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- PDB-3sjp: Structural characterization of a GII.4 2004 norovirus variant (TCH05) -

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Basic information

Entry
Database: PDB / ID: 3sjp
TitleStructural characterization of a GII.4 2004 norovirus variant (TCH05)
ComponentsCapsid
KeywordsVIRAL PROTEIN / Capsid protein
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorovirus Hu/GII.4/2004/NL
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsShanker, S. / Choi, J.-M. / Sankaran, B. / Atmar, R.L. / Estes, M.K. / Prasad, B.V.V.
CitationJournal: J.Virol. / Year: 2011
Title: Structural Analysis of Histo-Blood Group Antigen Binding Specificity in a Norovirus GII.4 Epidemic Variant: Implications for Epochal Evolution.
Authors: Shanker, S. / Choi, J.M. / Sankaran, B. / Atmar, R.L. / Estes, M.K. / Prasad, B.V.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7898
Polymers34,3311
Non-polymers4587
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.001, 72.966, 55.610
Angle α, β, γ (deg.)90.00, 97.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-83-

HOH

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Components

#1: Protein Capsid /


Mass: 34331.117 Da / Num. of mol.: 1 / Fragment: Protruding Domain (UNP Residues 221-531)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/2004/NL / Plasmid: pMal-C2E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5EGK8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE MUTATIONS ARE STRAIN SPECIFIC AS UNP DOES NOT HAVE THE STRAIN SPECIFIC SEQUENCE

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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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M Zinc Acetate, 0.1M MES, 15% v/v Ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.004→50 Å / Num. all: 23706 / Num. obs: 23043 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.054 / Rsym value: 0.041 / Net I/σ(I): 19.15
Reflection shellResolution: 2.004→2.04 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.82 / Rsym value: 0.273 / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OBS

2obs


Resolution: 2.004→28.108 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 1186 5.16 %
Rwork0.1982 --
obs0.2005 22999 96.81 %
all-22999 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.241 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.1709 Å20 Å21.3154 Å2
2---1.9401 Å2-0 Å2
3----3.2309 Å2
Refinement stepCycle: LAST / Resolution: 2.004→28.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 7 208 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072351
X-RAY DIFFRACTIONf_angle_d1.0213211
X-RAY DIFFRACTIONf_dihedral_angle_d12.988837
X-RAY DIFFRACTIONf_chiral_restr0.07360
X-RAY DIFFRACTIONf_plane_restr0.005422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.004-2.09520.30411470.23172670X-RAY DIFFRACTION96
2.0952-2.20560.27381430.21582805X-RAY DIFFRACTION100
2.2056-2.34380.3931390.27782720X-RAY DIFFRACTION97
2.3438-2.52460.26121580.20892806X-RAY DIFFRACTION100
2.5246-2.77850.24821550.19272806X-RAY DIFFRACTION100
2.7785-3.18010.24111530.19262781X-RAY DIFFRACTION99
3.1801-4.00470.2141390.18092433X-RAY DIFFRACTION87
4.0047-28.11110.20891520.18472792X-RAY DIFFRACTION97
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)
10.1948-0.05660.08610.3223-0.15210.92340.03370.025-0.0209-0.0067-0.0278-0.0652-0.13020.0727-0.01150.23650.00110.01230.21420.01140.181817.675365.39412.9022
20.6421-0.0875-0.38280.9558-0.07840.58260.1074-0.18540.06840.3513-0.129-0.0526-0.0135-0.1202-0.00840.3367-0.0292-0.04250.28070.01440.239723.217570.6123.7465
30.70581.07110.43381.70760.88470.8950.1707-0.1354-0.18020.2088-0.0788-0.29070.1205-0.0170.93820.16070.0150.00690.10930.04510.087825.255159.083511.0378
40.34220.390.02150.53930.21220.34150.0265-0.063-0.04210.028-0.0617-0.0339-0.02240.04230.00670.25060.00540.01210.23470.00060.187117.20163.0642-7.5627
50.23580.02130.1950.26790.20450.297-0.06390.2793-0.0347-0.20910.0878-0.1252-0.10630.00350.00040.3212-0.00180.04860.2422-0.00950.192819.652260.6604-15.0035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 221:292)
2X-RAY DIFFRACTION2chain 'A' and (resseq 293:379)
3X-RAY DIFFRACTION3chain 'A' and (resseq 380:428)
4X-RAY DIFFRACTION4chain 'A' and (resseq 429:500)
5X-RAY DIFFRACTION5chain 'A' and (resseq 501:531)

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