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- PDB-5mhs: T1L reovirus sigma1 complexed with 5C6 Fab fragments -

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Basic information

Entry
Database: PDB / ID: 5mhs
TitleT1L reovirus sigma1 complexed with 5C6 Fab fragments
Components
  • 5C6 Fab heavy chain
  • 5C6 Fab light chain
  • Outer capsid protein sigma-1
KeywordsIMMUNE SYSTEM / reovirus sigma1 / virus antibody complex / neutralization / VIRAL PROTEIN
Function / homology
Function and homology information


viral outer capsid / viral capsid / cell adhesion / symbiont entry into host cell / 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) / Adenovirus pIV-like, attachment domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein sigma-1
Similarity search - Component
Biological speciesReovirus type 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer capsid protein sigma-1
B: Outer capsid protein sigma-1
C: Outer capsid protein sigma-1
D: 5C6 Fab light chain
E: 5C6 Fab heavy chain
F: 5C6 Fab light chain
G: 5C6 Fab light chain
H: 5C6 Fab heavy chain
N: 5C6 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)200,7359
Polymers200,7359
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16340 Å2
ΔGint-121 kcal/mol
Surface area79280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.610, 129.080, 87.860
Angle α, β, γ (deg.)90.00, 101.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Outer capsid protein sigma-1 / Sigma1 / Cell attachment protein / Hemagglutinin


Mass: 19386.654 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reovirus type 1 (strain Lang) / Gene: S1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04506
#2: Antibody 5C6 Fab light chain


Mass: 23808.357 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody 5C6 Fab heavy chain


Mass: 23716.637 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 9.5-11.5% (w/v) PEG8000, 0.1 M MES (pH 5.5-6.5), 0.2 M zinc acetate
PH range: 5.5-6.5

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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: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→48.991 Å / Num. obs: 26263 / % possible obs: 99.9 % / Redundancy: 11.957 % / Biso Wilson estimate: 90.718 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.295 / Net I/σ(I): 7.94
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 12.4 % / CC1/2: 0.748 / Rrim(I) all: 1.619 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GU3 and 5MHR

4gu3

5mhr


Resolution: 3.7→48.991 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.57
RfactorNum. reflection% reflection
Rfree0.2779 1312 5 %
Rwork0.261 --
obs0.2618 26240 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.7→48.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11874 0 0 0 11874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412191
X-RAY DIFFRACTIONf_angle_d0.81316787
X-RAY DIFFRACTIONf_dihedral_angle_d10.5897009
X-RAY DIFFRACTIONf_chiral_restr0.0481909
X-RAY DIFFRACTIONf_plane_restr0.0062219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.84810.37961440.32612751X-RAY DIFFRACTION100
3.8481-4.02320.31621460.30922756X-RAY DIFFRACTION100
4.0232-4.23520.28861440.27282744X-RAY DIFFRACTION100
4.2352-4.50030.28891440.23192749X-RAY DIFFRACTION100
4.5003-4.84750.23531470.22392781X-RAY DIFFRACTION100
4.8475-5.33480.26051450.22692772X-RAY DIFFRACTION100
5.3348-6.10550.28931460.27292758X-RAY DIFFRACTION100
6.1055-7.68750.29921460.29122775X-RAY DIFFRACTION100
7.6875-48.99550.25371500.25692842X-RAY DIFFRACTION100

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