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- PDB-4wzt: Crystal structure of P domain from norovirus strain NSW0514 in co... -

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Basic information

Entry
Database: PDB / ID: 4wzt
TitleCrystal structure of P domain from norovirus strain NSW0514 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
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/Sydney/NSW0514/2012/AU
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 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: Atomic model / Data collection ...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 / 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 / _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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)69,4298
Polymers68,1222
Non-polymers1,3076
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint28 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.740, 104.740, 190.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: MET / End label comp-ID: MET

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERSERchain AAA224 - 5301 - 307
2LYSLYSchain BBB225 - 5302 - 307
Detailsbiological unit is the same as asym.

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Components

#1: Protein VP1


Mass: 34060.961 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/Sydney/NSW0514/2012/AU
Plasmid: MBP-HTSHP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4LM89
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 722 / 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: 3.84 Å3/Da / Density % sol: 67.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978174 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978174 Å / Relative weight: 1
ReflectionResolution: 1.85→48.26 Å / Num. obs: 89901 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 23.15 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.094 / Χ2: 0.937 / Net I/σ(I): 16.68 / Num. measured all: 585432
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
1.85-1.96.50.6270.9831.641990663765231.06398.3
1.9-1.950.7440.7062.3542181647264430.76399.6
1.95-2.010.8390.5782.8441128627162410.62399.5
2.01-2.070.880.4683.939409611360550.50599.1
2.07-2.140.9190.3784.6538018595558850.40898.8
2.14-2.210.9470.2925.937433571956780.31599.3
2.21-2.30.9680.2227.4636422556555390.23999.5
2.3-2.390.9790.1888.9435030537053470.20399.6
2.39-2.50.9850.16110.1833680513251090.17499.6
2.5-2.620.990.13212.532222492248980.14299.5
2.62-2.760.9940.10515.6230588469946650.11399.3
2.76-2.930.9950.08319.4528887443043940.08999.2
2.93-3.130.9980.06125.8827216419841610.06699.1
3.13-3.380.9990.04534.9725321394338940.04898.8
3.38-3.70.9990.03741.7723085361735600.0498.4
3.7-4.140.9990.03148.9120733330532350.03397.9
4.14-4.780.9990.02656.5617857294728570.02896.9
4.78-5.8510.02554.7115734251124410.02797.2
5.85-8.2810.02453.0512337200119130.02695.6
8.2810.01959.56161120710630.02188.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.63 Å48.26 Å
Translation4.63 Å48.26 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: 4OOS

4oos


Resolution: 1.91→48.258 Å / FOM work R set: 0.9003 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1791 4095 5 %
Rwork0.1537 77777 -
obs0.1549 81872 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.58 Å2 / Biso mean: 27.63 Å2 / Biso min: 9.7 Å2
Refinement stepCycle: final / Resolution: 1.91→48.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4781 0 88 722 5591
Biso mean--42.83 35.33 -
Num. residues----613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085034
X-RAY DIFFRACTIONf_angle_d1.1346879
X-RAY DIFFRACTIONf_chiral_restr0.047770
X-RAY DIFFRACTIONf_plane_restr0.006904
X-RAY DIFFRACTIONf_dihedral_angle_d12.5271807
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2802X-RAY DIFFRACTION4.264TORSIONAL
12B2802X-RAY DIFFRACTION4.264TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.93250.2861400.250126502790100
1.9325-1.95610.25341390.23032643278299
1.9561-1.98080.21961420.21162695283799
1.9808-2.00690.24381390.203226392778100
2.0069-2.03440.24621400.21352671281199
2.0344-2.06340.23491400.19912645278599
2.0634-2.09420.2411380.21662621275998
2.0942-2.1270.18531400.16882658279899
2.127-2.16180.20511390.1742637277699
2.1618-2.19910.18781410.163826732814100
2.1991-2.23910.17631410.156126872828100
2.2391-2.28220.18381400.146926592799100
2.2822-2.32870.19681420.146526832825100
2.3287-2.37940.18741410.146826792820100
2.3794-2.43470.19451420.14742695283799
2.4347-2.49560.18681400.143426712811100
2.4956-2.56310.16571410.14192676281799
2.5631-2.63850.18111420.138426912833100
2.6385-2.72370.19081420.13822689283199
2.7237-2.8210.16931410.13812688282999
2.821-2.93390.16981420.14382697283999
2.9339-3.06740.15731430.14492710285399
3.0674-3.22910.16891410.14232679282099
3.2291-3.43140.15351430.14772707285099
3.4314-3.69620.19061410.15472705284698
3.6962-4.0680.14951430.1392707285098
4.068-4.65630.14341420.11912713285597
4.6563-5.86480.16071440.13492741288597
5.8648-48.27340.18791460.18122768291493
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)
10.8184-0.1725-0.19690.26950.20241.8249-0.00690.0708-0.0419-0.0644-0.015-0.0320.03430.03760.02070.1334-0.02160.0230.14990.01550.160644.234513.6542-24.4516
21.5059-0.36870.22751.1608-0.60762.77470.03980.173-0.2767-0.1399-0.01550.05040.30170.07210.0130.175-0.00850.03470.1443-0.03620.196345.39594.1278-29.7147
30.6610.13140.04571.29140.49811.5317-0.047-0.1831-0.02940.2032-0.005-0.02140.03730.07670.05420.153-0.00510.01760.22610.04150.15742.650614.9748-2.3435
41.91290.091-0.37692.42860.26481.3893-0.02520.12780.07460.10650.0564-0.1755-0.12060.0141-0.03370.12780.0093-0.01820.15460.00570.121630.490329.4066-23.3768
51.8913-0.6238-0.25692.9343-0.45330.9657-0.02730.1171-0.2936-0.1303-0.03080.34080.1155-0.27740.04280.1424-0.0412-0.02490.2463-0.03820.23919.756312.4318-27.3126
61.1237-0.2521-0.08261.78520.57021.51350.08070.11810.2976-0.12450.0231-0.2936-0.35770.1457-0.06810.2146-0.01260.01860.18060.03710.232832.637438.7232-26.0731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 224 through 352 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 353 through 418 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 419 through 530 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 225 through 292 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 293 through 398 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 399 through 530 )B0

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