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- PDB-4z4s: Crystal structure of GII.10 P domain in complex with 150mM fucose -

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Basic information

Entry
Database: PDB / ID: 4z4s
TitleCrystal structure of GII.10 P domain in complex with 150mM fucose
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / fucose / norovirus / 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
beta-L-fucopyranose / NITRATE ION / Capsid protein
Similarity search - Component
Biological speciesNorovirus GII.10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKoromyslova, A.D. / Leuthold, M.M. / Hansman, G.S.
CitationJournal: Virology / Year: 2015
Title: The sweet quartet: Binding of fucose to the norovirus capsid.
Authors: Koromyslova, A.D. / Leuthold, M.M. / Bowler, M.W. / Hansman, G.S.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 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 / 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_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: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,16614
Polymers69,0132
Non-polymers1,15312
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint12 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.090, 78.681, 68.811
Angle α, β, γ (deg.)90.000, 99.610, 90.000
Int Tables number4
Space group name H-MP1211
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
1LYSLYSchain AAA225 - 5382 - 315
2SERSERchain BBB224 - 5381 - 315

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Components

#1: Protein Capsid protein


Mass: 34506.660 Da / Num. of mol.: 2 / Fragment: Protruding domain, UNP residues 224-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.10 / Plasmid: pMBP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5F4T5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: sodium nitrate, bis-tris propane, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.984463 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 20, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984463 Å / Relative weight: 1
ReflectionResolution: 1.799→43.08 Å / Num. obs: 63903 / % possible obs: 99 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06395 / Net I/σ(I): 13.76
Reflection shellResolution: 1.799→1.863 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.2973 / Mean I/σ(I) obs: 4.06 / Rejects: 0 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.11 Å43.08 Å
Translation7.11 Å43.08 Å

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Processing

Software
NameVersionClassification
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONU

3onu


Resolution: 1.8→43.08 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 16.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1821 3193 5 %
Rwork0.1449 60688 -
obs0.1468 63881 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.22 Å2 / Biso mean: 18.6541 Å2 / Biso min: 5.25 Å2
Refinement stepCycle: final / Resolution: 1.8→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 80 737 5589
Biso mean--17.12 29.45 -
Num. residues----626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155065
X-RAY DIFFRACTIONf_angle_d1.4476945
X-RAY DIFFRACTIONf_chiral_restr0.084788
X-RAY DIFFRACTIONf_plane_restr0.009916
X-RAY DIFFRACTIONf_dihedral_angle_d11.9951782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2822X-RAY DIFFRACTION6.947TORSIONAL
12B2822X-RAY DIFFRACTION6.947TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.799-1.82590.2521330.19962523265695
1.8259-1.85440.25091380.17672617275599
1.8544-1.88480.20471370.16962609274699
1.8848-1.91730.22881390.15992644278399
1.9173-1.95210.2211400.15962645278599
1.9521-1.98970.20831360.16162597273399
1.9897-2.03030.19391410.15252667280899
2.0303-2.07450.22721380.15772627276599
2.0745-2.12270.19741400.143826552795100
2.1227-2.17580.20981380.143626342772100
2.1758-2.23460.18171410.145126672808100
2.2346-2.30040.18771390.142626472786100
2.3004-2.37460.19431400.139426532793100
2.3746-2.45950.18571390.143826462785100
2.4595-2.55790.16561400.143926492789100
2.5579-2.67430.21291380.142926262764100
2.6743-2.81530.15561400.14842662280299
2.8153-2.99170.17751390.15282651279099
2.9917-3.22260.17731390.1452640277999
3.2226-3.54670.1661410.14342664280599
3.5467-4.05960.16471400.13322655279599
4.0596-5.11340.15191390.11582655279498
5.1134-43.0940.15031380.14392655279397
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)
10.5218-0.2634-0.27621.2990.47591.77050.00780.03240.0393-0.0315-0.00430.0022-0.08980.055-0.0090.0788-0.0059-0.01450.0750.01280.08528.91438.88810.7693
22.83840.0345-0.08352.27440.01532.8639-0.0007-0.46470.11130.46030.0368-0.2461-0.26680.2178-0.05020.1664-0.0016-0.0410.1209-0.0080.12049.6359.070134.9347
30.54660.0335-0.12580.6879-0.21281.2468-0.00510.06910.0706-0.04990.03490.0527-0.1009-0.0452-0.02620.0687-0.0007-0.00560.07540.00460.08423.41067.784111.8718
43.35991.4416-0.28253.02920.21612.3222-0.06610.1262-0.2907-0.3230.0278-0.24270.19720.23370.03660.16680.00880.01230.1552-0.00590.080214.4912-4.5681-7.3248
51.52740.3173-0.29940.5261-1.52384.7189-0.05430.256-0.1833-0.30150.0268-0.13580.24280.33010.01840.2459-0.02310.05140.1928-0.03460.111217.0544-3.6597-12.9629
61.71850.5504-0.09360.9106-0.05940.66680.01550.0721-0.0060.0352-0.005-0.05680.04610.1026-0.01080.0710.011-0.00930.07970.00850.074122.3296-6.274721.7224
71.7794-0.31760.22241.0271-0.06380.86140.0175-0.0889-0.2380.0540.01850.08470.1403-0.0604-0.02780.107-0.0197-0.00640.06590.01880.10617.584-13.698927.511
81.26980.48760.25450.7369-0.1681.20790.0257-0.0632-0.00150.1353-0.0024-0.2431-0.01020.1672-0.01320.0795-0.012-0.03230.09190.00230.107227.0674-1.106331.3525
92.6396-0.0342-0.06661.17810.43961.91920.01110.14320.1243-0.0480.0185-0.1724-0.09860.1693-0.01940.0728-0.0040.0020.12120.0130.134436.64790.684919.6584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 332 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 333 through 354 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 355 through 472 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 473 through 521 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 522 through 538 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 224 through 295 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 296 through 426 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 427 through 455 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 456 through 538 )B0

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