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- PDB-5mhr: T3D reovirus sigma1 complexed with 9BG5 Fab fragments -

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Basic information

Entry
Database: PDB / ID: 5mhr
TitleT3D reovirus sigma1 complexed with 9BG5 Fab fragments
Components
  • 9BG5 Fab heavy chain
  • 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
  • Viral attachment protein sigma 1
KeywordsIMMUNE SYSTEM / reovirus sigma1 / virus antibody complex / neutralization / VIRAL PROTEIN
Function / homology
Function and homology information


virion component / cell adhesion / virion attachment to host cell
Similarity search - Function
Virus attachment protein , globular domain / Viral attachment sigma 1, reoviral / Reovirus viral attachment protein sigma 1 / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Viral attachment protein sigma 1
Similarity search - Component
Biological speciesReovirus sp.
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStehle, T. / Dietrich, M.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthR01 AI118887 United States
CitationJournal: J. Virol. / Year: 2017
Title: Structural Insights into Reovirus sigma 1 Interactions with Two Neutralizing Antibodies.
Authors: Dietrich, M.H. / Ogden, K.M. / Katen, S.P. / Reiss, K. / Sutherland, D.M. / Carnahan, R.H. / Goff, M. / Cooper, T. / Dermody, T.S. / Stehle, T.
History
DepositionNov 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Viral attachment protein sigma 1
B: Viral attachment protein sigma 1
C: Viral attachment protein sigma 1
D: Viral attachment protein sigma 1
E: Viral attachment protein sigma 1
F: Viral attachment protein sigma 1
G: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
H: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
I: 9BG5 Fab heavy chain
J: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
K: 9BG5 Fab heavy chain
L: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
M: 9BG5 Fab heavy chain
N: 9BG5 Fab heavy chain
O: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
P: 9BG5 Fab heavy chain
Q: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
R: 9BG5 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)388,38718
Polymers388,38718
Non-polymers00
Water00
1
A: Viral attachment protein sigma 1
B: Viral attachment protein sigma 1
C: Viral attachment protein sigma 1
H: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
I: 9BG5 Fab heavy chain
J: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
K: 9BG5 Fab heavy chain
Q: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
R: 9BG5 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)194,1949
Polymers194,1949
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Viral attachment protein sigma 1
E: Viral attachment protein sigma 1
F: Viral attachment protein sigma 1
G: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
L: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
M: 9BG5 Fab heavy chain
N: 9BG5 Fab heavy chain
O: 9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain
P: 9BG5 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)194,1949
Polymers194,1949
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.163, 109.306, 131.699
Angle α, β, γ (deg.)103.13, 113.56, 103.48
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Viral attachment protein sigma 1


Mass: 17921.033 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reovirus sp. / Gene: S1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86335
#2: Antibody
9BG5 Fab light chain,LOC100046793 protein,MAb 110 light chain


Mass: 23282.822 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: DUE TO POORLY DEFINED ELECTRON DENSITY THE CONSTANT REGION OF THE FAB FRAGMENT WAS NOT BUILT FOR CHAIN J AND CHAIN L
Source: (natural) Mus musculus (house mouse)
#3: Antibody
9BG5 Fab heavy chain


Mass: 23527.369 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: DUE TO POORLY DEFINED ELECTRON DENSITY THE CONSTANT REGION OF THE FAB FRAGMENT WAS NOT BUILT FOR CHAIN K AND CHAIN M
Source: (natural) Mus musculus (house mouse)
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: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 11% (w/v) PEG8000, 0.1 M Tris pH 7.0, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.045 Å / Num. obs: 94667 / % possible obs: 98.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 55.9 Å2 / Net I/σ(I): 13.08
Reflection shellResolution: 3→3.08 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.89 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Cootmodel building
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OJ5 AND 1FIG

2oj5

1fig


Resolution: 3→49.05 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.66
RfactorNum. reflection% reflection
Rfree0.247 4734 5 %
Rwork0.212 --
obs0.214 94661 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22593 0 0 0 22593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423212
X-RAY DIFFRACTIONf_angle_d0.66131812
X-RAY DIFFRACTIONf_dihedral_angle_d10.45913365
X-RAY DIFFRACTIONf_chiral_restr0.0493592
X-RAY DIFFRACTIONf_plane_restr0.0054067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.03410.35341610.31123049X-RAY DIFFRACTION98
3.0341-3.06980.35971520.30982902X-RAY DIFFRACTION98
3.0698-3.10720.35111590.29763007X-RAY DIFFRACTION98
3.1072-3.14650.31491570.2832983X-RAY DIFFRACTION99
3.1465-3.18790.31121570.28272991X-RAY DIFFRACTION99
3.1879-3.23160.30821580.26813000X-RAY DIFFRACTION99
3.2316-3.27780.33061580.26443004X-RAY DIFFRACTION99
3.2778-3.32670.30141570.25272975X-RAY DIFFRACTION99
3.3267-3.37860.30031590.2533029X-RAY DIFFRACTION99
3.3786-3.4340.32851580.24692996X-RAY DIFFRACTION99
3.434-3.49320.29611560.24632979X-RAY DIFFRACTION99
3.4932-3.55670.28551610.23163050X-RAY DIFFRACTION99
3.5567-3.62510.25691550.22542937X-RAY DIFFRACTION99
3.6251-3.69910.24841570.21142991X-RAY DIFFRACTION99
3.6991-3.77950.23881580.20883007X-RAY DIFFRACTION99
3.7795-3.86740.23711590.21323023X-RAY DIFFRACTION99
3.8674-3.9640.23491570.19752972X-RAY DIFFRACTION99
3.964-4.07120.2141570.19362987X-RAY DIFFRACTION99
4.0712-4.19090.20351570.18762984X-RAY DIFFRACTION99
4.1909-4.32610.22581580.18043007X-RAY DIFFRACTION99
4.3261-4.48060.20371580.17343001X-RAY DIFFRACTION99
4.4806-4.65990.20651600.17593033X-RAY DIFFRACTION99
4.6599-4.87180.18241580.16373009X-RAY DIFFRACTION99
4.8718-5.12840.22051560.17162962X-RAY DIFFRACTION99
5.1284-5.44930.20731610.17933056X-RAY DIFFRACTION99
5.4493-5.86940.23391560.20142961X-RAY DIFFRACTION99
5.8694-6.45890.24291590.21063025X-RAY DIFFRACTION99
6.4589-7.39080.25631580.21753002X-RAY DIFFRACTION99
7.3908-9.30120.22811580.21013001X-RAY DIFFRACTION99
9.3012-49.05140.25111590.2193004X-RAY DIFFRACTION99

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