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- PDB-4xc5: CRYSTAL STRUCTURE OF THE T1L REOVIRUS ATTACHMENT PROTEIN SIGMA1 -

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Basic information

Entry
Database: PDB / ID: 4xc5
TitleCRYSTAL STRUCTURE OF THE T1L REOVIRUS ATTACHMENT PROTEIN SIGMA1
ComponentsOuter capsid protein sigma-1
KeywordsVIRAL PROTEIN / TRIPLE BETA-SPIRAL / BETA-BARREL / BETA-SPIRAL REPEAT / GREEK KEY MOTIF / VIRAL ATTACHMENT PROTEIN / GM2 GLYCAN ALPHA-2 / 3-SIALYLLACTOSE / JUNCTIONAL ADHESION MOLECULE A / VIRAL CAPSID
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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Outer capsid protein sigma-1
Similarity search - Component
Biological speciesMammalian orthoreovirus 1 Lang
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsReiss, K. / Stehle, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthR01 AI076983 United States
CitationJournal: J.Virol. / Year: 2015
Title: Structure of Serotype 1 Reovirus Attachment Protein sigma 1 in Complex with Junctional Adhesion Molecule A Reveals a Conserved Serotype-Independent Binding Epitope.
Authors: Stettner, E. / Dietrich, M.H. / Reiss, K. / Dermody, T.S. / Stehle, T.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Jul 13, 2016Group: Data collection
Revision 2.0Jan 10, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,94119
Polymers73,9403
Non-polymers1,00116
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-101 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.930, 112.960, 113.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-502-

MG

21B-502-

MG

31C-502-

MG

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 24646.564 Da / Num. of mol.: 3 / Fragment: UNP residues 308-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalian orthoreovirus 1 Lang / Gene: S1 / Plasmid: PQE-80L / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P04506

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Non-polymers , 5 types, 110 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES/ imidazole (pH 6.3-6.9), 11 % PEG 4000, 22 % glycerol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, and 0.02 M sodium oxamate
PH range: 6.3-6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 36975 / % possible obs: 98.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 37.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.7
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 1.318 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.561 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4odb

4odb


Resolution: 2.2→42.32 Å / Cor.coef. Fo:Fc: 0.9337 / Cor.coef. Fo:Fc free: 0.9128 / SU R Cruickshank DPI: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 3722 10.07 %RANDOM
Rwork0.1899 ---
obs0.1932 36973 99.71 %-
Displacement parametersBiso mean: 38.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.5939 Å20 Å20 Å2
2--1.2134 Å20 Å2
3----0.6195 Å2
Refine analyzeLuzzati coordinate error obs: 0.245 Å
Refinement stepCycle: 1 / Resolution: 2.2→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3797 0 60 94 3951
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013946HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15379HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1273SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes569HARMONIC5
X-RAY DIFFRACTIONt_it3946HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion16.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion521SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4321SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2652 292 10.26 %
Rwork0.238 2554 -
all0.2408 2846 -
obs--99.71 %

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