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- PDB-1fn9: CRYSTAL STRUCTURE OF THE REOVIRUS OUTER CAPSID PROTEIN SIGMA 3 -

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Basic information

Entry
Database: PDB / ID: 1fn9
TitleCRYSTAL STRUCTURE OF THE REOVIRUS OUTER CAPSID PROTEIN SIGMA 3
ComponentsOUTER-CAPSID PROTEIN SIGMA 3
KeywordsVIRAL PROTEIN / Zinc binding motif
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / protein serine/threonine kinase inhibitor activity / viral life cycle / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Outer-capsid protein sigma 3, large lobe / Outer-capsid protein sigma 3, large lobe / Outer-capsid protein sigma 3, small lobe / Outer-capsid protein sigma 3, small lobe / Reovirus, outer capsid sigma 3 / Reovirus, outer capsid sigma-3 domain superfamily / Reovirus outer capsid protein, Sigma 3 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Outer capsid protein sigma-3 / Outer-capsid protein sigma 3
Similarity search - Component
Biological speciesReovirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsOlland, A.M. / Jane-Valbuena, J. / Schiff, L.A. / Nibert, M.L. / Harrison, S.C.
CitationJournal: EMBO J. / Year: 2001
Title: Structure of the reovirus outer capsid and dsRNA-binding protein sigma3 at 1.8 A resolution.
Authors: Olland, A.M. / Jane-Valbuena, J. / Schiff, L.A. / Nibert, M.L. / Harrison, S.C.
History
DepositionAug 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER-CAPSID PROTEIN SIGMA 3
B: OUTER-CAPSID PROTEIN SIGMA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4674
Polymers82,3362
Non-polymers1312
Water13,619756
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-17 kcal/mol
Surface area30600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.898, 82.564, 132.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein OUTER-CAPSID PROTEIN SIGMA 3


Mass: 41168.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reovirus sp. / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q98639, UniProt: P03527*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 756 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 302 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: PEG 6000, sodium chloride, magnesium chloride, tris-HCl, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 302K
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
210 mMTris1droppH8.0
310 mM1dropMgCl2
4800 mM1dropNaCl
550 mMTris-HCl1droppH8.3
61-3 %PEG60001drop
710 mMTris1reservoir
810 mM1reservoirMgCl2
950 mMTris-HCl1reservoir
101-3 %PEG60001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11981
21981
31981
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODEOTHER11.5418
SYNCHROTRONNSLS X12C21.04
SYNCHROTRONNSLS X2531
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJan 1, 1998
BRANDEIS - B1.22CCDJan 1, 1999
BRANDEIS - B43CCDOct 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.041
311
ReflectionResolution: 1.8→25 Å / Num. obs: 79737 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 16.2 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.107 / Num. unique all: 7547 / % possible all: 96
Reflection
*PLUS
Redundancy: 5.7 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→500 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.195 2390 random
Rwork0.169 --
obs-78928 -
Refinement stepCycle: LAST / Resolution: 1.8→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5764 0 2 756 6522
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.54
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 500 Å / σ(F): 0 / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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