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- PDB-4wze: Crystal structure of P domain from norovirus strain Saga4 in comp... -

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Basic information

Entry
Database: PDB / ID: 4wze
TitleCrystal structure of P domain from norovirus strain Saga4 in complex with HBGA type Ley (tetraglycan)
ComponentsVP1
KeywordsVIRAL PROTEIN / Protruding domain
Function / homology
Function and homology information


virion component / host cell cytoplasm / metal ion binding
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
Lewis Y antigen, alpha anomer / ACETATE ION / VP1
Similarity search - Component
Biological speciesNorovirus Hu/GII-4/Saga4/2006/JP
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Human noroviruses' fondness for histo-blood group antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_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_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3496
Polymers67,8802
Non-polymers1,4694
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint21 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.020, 58.500, 113.860
Angle α, β, γ (deg.)90.000, 108.100, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asym.

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Components

#1: Protein VP1


Mass: 33939.953 Da / Num. of mol.: 2 / Fragment: P DOMAIN (UNP residues 225-530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII-4/Saga4/2006/JP / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5BTR7
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis Y antigen / alpha anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 675.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis Y antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3-2/a3-b1_a4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 45.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 1.45→48.16 Å / Num. obs: 102227 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 26.418 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.035 / Χ2: 1.023 / Net I/σ(I): 10.16 / Num. measured all: 234946
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.45-1.492.20.8710.4551.816667792074360.58293.9
1.49-1.530.9320.3232.3315527772571950.41793.1
1.53-1.570.9510.2722.9116994748872220.34596.4
1.57-1.620.9710.2013.6716490731370570.25696.5
1.62-1.670.9790.1654.4515786705367900.21196.3
1.67-1.730.9870.1315.2714877680864890.16895.3
1.73-1.80.9930.0976.5213401656161380.12493.6
1.8-1.870.9950.0778.3614428638161550.09896.5
1.87-1.960.9970.06110.1513754612458450.07895.4
1.96-2.050.9980.04412.2113147579655820.05696.3
2.05-2.160.9980.03814.0512188555352750.04895
2.16-2.290.9990.03115.110487524748140.0491.7
2.29-2.450.9990.02816.7711492498348280.03696.9
2.45-2.650.9990.02617.9210606459244490.03396.9
2.65-2.90.9990.02319.679544423740560.02995.7
2.9-3.240.9990.01920.688045385836190.02593.8
3.24-3.740.9990.01722.957445340631990.02293.9
3.74-4.590.9990.01723.66565289027780.02196.1
4.59-6.490.9990.01723.244654226320960.02292.6
6.490.9990.02123.282849128012040.02794.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.15 Å48.16 Å
Translation7.15 Å48.16 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OOX

4oox


Resolution: 1.46→31.759 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 46.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 4998 5 %
Rwork0.1774 --
obs0.1791 100015 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.73 Å2 / Biso mean: 25.2339 Å2 / Biso min: 6.87 Å2
Refinement stepCycle: final / Resolution: 1.46→31.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 100 542 5417
Biso mean--41.66 32.34 -
Num. residues----616

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