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- PDB-4rox: Crystal Structure of P Domain of Hawaii Norovirus (GII.1) -

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Basic information

Entry
Database: PDB / ID: 4rox
TitleCrystal Structure of P Domain of Hawaii Norovirus (GII.1)
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / Virus Binding / HBGA / Virus surface / Protruding domain / Surface domain
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.1/7EK/Hawaii/1971/USA
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: mSphere / Year: 2016
Title: Structural Constraints on Human Norovirus Binding to Histo-Blood Group Antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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 protein VP1
B: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7369
Polymers67,3012
Non-polymers4347
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-1 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.060, 78.160, 74.660
Angle α, β, γ (deg.)90.00, 122.42, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 221 - 525 / Label seq-ID: 1 - 305

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Capsid protein VP1 /


Mass: 33650.586 Da / Num. of mol.: 2 / Fragment: P domain residues 225-525
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.1/7EK/Hawaii/1971/USA / Strain: Hu/NLV/Hawaii virus/1971/US / Gene: VP1, U07611 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J9XXB7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M KCl, 20% w/v PEG 3350, 2ul drops with 1:1 protein:precipitant ratio, VAPOR DIFFUSION, HANGING DROP, temperature 291K, vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979961 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2014
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979961 Å / Relative weight: 1
ReflectionResolution: 1.86→37.33 Å / Num. obs: 110624 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.89 Å2 / Rmerge(I) obs: 0.053 / Χ2: 0.915 / Net I/σ(I): 8.92
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.86-1.910.5380.6041.3114866821279740.81697.1
1.91-1.960.6850.4351.915208805580040.58899.4
1.96-2.020.8150.3262.4314918782277770.44299.4
2.02-2.080.8680.2483.2714443761775460.33699.1
2.08-2.150.9190.196414037735373110.26599.4
2.15-2.220.9410.1594.9613644713570800.21599.2
2.22-2.310.9630.1265.9513174692768700.17299.2
2.31-2.40.970.1086.9212740663765980.14699.4
2.4-2.510.9730.0987.7712175635463140.13399.4
2.51-2.630.980.0819.1511651607360300.1199.3
2.63-2.770.9880.06610.6711028578457330.0999.1
2.77-2.940.9920.05512.5510479548554510.07699.4
2.94-3.140.9930.04415.079634510050520.06199.1
3.14-3.40.9940.03917.249051483347900.05499.1
3.4-3.720.9950.03618.858061436042990.0598.6
3.72-4.160.9950.03220.687426401839640.04498.7
4.16-4.80.9950.03221.226286347934300.04498.6
4.8-5.880.9960.02921.885707298229610.0499.3
5.88-8.320.9960.02921.384386231522860.04198.7
8.32-37.330.9950.02921.72092126211540.0491.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.11 Å39.75 Å
Translation5.11 Å39.75 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1690)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→37.33 Å / SU ML: 0.21 / σ(F): 1.04 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 5265 4.98 %
Rwork0.1773 100402 -
obs0.1785 105667 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.61 Å2 / Biso mean: 37.68 Å2 / Biso min: 17.57 Å2
Refinement stepCycle: LAST / Resolution: 1.89→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 28 306 4933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044775
X-RAY DIFFRACTIONf_angle_d0.8926533
X-RAY DIFFRACTIONf_chiral_restr0.035729
X-RAY DIFFRACTIONf_plane_restr0.005865
X-RAY DIFFRACTIONf_dihedral_angle_d12.041720
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2802X-RAY DIFFRACTION1.007TORSIONAL
12B2802X-RAY DIFFRACTION1.007TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.91150.35751710.332233343505100
