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- PDB-3s6z: Structure of reovirus attachment protein sigma1 in complex with a... -

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Basic information

Entry
Database: PDB / ID: 3s6z
TitleStructure of reovirus attachment protein sigma1 in complex with alpha-2,8-disialyllactose
ComponentsOuter capsid protein sigma-1
KeywordsVIRAL PROTEIN / triple beta-spiral / beta-barrel / beta-spiral repeat / greek key motif / trimer / Viral attachment protein / sialic acid receptor 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
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 / 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 / molecular replacement / Resolution: 2.28 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 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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)107,6085
Polymers106,0823
Non-polymers1,5252
Water12,881715
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24820 Å2
ΔGint-140 kcal/mol
Surface area38140 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-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 762.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-2/a3-b2_b8-c2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 0.9755 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2.28→48.058 Å / Num. all: 78294 / Num. obs: 75918 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.28-2.340.4353.17198.9
2.34-2.40.3533.75198.7
2.4-2.470.3134.35198.2
2.47-2.550.2595.23198.3
2.55-2.630.1986.67198.5
2.63-2.730.1598.15198.1
2.73-2.830.12310.27197.7
2.83-2.940.09712.59197.7
2.94-3.070.07715.58197.5
3.07-3.220.0619.45197
3.22-3.40.0522.81197
3.4-3.610.03927.5195.7
3.61-3.850.03331.91196
3.85-4.160.02934.83194.6
4.16-4.560.02441.18194.8
4.56-5.10.02343.17194.5
5.1-5.890.02243.34193.6
5.89-7.210.0248.27195.1
7.21-10.20.01756.78193.5
10.2-48.0580.01463.27187.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.397 / Cor.coef. Fo:Fc: 0.6 / Cor.coef. Io to Ic: 0.605
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
AMoREphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→48.058 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.68 / σ(F): 2 / Phase error: 19.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 3828 5.04 %
Rwork0.173 --
obs0.1753 75914 96.03 %
all-78294 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.685 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.2371 Å20 Å2-0 Å2
2---4.8497 Å2-0 Å2
3---9.0868 Å2
Refinement stepCycle: LAST / Resolution: 2.28→48.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6663 0 104 715 7482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066925
X-RAY DIFFRACTIONf_angle_d1.0189454
X-RAY DIFFRACTIONf_dihedral_angle_d14.9092513
X-RAY DIFFRACTIONf_chiral_restr0.0661100
X-RAY DIFFRACTIONf_plane_restr0.0041226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.3610.29723480.25176568X-RAY DIFFRACTION89
2.361-2.45560.31313890.24087282X-RAY DIFFRACTION99
2.4556-2.56730.3113890.23437293X-RAY DIFFRACTION98
2.5673-2.70270.25853920.18867279X-RAY DIFFRACTION98
2.7027-2.8720.21033750.16167281X-RAY DIFFRACTION98
2.872-3.09370.20653820.15787326X-RAY DIFFRACTION98
3.0937-3.40490.22023740.1727248X-RAY DIFFRACTION97
3.4049-3.89740.20413950.16087217X-RAY DIFFRACTION96
3.8974-4.90960.17653970.12997166X-RAY DIFFRACTION94
4.9096-48.06890.21173870.18677426X-RAY DIFFRACTION94
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)
11.2799-0.7341-0.03154.1817-0.06882.11320.0869-0.0214-0.5191-0.1429-0.1134-0.15010.2827-0.00030.06230.1592-0.0674-0.01410.20420.00390.334332.5230.056513.5065
20.78650.32460.08460.28570.08550.0250.0381-0.0718-0.2143-0.0071-0.12540.09380.3376-0.0889-0.05431.3169-0.0770.00890.29050.02111.358222.9507168.895711.9936
31.10240.3649-0.01742.03220.01211.2471-0.0206-0.02960.2433-0.16230.02030.1637-0.1361-0.16460.00690.09810.0151-0.01230.18120.02840.133311.582696.881518.318
41.53881.2888-0.09513.02320.62582.24060.05660.0072-0.4209-0.3416-0.0820.09840.1609-0.02460.08220.16940.0099-0.09760.1713-0.01730.297532.0255232.62319.5842
50.16350.01380.14790.00210.01120.13310.0085-0.0383-0.0978-0.0139-0.12090.0140.11160.0112-0.25641.03-0.1321-0.0220.16160.07071.050826.8563166.702212.5671
61.6079-0.2670.03741.8406-0.2341.4906-0.0596-0.1880.14210.13240.05350.011-0.12460.17380.00770.0981-0.0045-0.00810.1953-0.02190.091332.226797.207425.4053
71.19390.5655-0.40213.2704-1.28271.85440.1003-0.0182-0.5438-0.2978-0.18960.23850.2769-0.0960.10450.1904-0.0114-0.09270.2686-0.01460.44728.0509230.23511.7446
80.3174-0.03220.00060.19630.02360.3620.0603-0.0037-0.0676-0.0237-0.08650.03180.0714-0.00220.24181.296-0.1274-0.00660.2630.05151.311225.1118166.79458.7927
91.2609-0.1793-0.09841.63590.46231.194-0.06070.29540.1797-0.22390.113-0.1229-0.21570.1235-0.04630.1641-0.0648-0.00070.25320.03350.124427.622396.37963.5967
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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