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- PDB-3r6k: Crystal Structure of the Capsid P Domain from Norwalk Virus Strai... -

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Basic information

Entry
Database: PDB / ID: 3r6k
TitleCrystal Structure of the Capsid P Domain from Norwalk Virus Strain Hiroshima/1999 in complex with HBGA type B (triglycan)
ComponentsVP1 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
Biological speciesNorwalk-like virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHansman, G.S. / Biertumpfel, C. / McLellan, J.S. / Georgiev, I. / Chen, L. / Zhou, T. / 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
DepositionMar 21, 2011Deposition 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 / pdbx_struct_special_symmetry / 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 / _pdbx_struct_special_symmetry.label_asym_id / _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: VP1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0274
Polymers33,4151
Non-polymers6133
Water4,107228
1
A: VP1 protein
hetero molecules

A: VP1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0548
Polymers66,8292
Non-polymers1,2256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5310 Å2
ΔGint18 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.388, 100.279, 82.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-27-

HOH

21A-55-

HOH

31A-535-

HOH

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Components

#1: Protein VP1 protein


Mass: 33414.504 Da / Num. of mol.: 1 / Fragment: unp residues 225-525
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk-like virus / Strain: Hiroshima/1999/JP / Gene: Capsid protein / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q54AD6
#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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
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, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Sep 12, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→24.446 Å / Num. obs: 37085 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 22.53 Å2 / Rsym value: 0.086 / Net I/σ(I): 18.26
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.99 / Num. unique all: 2432 / Rsym value: 0.395 / % possible all: 61.2

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASER(2.1.4)phasing
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ONU

3onu


Resolution: 1.6→24.446 Å / SU ML: 0.19 / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1844 5.01 %RANDOM
Rwork0.2194 ---
obs0.2203 36791 91.28 %-
all-36791 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.6823 Å20 Å2-0 Å2
2--9.8361 Å2-0 Å2
3----4.8471 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 41 228 2607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052447
X-RAY DIFFRACTIONf_angle_d0.933349
X-RAY DIFFRACTIONf_dihedral_angle_d16.129898
X-RAY DIFFRACTIONf_chiral_restr0.061379
X-RAY DIFFRACTIONf_plane_restr0.004439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5999-1.64310.3414900.30531750X-RAY DIFFRACTION60
1.6431-1.69140.3091210.27412414X-RAY DIFFRACTION83
1.6914-1.7460.32141670.24332819X-RAY DIFFRACTION97
1.746-1.80840.23121270.22792911X-RAY DIFFRACTION99
1.8084-1.88080.31491440.24612912X-RAY DIFFRACTION99
1.8808-1.96640.47281280.42752200X-RAY DIFFRACTION76
1.9664-2.070.25251590.22832925X-RAY DIFFRACTION100
2.07-2.19960.25691500.22832913X-RAY DIFFRACTION99
2.1996-2.36930.34461360.31632476X-RAY DIFFRACTION84
2.3693-2.60750.25851600.21032938X-RAY DIFFRACTION100
2.6075-2.98420.23221460.21232966X-RAY DIFFRACTION100
2.9842-3.75760.21471570.19342805X-RAY DIFFRACTION94
3.7576-24.44880.16411590.17092918X-RAY DIFFRACTION94
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)
10.3442-0.01940.08690.2186-0.05470.47850.15150.003-0.03980.015-0.0971-0.01540.36530.40490.01350.12960.0926-0.04840.2182-0.01590.148110.4807-29.6507-15.061
20.3596-0.01280.05140.0609-0.10240.42470.2955-0.0715-0.0895-0.0116-0.0346-0.04180.72890.38380.22450.33520.2348-0.15540.04040.00060.13589.685-35.8929-14.0114
30.3580.18060.1140.39510.01970.15560.0132-0.15830.07340.2143-0.16620.0305-0.0819-0.17610.02520.1455-0.07430.01810.2737-0.08160.165-0.3064-12.282-0.5655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 225:328)
2X-RAY DIFFRACTION2(chain A and resid 329:460)
3X-RAY DIFFRACTION3(chain A and resid 461:525)

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