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- PDB-4gu3: Crystal structure of the T1L reovirus attachment protein sigma1 i... -

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Basic information

Entry
Database: PDB / ID: 4gu3
TitleCrystal structure of the T1L reovirus attachment protein sigma1 in complex with the GM2 glycan
ComponentsOuter capsid protein sigma-1
KeywordsVIRAL PROTEIN / TRIPLE BETA-SPIRAL / BETA-BARREL / BETA-SPIRAL REPEAT / GREEK KEY MOTIF / VIRAL ATTACHMENT PROTEIN / GM2 GLYCAN 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
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) / Adenovirus pIV-like, attachment domain / Laminin / Ribbon / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein sigma-1
Similarity search - Component
Biological speciesMammalian orthoreovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsReiss, K. / Stehle, T.
CitationJournal: Plos Pathog. / Year: 2012
Title: The GM2 Glycan Serves as a Functional Coreceptor for Serotype 1 Reovirus.
Authors: Reiss, K. / Stencel, J.E. / Liu, Y. / Blaum, B.S. / Reiter, D.M. / Feizi, T. / Dermody, T.S. / Stehle, T.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
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.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)76,0126
Polymers73,5013
Non-polymers2,5103
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-92 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.460, 147.460, 164.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 24500.469 Da / Num. of mol.: 3 / Fragment: UNP residues 261-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalian orthoreovirus 1 / Strain: Lang / Gene: S1 / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2(DE3) / References: UniProt: P04506
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)]beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3[DGalpNAcb1-4]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b3-c2_b4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE

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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: 7.02 Å3/Da / Density % sol: 82.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Na Cacodylate, 1.25 M (NH4)2SO4 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. all: 24455 / Num. obs: 24422 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 61.26 Å2
Reflection shellResolution: 3.6→3.69 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→46.31 Å / Cor.coef. Fo:Fc: 0.9058 / Cor.coef. Fo:Fc free: 0.8895 / SU R Cruickshank DPI: 0.686 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 2485 10.18 %RANDOM
Rwork0.1847 ---
obs0.1866 24418 99.95 %-
all-24455 --
Displacement parametersBiso mean: 90.76 Å2
Baniso -1Baniso -2Baniso -3
1--15.4403 Å20 Å20 Å2
2---15.4403 Å20 Å2
3---30.8806 Å2
Refine analyzeLuzzati coordinate error obs: 0.679 Å
Refinement stepCycle: LAST / Resolution: 3.6→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 171 0 4947
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015079HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.116971HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1677SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0.0091109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0.0177724HARMONIC5
X-RAY DIFFRACTIONt_it5079HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion17.25
X-RAY DIFFRACTIONt_chiral_improper_torsion727SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5736SEMIHARMONIC4
LS refinement shellResolution: 3.6→3.76 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2501 279 9.45 %
Rwork0.2312 2673 -
all0.233 2952 -
obs--99.95 %

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