1.9115-1.9340.33311790.29023404358399
1.934-1.95760.29131780.27933853563100
1.9576-1.98230.26421710.260632813452100
1.9823-2.00840.27081780.242133733551100
2.0084-2.03590.2151800.22734223602100
2.0359-2.0650.24251740.21523282345699
2.065-2.09580.20541800.21343393357399
2.0958-2.12860.25891710.204332963467100
2.1286-2.16350.24451770.207333873564100
2.1635-2.20080.20531780.206833303508100
2.2008-2.24080.21081790.19973371355099
2.2408-2.28390.19981730.19133342351599
2.2839-2.33050.211730.184533243497100
2.3305-2.38120.20781750.176933163491100
2.3812-2.43650.2281820.179434133595100
2.4365-2.49750.20571780.182533883566100
2.4975-2.5650.22091720.181933463518100
2.565-2.64040.21341720.190132723444100
2.6404-2.72560.21491760.18273355353199
2.7256-2.8230.23991740.181833513525100
2.823-2.9360.21371760.176833703546100
2.936-3.06960.18691810.1733401358299
3.0696-3.23130.19641710.17223297346899
3.2313-3.43360.20791760.17213333350999
3.4336-3.69850.19351720.16473334350699
3.6985-4.07030.18211760.14843337351399
4.0703-4.65830.16751790.14043378355799
4.6583-5.86530.14141700.148633183488100
5.8653-37.33720.18841730.16723269344296
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)
11.36140.0553-0.53152.33380.30561.60480.0667-0.01530.1295-0.08580.03350.1573-0.21810.0335-0.04470.2173-0.0304-0.00730.16970.00040.1874-10.55425.032175.5594
21.65640.9916-0.70713.3486-0.33841.0454-0.07240.11460.2426-0.1760.17130.6476-0.1145-0.221-0.13160.33550.0445-0.08240.29290.05830.3674-24.25377.417371.1444
31.7368-0.3541-0.57631.78220.56692.4283-0.0316-0.07770.0269-0.26830.138-0.3556-0.00070.4648-0.07980.2142-0.04110.03430.2776-0.04020.24494.3247-2.542870.8405
42.7820.51130.82352.3068-0.09081.8214-0.088-0.07450.03490.12830.1136-0.0121-0.13950.30430.00220.20590.0097-0.00350.2448-0.02570.1701-9.7094-4.783491.7302
51.51220.49090.46094.43210.8922.6026-0.2196-0.3233-0.11970.38540.08740.55540.17020.0050.14830.29320.04330.05710.25110.04610.3023-21.6023-13.965196.6786
63.3190.75620.7133.37671.19163.3746-0.07410.0884-0.3063-0.38410.16810.17930.273-0.1849-0.13690.245-0.0099-0.00020.14750.01090.2151-14.4933-17.499178.7979
73.5235-3.12124.07863.9285-2.59886.1595-0.36660.2663-0.0786-0.236-0.06790.15490.00470.02770.64020.5789-0.0157-0.00230.3024-0.00530.3975-20.7433-23.588870.4469
80.83010.0039-0.38093.3353-1.62863.1843-0.04240.2143-0.1516-0.54030.12970.33710.2712-0.1775-0.090.3144-0.0655-0.06490.2526-0.02670.3619-23.5675-18.29673.0884
97.5958-3.7669-3.87417.2843.94537.54540.04230.3691-0.1965-1.15260.29140.1452-0.02540.263-0.26880.3997-0.0824-0.06020.18410.05160.3229-23.0083-14.813167.5629
101.71160.3998-0.1141.65560.47622.0594-0.1049-0.1878-0.04950.31810.08120.23280.12140.01230.02610.22760.05310.03480.20810.04520.2221-18.3154-12.091193.7417
112.59090.4166-0.98535.0402-0.11722.8553-0.0582-0.52850.08310.46080.20420.17160.10690.2043-0.16980.32540.06760.03790.32970.00270.1755-16.1374-4.8518103.407
124.29-1.52390.21582.4003-1.96473.4592-0.0852-0.7696-0.01610.64090.1593-0.1081-0.09320.7861-0.04440.44310.1121-0.08040.5971-0.07860.2342-8.3635-6.6115108.2239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 221 through 330 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 331 through 409 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 410 through 525 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 222 through 247 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 248 through 267 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 268 through 293 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 294 through 316 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 317 through 370 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 371 through 389 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 390 through 479 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 480 through 508 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 509 through 525 )B0

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