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- PDB-3q3a: Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 0... -

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Basic information

Entry
Database: PDB / ID: 3q3a
TitleCrystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type H2 (triglycan)
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Norovirus / P-Domain / Capsid / Receptor / Histo Blood Group Antigen (HBGA)
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / 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 ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / 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: 1.4 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 1.2Nov 2, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_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)71,78829
Polymers69,6102
Non-polymers2,17827
Water13,475748
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-13 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.168, 79.104, 68.912
Angle α, β, γ (deg.)90.00, 99.54, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit is also biological unit.

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Components

#1: Protein Capsid protein


Mass: 34804.953 Da / Num. of mol.: 2 / Fragment: unp residues 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 beta-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-2DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1b_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
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: 1.4→28.171 Å / Num. obs: 135108 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.74 % / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.04 / Net I/σ(I): 21.33
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 3.69 % / Mean I/σ(I) obs: 2.32 / Num. unique all: 9985 / Rsym value: 0.672 / % possible all: 99.9

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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: 1.4→28.171 Å / SU ML: 0.15 / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 6863 5.08 %RANDOM
Rwork0.1689 ---
obs0.1698 135108 99.82 %-
all-135210 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.958 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 23.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.1027 Å2-0 Å2-2.7216 Å2
2---1.3517 Å20 Å2
3---1.4544 Å2
Refinement stepCycle: LAST / Resolution: 1.4→28.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 145 748 5725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095155
X-RAY DIFFRACTIONf_angle_d1.2447015
X-RAY DIFFRACTIONf_dihedral_angle_d15.0611856
X-RAY DIFFRACTIONf_chiral_restr0.087781
X-RAY DIFFRACTIONf_plane_restr0.007922
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4-1.41590.30762450.271442644264100
1.4159-1.43260.28032500.257642074207100
1.4326-1.450.27872190.255242764276100
1.45-1.46840.26332380.243742684268100
1.4684-1.48770.26452370.233942624262100
1.4877-1.50810.24492550.227742054205100
1.5081-1.52960.24482240.218642984298100
1.5296-1.55250.23392160.212642734273100
1.5525-1.57670.22372280.201842634263100
1.5767-1.60260.24582220.193642894289100
1.6026-1.63020.23132320.195842474247100
1.6302-1.65980.20722410.184942514251100
1.6598-1.69180.18692300.177242914291100
1.6918-1.72630.18482210.173842714271100
1.7263-1.76380.21342110.171142814281100
1.7638-1.80480.19552240.163542924292100
1.8048-1.850.1632280.156342744274100
1.85-1.90.19412330.158842704270100
1.9-1.95590.17072450.156442304230100
1.9559-2.0190.18792200.156143074307100
2.019-2.09110.17322080.156343114311100
2.0911-2.17480.18062190.159142814281100
2.1748-2.27380.17362410.158642514251100
2.2738-2.39360.1662620.151342574257100
2.3936-2.54350.16822130.157743264326100
2.5435-2.73970.18662200.168142764276100
2.7397-3.01510.17972140.165443094309100
3.0151-3.45070.19792170.161943264326100
3.4507-4.3450.15442400.146943054305100
4.345-28.17690.17042100.1614386438699
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)
10.1304-0.0550.12540.26280.02390.3246-0.01990.05440.0189-0.05990.02140.0296-0.09590.0667-0.01390.0534-0.00660.00950.0269-0.00640.0078.45238.286110.027
20.50380.0588-0.04840.8516-0.3620.7939-0.0036-0.02910.06490.08760.05410.0245-0.2025-0.0261-0.03740.10140.01060.00550.0552-0.00080.06363.911614.28119.2908
30.50410.12880.12220.70920.09630.0377-0.01840.1655-0.0513-0.30730.070.0013-0.05340.0472-0.02620.1126-0.02290.03810.1024-0.0384-0.043412.9142-1.3125-4.4304
40.37420.17880.29140.49040.09580.23670.04470.0735-0.09440.04780.0138-0.14740.03050.0724-0.04820.0103-0.0001-0.01860.0299-0.00560.07920.197-5.120623.5308
50.6303-0.15570.26660.5833-0.12220.49570.0246-0.0375-0.19130.06190.0419-0.0070.0983-0.0411-0.07820.0223-0.0048-0.02320.00670.02240.06049.4241-11.842627.2449
60.17930.28490.31891.03930.25060.66760.00190.14-0.16730.03790.0828-0.4318-0.03460.1722-0.09410.0552-0.0078-0.01560.1465-0.04440.235333.92763.192922.4811
70.86570.9540.27371.12580.21060.19810.2031-0.2264-0.05880.10480.07520.07390.219-0.5021-0.27790.1803-0.0534-0.02340.20850.05940.14821.46184.89539.9479
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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