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- PDB-4x07: Crystal structure of P domain from norovirus strain Saga4 in comp... -

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Basic information

Entry
Database: PDB / ID: 4x07
TitleCrystal structure of P domain from norovirus strain Saga4 in complex with HBGA type A (triglycan)
ComponentsVP1
KeywordsVIRAL PROTEIN / Viral capsid 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
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 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
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 / 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 / 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_struct_special_symmetry.label_asym_id / _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.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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9436
Polymers67,7662
Non-polymers1,1774
Water14,358797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint7 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.960, 58.640, 114.590
Angle α, β, γ (deg.)90.000, 105.490, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-785-

HOH

21A-1058-

HOH

31B-785-

HOH

41B-1044-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein VP1


Mass: 33882.902 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 BL21(DE3) (bacteria) / References: UniProt: B5BTR7
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}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.: 797 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 3M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97246 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: 0.97246 Å / Relative weight: 1
ReflectionResolution: 1.28→48.01 Å / Num. obs: 157018 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 14.39 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.071 / Χ2: 1.104 / Net I/σ(I): 7.42 / Num. measured all: 708898
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
1.28-1.323.60.9280.4191.963436311825109600.50192.7
1.32-1.350.9660.3522.995347411502114790.39799.8
1.35-1.390.9760.2853.485061911232112050.32399.8
1.39-1.430.9830.2543.965069910851108240.28699.8
1.43-1.480.9830.2284.554716410506104080.25899.1
1.48-1.530.990.1745.44857310202101780.19699.8
1.53-1.590.9930.1466.1345995986098520.16499.9
1.59-1.660.9940.1226.9843452942994100.13799.8
1.66-1.730.9950.1087.7442239915391360.12199.8
1.73-1.810.9960.0938.9841826863186110.10599.8
1.81-1.910.9950.0889.7337465830880410.09996.8
1.91-2.030.9950.07610.5932095784175100.08695.8
2.03-2.170.9970.07111.232704733272470.0898.8
2.17-2.340.9970.06612.9828095690462220.07390.1
2.34-2.560.9970.06212.230397630462740.06999.5
2.56-2.870.9970.05911.8325904575057010.06799.1
2.87-3.310.9980.05812.822732506249880.06598.5
3.31-4.050.9970.05215.117450432538450.05888.9
4.05-5.730.9980.04312.7714706334832610.04997.4
5.730.9970.04913.068946188618660.05598.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.14 Å48.01 Å
Translation7.14 Å48.01 Å

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Processing

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

4oox


Resolution: 1.46→43.183 Å / FOM work R set: 0.5293 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 45.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 5304 5 %
Rwork0.1653 100871 -
obs0.1667 106175 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.34 Å2 / Biso mean: 17.47 Å2 / Biso min: 3.9 Å2
Refinement stepCycle: final / Resolution: 1.46→43.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 80 797 5649
Biso mean--35.98 27.34 -
Num. residues----614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075080
X-RAY DIFFRACTIONf_angle_d1.2046964
X-RAY DIFFRACTIONf_chiral_restr0.075766
X-RAY DIFFRACTIONf_plane_restr0.006914
X-RAY DIFFRACTIONf_dihedral_angle_d15.041904
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 (%)
1.46-1.47660.2521760.26823343351999
1.4766-1.4940.29381770.24643379355699
1.494-1.51220.27511810.233234323613100
1.5122-1.53130.20851800.234334173597100
1.5313-1.55150.26891800.226634303610100
1.5515-1.57270.23561790.215833903569100
1.5727-1.59520.25011810.210834293610100
1.5952-1.6190.23381790.213534043583100
1.619-1.64430.23461790.210234043583100
1.6443-1.67130.23651820.201234493631100
1.6713-1.70010.22631780.197833913569100
1.7001-1.7310.22871830.189834553638100
1.731-1.76430.19761780.186933933571100
1.7643-1.80030.2211800.1834103590100
1.8003-1.83950.21841820.180734573639100
1.8395-1.88230.19621780.17713385356399
1.8823-1.92930.2231620.19683065322789
1.9293-1.98150.18431720.15943272344495
1.9815-2.03980.21091810.15833441362299
2.0398-2.10560.17081780.15073394357298
2.1056-2.18090.19191780.15183397357599
2.1809-2.26820.2061550.16162984313987
2.2682-2.37140.17081700.13363233340394
2.3714-2.49640.17261810.147134393620100
2.4964-2.65280.18611800.14173420360099
2.6528-2.85760.16441810.15513435361699
2.8576-3.14510.17231810.15153422360399
3.1451-3.60.17861730.14433315348895
3.6-4.53490.14591640.13663118328290
4.5349-43.20150.19971750.16383368354394

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