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- PDB-3q38: Crystal structure of P domain from norwalk virus strain vietnam 0... -

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Basic information

Entry
Database: PDB / ID: 3q38
TitleCrystal structure of P domain from norwalk virus strain vietnam 026 in complex with HBGA type B (triglycan)
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / Norovirus / P-Domain / Capsid / Receptor / Histo Blood Group Antigen (HBGA)
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
IMIDAZOLE / Capsid protein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsHansman, G.S. / Biertumpfel, C. / Chen, L. / Georgiev, I. / McLellan, J.S. / Katayama, K. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2011
Title: Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability.
Authors: Hansman, G.S. / Biertumpfel, C. / Georgiev, I. / McLellan, J.S. / Chen, L. / Zhou, T. / Katayama, K. / Kwong, P.D.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,69228
Polymers69,6102
Non-polymers2,08226
Water14,862825
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-14 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.227, 79.028, 69.637
Angle α, β, γ (deg.)90.00, 99.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein / Capsid


Mass: 34804.953 Da / Num. of mol.: 2 / Fragment: unp reisdues 224-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Strain: Vietnam 026 / Gene: Capsid protein / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5F4T5
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 825 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Imidazole, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→29.038 Å / Num. obs: 178400 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.041 / Net I/σ(I): 18.92
Reflection shellResolution: 1.28→1.31 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.14 / Num. unique all: 13137 / Rsym value: 0.725 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASER(2.1.4)phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ONU

3onu


Resolution: 1.28→29.038 Å / SU ML: 0.13 / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 8988 5.04 %RANDOM
Rwork0.1667 ---
obs0.1675 178393 99.83 %-
all-178400 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.71 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 21.433 Å2
Baniso -1Baniso -2Baniso -3
1--0.8882 Å2-0 Å2-1.8004 Å2
2---0.6755 Å20 Å2
3---1.5637 Å2
Refinement stepCycle: LAST / Resolution: 1.28→29.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4829 0 139 825 5793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115187
X-RAY DIFFRACTIONf_angle_d1.3577065
X-RAY DIFFRACTIONf_dihedral_angle_d13.6831870
X-RAY DIFFRACTIONf_chiral_restr0.095787
X-RAY DIFFRACTIONf_plane_restr0.008930
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.28-1.29450.28143320.279155375537100
1.2945-1.30980.26132780.260356625662100
1.3098-1.32570.27672870.256556345634100
1.3257-1.34250.28252920.247956395639100
1.3425-1.36020.23312790.242356715671100
1.3602-1.37880.25223010.228155985598100
1.3788-1.39850.22322800.217356795679100
1.3985-1.41940.22623160.211956155615100
1.4194-1.44160.24133030.205856295629100
1.4416-1.46520.21713080.190856285628100
1.4652-1.49050.20283140.189556165616100
1.4905-1.51760.19813190.18356275627100
1.5176-1.54680.20873030.176656465646100
1.5468-1.57830.19222860.169556215621100
1.5783-1.61260.18673080.162456465646100
1.6126-1.65020.19723070.164456445644100
1.6502-1.69140.17273220.159756035603100
1.6914-1.73710.1742720.154456925692100
1.7371-1.78830.1662960.148556325632100
1.7883-1.8460.15633020.140956435643100
1.846-1.91190.15913030.148956405640100
1.9119-1.98850.16193200.148156755675100
1.9885-2.07890.15392800.147956375637100
2.0789-2.18850.15812840.152156665666100
2.1885-2.32560.16063210.155256715671100
2.3256-2.5050.17063170.155256425642100
2.505-2.7570.17842870.164256585658100
2.757-3.15550.18642860.170156985698100
3.1555-3.9740.17832960.156956925692100
3.974-29.04530.16252890.15335764576499
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)
10.27170.0430.15770.5850.08090.8732-0.01330.06960.0129-0.05580.00870.0389-0.09340.0418-0.00680.0914-0.00640.0040.0797-0.00250.06818.29497.383310.2468
20.75490.0858-0.06420.9332-0.42081.1776-0.0054-0.02840.10190.08920.03590.0343-0.2127-0.0379-0.03120.0880.0110.00610.0361-0.0060.05873.745313.458419.4574
30.64490.14390.10090.61660.06070.3769-0.07480.1663-0.0549-0.23740.0705-0.02090.01180.1058-0.00230.1496-0.02640.02280.1466-0.02510.057612.8773-2.7507-4.132
40.52050.20490.2760.74070.18020.39540.05190.0042-0.07270.066-0.0044-0.12090.04610.0769-0.04170.06540.0008-0.01370.07650.0010.10420.094-5.914623.8699
50.8964-0.21990.1940.7195-0.0990.63940.0325-0.0862-0.2180.07040.03170.0270.1089-0.0319-0.06950.0944-0.0088-0.01540.06430.02360.11559.2654-12.623127.6505
60.41030.19650.24910.88040.24450.59690.0240.0797-0.09020.01870.0725-0.3396-0.04060.1754-0.09270.0564-0.01-0.00560.125-0.03510.177233.79482.297122.8082
75.36412.59972.98433.04952.28924.4793-0.31160.34770.0926-0.12510.43260.08310.2388-0.0048-0.08130.3875-0.0801-0.08840.33830.06580.26551.70775.125441.1842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 224:307)
2X-RAY DIFFRACTION2(chain A and resid 308:432)
3X-RAY DIFFRACTION3(chain A and resid 433:538)
4X-RAY DIFFRACTION4(chain B and resid 224:300)
5X-RAY DIFFRACTION5(chain B and resid 301:434)
6X-RAY DIFFRACTION6(chain B and resid 435:538)
7X-RAY DIFFRACTION7(chain L)

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