Authors: Hellert, J. / Buchrieser, J. / Larrous, F. / Minola, A. / de Melo, G.D. / Soriaga, L. / England, P. / Haouz, A. / Telenti, A. / Schwartz, O. / Corti, D. / Bourhy, H. / Rey, F.A.
History
DepositionDec 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: 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_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 2024Group: 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
G: Glycoprotein,Glycoprotein
A: Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7686
Polymers40,6212
Non-polymers1464
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-42 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.945, 81.945, 155.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1333-

HOH

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Components

#1: Protein Glycoprotein,Glycoprotein


Mass: 13100.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies lyssavirus / Plasmid: pMT / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8JUA9
#2: Antibody Single-chain Fv / Single-chain variable fragment


Mass: 27520.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / Plasmid: pMT / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.7 uL of 18 mg/mL complex in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.7 uL of reservoir solution containing 100 mM Tris-Cl pH 8.0, 300 mM CaCl2, 22% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 1, 2019
Details: Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.587→46.506 Å / Num. obs: 15457 / % possible obs: 89.5 % / Redundancy: 25.7 % / Biso Wilson estimate: 84.61 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.106 / Rsym value: 0.103 / Net I/σ(I): 21.374
Reflection shellResolution: 2.587→2.72 Å / Redundancy: 28.1 % / Num. unique obs: 774 / CC1/2: 0.66 / Rpim(I) all: 0.705 / Rrim(I) all: 3.758 / Rsym value: 3.69 / % possible all: 33.3

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
STARANISOdata scaling
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phyre2 homology model of RVC20 scFv

