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- PDB-3s6x: Structure of reovirus attachment protein sigma1 in complex with a... -

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Basic information

Entry
Database: PDB / ID: 3s6x
TitleStructure of reovirus attachment protein sigma1 in complex with alpha-2,3-sialyllactose
ComponentsOuter capsid protein sigma-1
KeywordsVIRAL PROTEIN / triple beta-spiral / beta-barrel / beta-spiral repeat / greek key motif / trimer / Viral attachment protein / sialic acid receptors Junctional adhesion molecule A / Viral capsid
Function / homology
Function and homology information


viral outer capsid / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3380 / Laminin - #20 / Laminin / reovirus attachment protein sigma1; domain 1 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3380 / Laminin - #20 / Laminin / reovirus attachment protein sigma1; domain 1 / 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 / Other non-globular / Laminin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Ribbon / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein sigma-1
Similarity search - Component
Biological speciesReovirus type 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsReiter, D.M. / Dermody, T.S. / Stehle, T.
CitationJournal: Plos Pathog. / Year: 2011
Title: Crystal structure of reovirus attachment protein sigma1 in complex with sialylated oligosaccharides
Authors: Reiter, D.M. / Frierson, J.M. / Halvorson, E.E. / Kobayashi, T. / Dermody, T.S. / Stehle, T.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / 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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr2_auth_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)107,9836
Polymers106,0823
Non-polymers1,9013
Water14,628812
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25260 Å2
ΔGint-136 kcal/mol
Surface area37700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.150, 333.180, 58.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 35360.777 Da / Num. of mol.: 3 / Fragment: Head and body, residues 170-445 / Mutation: T249I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reovirus type 3 / Strain: Dearing / Gene: S1 / Plasmid: PQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: P03528
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 633.552 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 812 / 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: 4 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG200, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9185 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 2.25→38.611 Å / Num. all: 82127 / Num. obs: 78323 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.25-2.31189.7
2.31-2.37188.9
2.37-2.44187.8
2.44-2.52188.8
2.52-2.6192.4
2.6-2.69193.2
2.69-2.79195.9
2.79-2.9198
2.9-3.03197.9
3.03-3.181100
3.18-3.351100
3.35-3.561100
3.56-3.8199.9
3.8-4.11199.7
4.11-4.5199.8
4.5-5.03199.7
5.03-5.81199.8
5.81-7.12199.9
7.12-10.06199.9
10.06-38.611195.4

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Processing

Software
NameVersionClassification
XDSdata scaling
AMoREphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→38.611 Å / SU ML: 0.63 / σ(F): 2 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1989 3956 5.05 %
Rwork0.1576 --
obs0.1597 78322 95.37 %
all-82127 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.64 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7915 Å20 Å20 Å2
2---4.6597 Å2-0 Å2
3---9.4511 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6655 0 129 812 7596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066955
X-RAY DIFFRACTIONf_angle_d0.9859499
X-RAY DIFFRACTIONf_dihedral_angle_d17.8452535
X-RAY DIFFRACTIONf_chiral_restr0.0631115
X-RAY DIFFRACTIONf_plane_restr0.0031226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.33040.2923820.24666818X-RAY DIFFRACTION89
2.3304-2.42370.2563560.21316825X-RAY DIFFRACTION89
2.4237-2.5340.28953530.20376763X-RAY DIFFRACTION88
2.534-2.66760.21533790.16577220X-RAY DIFFRACTION93
2.6676-2.83460.21573860.15977456X-RAY DIFFRACTION96
2.8346-3.05340.19364010.157610X-RAY DIFFRACTION98
3.0534-3.36050.20184110.1627776X-RAY DIFFRACTION100
3.3605-3.84640.19384240.157827X-RAY DIFFRACTION100
3.8464-4.84460.15324380.1157876X-RAY DIFFRACTION100
4.8446-38.61640.19364260.16778195X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35790.77080.14755.12960.19521.94820.1451-0.17680.60390.1156-0.22250.2271-0.354-0.00660.08290.18030.03860.02440.2632-0.09410.405432.6338-63.152415.7499
20.9066-0.6871-0.17862.1498-0.12410.12470.01480.04610.1807-0.0963-0.06050.017-0.6433-0.0581-0.13791.24250.0856-0.0250.3724-0.07331.576422.7316-2.074517.2731
31.5485-0.88260.12073.4722-0.04371.1994-0.0527-0.0205-0.22870.11130.01540.24120.1274-0.18810.0480.1102-0.01970.01630.2680.020.139211.210369.875410.9755
41.6143-1.32880.02552.66330.54612.18570.0323-0.260.49360.3968-0.02280.3551-0.3745-0.12990.00960.2830.02170.14860.2547-0.10680.46631.9659-65.824519.4904
50.21410.247-0.22072.385-0.08320.2369-0.02650.0150.04050.0342-0.2701-0.0537-0.1844-0.0165-0.02511.28190.14410.08940.35390.00411.485426.67420.083216.8072
61.97680.5717-0.13833.6158-0.46491.1886-0.04040.2159-0.1523-0.0397-0.0452-0.02370.10670.11280.08430.10790.00760.00810.2357-0.00820.107331.950269.53863.9549
71.3235-0.2880.4331.9487-0.87131.51850.0877-0.01920.58890.3766-0.24690.5506-0.3813-0.13380.1080.27610.03350.07470.3368-0.10790.561928.0864-63.22517.2864
80.24890.0622-0.16461.18890.04610.28880.21920.05390.11730.083-0.2387-0.0057-0.104-0.00560.10521.40890.13150.05890.3343-0.01041.460424.9180.001520.526
91.4980.2810.10533.49620.42371.3094-0.0691-0.3632-0.160.27780.0267-0.06020.18790.0720.04110.150.05460.01040.28950.03770.128727.449270.509425.511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 166:237)
2X-RAY DIFFRACTION2(chain A and resid 238:287)
3X-RAY DIFFRACTION3(chain A and resid 288:455)
4X-RAY DIFFRACTION4(chain B and resid 161:237)
5X-RAY DIFFRACTION5(chain B and resid 238:291)
6X-RAY DIFFRACTION6(chain B and resid 292:455)
7X-RAY DIFFRACTION7(chain C and resid 165:239)
8X-RAY DIFFRACTION8(chain C and resid 240:288)
9X-RAY DIFFRACTION9(chain C and resid 289:455)

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