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- PDB-2bt7: Structure of the C-terminal receptor-binding domain of avian reov... -

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Basic information

Entry
Database: PDB / ID: 2bt7
TitleStructure of the C-terminal receptor-binding domain of avian reovirus fibre sigmaC, Cd crystal form
ComponentsSIGMA C
KeywordsVIRAL PROTEIN / ORTHOREOVIRUS / TRIPLE BETA-SPIRAL / BETA-BARREL
Function / homology
Function and homology information


Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) - #40 / Reovirus sigma C capsid protein, C-terminal / Reovirus sigma C capsid protein triple beta spiral / Reovirus sigma C capsid protein C-terminal domain / Reovirus sigma C capsid protein triple beta spiral / reovirus attachment protein sigma1; domain 1 / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Laminin / Ribbon / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAVIAN ORTHOREOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsGuardado Calvo, P. / Fox, G.C. / Hermo Parrado, X.L. / Llamas-Saiz, A.L. / van Raaij, M.J.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Structure of the Carboxy-Terminal Receptor-Binding Domain of Avian Reovirus Fibre Sigmac
Authors: Guardado Calvo, P. / Fox, G.C. / Hermo Parrado, X.L. / Llamas-Saiz, A.L. / Costas, C. / Martinez-Costas, J. / Benavente, J. / van Raaij, M.J.
#1: Journal: Embo J. / Year: 2002
Title: Crystal Structure of Reovirus Attachment Protein Sigma1 Reveals Evolutionary Relationship to Adenovirus Fiber
Authors: Chappell, J.D. / Prota, A.E. / Dermody, T.S. / Stehle, T.
#2: Journal: J.Virol. / Year: 1997
Title: Protein Architecture of Avian Reovirus S1133 and Identification of the Cell Attachment Protein
Authors: Martinez-Costas, J. / Grande, A. / Varela, R. / Garcia-Martinez, C. / Benavente, J.
#3: Journal: Virology / Year: 2000
Title: Oligomerization and Cell-Binding Properties of the Avian Reovirus Cell-Attachment Protein Sigmac
Authors: Grande, A. / Rodriguez, E. / Costas, C. / Everitt, E. / Benavente, J.
#4: Journal: Virology / Year: 2001
Title: The Avian Reovirus Genome Segment S1 is a Functionally Tricistronic Gene that Expresses One Structure and Two Nonstructural Proteins in Infected Cells
Authors: Bodelon, G. / Labrada, L. / Martinez-Costas, J. / Benavente, J.
#5: Journal: J.Gen.Virol. / Year: 2002
Title: Subunit Composition and Conformational Stability of the Oligomeric Form of the Avian Reovirus Cell-Attachment Protein Sigmac
Authors: Grande, A. / Costas, C. / Benavente, J.
History
DepositionMay 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIGMA C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6454
Polymers18,3241
Non-polymers3213
Water2,162120
1
A: SIGMA C
hetero molecules

A: SIGMA C
hetero molecules

A: SIGMA C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,93612
Polymers54,9733
Non-polymers9639
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.075, 73.075, 69.928
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1329-

CD

21A-2043-

HOH

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Components

#1: Protein SIGMA C / AVIAN REOVIRUS FIBRE SIGMAC


Mass: 18324.336 Da / Num. of mol.: 1
Fragment: C-TERMINAL RECEPTOR-BINDING REGION, RESIDUES 157-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIAN ORTHOREOVIRUS / Strain: S1133
Description: THE AVIAN REOVIRUS STRAIN S1133 WAS ORIGINALLY PROVIDED BY DR. PHILIP I. MARCUS WHEN DR. J.BENAVENTE WAS A ROCHE VISITING SCIENTIST IN THE LABORATORY OF DR. A. SHATKIN
Plasmid: PET28CPLUS / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: O12287
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: IN PROCESS OF SUBMISSION TO PDB
Crystal growpH: 8.5
Details: 100 MM TRIS-HCL PH 8.5, 1.5 M AMMONIUM SULPHATE, 12 % GLYCEROL, 10 MM CADMIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97959
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 30, 2005 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.32→36.5 Å / Num. obs: 9602 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 48.06 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.1
Reflection shellResolution: 2.32→2.45 Å / Redundancy: 10 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.1 / % possible all: 71.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→69.84 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.059 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 929 10 %RANDOM
Rwork0.183 ---
obs0.189 8348 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å21.01 Å20 Å2
2--2.02 Å20 Å2
3----3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.35→69.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 7 120 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211318
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.941796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3635169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81422.54555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18315194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.231510
X-RAY DIFFRACTIONr_chiral_restr0.1140.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021005
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2506
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.2882
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9123866
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.23851370
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1387506
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.14610426
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 67
Rwork0.25 541

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