Resolution: 2.587→46.506 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.05
RfactorNum. reflection% reflection
Rfree0.225 1545 10 %
Rwork0.1898 --
obs0.1932 15454 89.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 294.92 Å2 / Biso mean: 105.8974 Å2 / Biso min: 58.68 Å2
Refinement stepCycle: final / Resolution: 2.587→46.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 818 88 3229
Biso mean--84.94 93.35 -
Num. residues----195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032382
X-RAY DIFFRACTIONf_angle_d0.6073228
X-RAY DIFFRACTIONf_chiral_restr0.042351
X-RAY DIFFRACTIONf_plane_restr0.004403
X-RAY DIFFRACTIONf_dihedral_angle_d13.4551394
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5873-2.67080.4197250.351722716
2.6708-2.76620.35081120.3394100073
2.7662-2.8770.34111410.2836127192
2.877-3.00790.35461550.28941394100
3.0079-3.16640.29311530.24371385100
3.1664-3.36480.23591540.2261385100
3.3648-3.62450.24231570.20451409100
3.6245-3.9890.20081580.17181421100
3.989-4.56580.17141580.14391421100
4.5658-5.75080.20461600.14891445100
5.7508-46.5060.231720.20441551100
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)
19.82752.5219-4.23972.59470.60232.974-0.2809-1.615-0.61540.66861.02230.52651.30950.326-0.72061.08470.10040.07881.76450.621.4128-1.0224-35.8708-8.9941
28.5887-5.7089-5.68723.87393.22519.87140.9469-3.6277-2.37141.9986-1.47441.40012.054-3.57470.72871.9564-0.6887-0.08213.20520.87671.4793.6689-33.32165.4038
33.1777-1.6814-3.41336.67023.59414.23391.0868-1.6726-0.5960.9473-0.1721-2.31031.1199-1.6044-1.09280.796-0.2004-0.33471.39190.51031.202512.9883-30.6188-6.3226
47.27991.5384.75937.6612-1.84894.18050.1822-1.9735-1.68690.0860.4606-0.26480.3141-0.0742-0.72350.7296-0.12950.10121.27490.47620.94688.734-31.2521-10.8023
56.4591-6.10925.97785.737-5.68835.5683-0.2967-3.2525-0.89131.8625-0.2319-0.6892-0.17060.79470.21040.9277-0.06880.00652.37540.65141.39459.1614-33.1294-3.7477
66.1167-5.19664.4534.4034-3.76913.2437-0.1177-1.08381.08682.08171.5084-0.0586-2.53523.9441-1.06952.3229-0.1713-0.77431.98360.31391.755516.3182-21.9648-4.2545
74.0663-4.0480.13454.1658-0.76572.2611-1.0823-0.2855-0.06180.4722-0.1332-1.16953.61050.08021.16141.60050.08340.18731.57660.24190.998519.4508-32.346-10.4728
86.9351-5.8089-4.68994.90693.72353.33461.51072.2925-0.2874-1.4671-1.94090.6371-0.3251-1.5271-0.08151.1092-0.0284-0.06951.30840.01020.826-15.9382-27.882-31.0558
95.5048-1.797-3.4232.70310.36251.94120.27340.01820.3573-0.2398-0.33561.7208-0.23-0.86470.28770.6066-0.0389-0.08470.93810.14761.0165-20.7039-18.6392-18.4711
106.0153-1.5176-5.87622.24321.1595.8304-0.08051.923-1.454-0.182-0.52470.465-0.25580.52141.1541.1639-0.0360.02591.02680.07291.1061-10.0786-38.2594-25.7338
118.3852-1.9476-0.48737.5138-0.29114.6020.0087-0.898-0.56160.41360.1148-0.02060.2766-0.1911-0.11380.4833-0.0852-0.05190.93670.18180.6044-10.4948-24.9186-17.3262
127.2652-4.361-3.27746.70.22944.50530.3329-0.53510.4167-0.2418-0.2211-0.83510.30330.4183-0.110.5034-0.1941-0.07580.7610.07130.6936-5.6649-24.4943-22.5959
135.5227-2.0287-5.23623.31740.76555.23690.67090.76970.6822-0.37690.3019-0.5547-0.1923-1.7216-0.88220.6869-0.0834-0.04061.00370.24520.9136-17.8734-12.5194-23.3091
148.231-2.89926.54297.0301-3.7947.99960.0072-0.2687-0.0014-0.13850.53480.0801-0.9026-0.993-0.64210.4987-0.04910.05070.6065-0.01170.61425.183-11.2669-34.5162
158.06540.04820.31467.3648-1.21827.64610.2276-0.1261-0.7044-0.47490.1585-0.0290.38440.0992-0.42850.4762-0.00210.00750.60810.04260.48434.7832-21.3998-34.7837
163.80410.7236-2.1474.9908-0.873.9287-0.03350.1885-0.1234-0.26190.09410.1229-0.2622-0.5467-0.13950.5078-0.04490.01690.76610.03270.62560.5678-16.2831-34.7091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 41 through 196 )G41 - 196
2X-RAY DIFFRACTION2chain 'G' and (resid 197 through 218 )G197 - 218
3X-RAY DIFFRACTION3chain 'G' and (resid 219 through 227 )G219 - 227
4X-RAY DIFFRACTION4chain 'G' and (resid 228 through 234 )G228 - 234
5X-RAY DIFFRACTION5chain 'G' and (resid 235 through 244 )G235 - 244
6X-RAY DIFFRACTION6chain 'G' and (resid 245 through 249 )G245 - 249
7X-RAY DIFFRACTION7chain 'G' and (resid 250 through 255 )G250 - 255
8X-RAY DIFFRACTION8chain 'A' and (resid 1 through 7 )A1 - 7
9X-RAY DIFFRACTION9chain 'A' and (resid 8 through 25 )A8 - 25
10X-RAY DIFFRACTION10chain 'A' and (resid 26 through 34 )A26 - 34
11X-RAY DIFFRACTION11chain 'A' and (resid 35 through 82 )A35 - 82
12X-RAY DIFFRACTION12chain 'A' and (resid 82A through 103 )A82A - 103
13X-RAY DIFFRACTION13chain 'A' and (resid 104 through 113 )A104 - 113
14X-RAY DIFFRACTION14chain 'A' and (resid 1000 through 1018 )A1000 - 1018
15X-RAY DIFFRACTION15chain 'A' and (resid 1019 through 1075 )A1019 - 1075
16X-RAY DIFFRACTION16chain 'A' and (resid 1076 through 1107 )A1076 - 1107

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