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- PDB-4z4u: Crystal structure of GII.10 P domain in complex with 37.5mM fucose -

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Basic information

Entry
Database: PDB / ID: 4z4u
TitleCrystal structure of GII.10 P domain in complex with 37.5mM 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 / Capsid protein
Similarity search - Component
Biological speciesNorovirus GII.10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 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)69,83812
Polymers69,0132
Non-polymers82510
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint13 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.317, 78.774, 68.512
Angle α, β, γ (deg.)90.000, 99.520, 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: 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.: 8 / 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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
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: 1.885→43.15 Å / Num. obs: 54715 / % possible obs: 98.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.07839 / Net I/σ(I): 11.56
Reflection shellResolution: 1.885→1.953 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.6084 / Mean I/σ(I) obs: 1.81 / Rejects: 0 / % possible all: 95.03

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.15 Å43.19 Å
Translation7.15 Å43.19 Å

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Processing

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

3onu


Resolution: 1.89→43.1 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 2736 5 %
Rwork0.1571 51957 -
obs0.1592 54693 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.04 Å2 / Biso mean: 28.3045 Å2 / Biso min: 10.06 Å2
Refinement stepCycle: final / Resolution: 1.89→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 58 540 5333
Biso mean--31.15 35.81 -
Num. residues----620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074960
X-RAY DIFFRACTIONf_angle_d1.0626788
X-RAY DIFFRACTIONf_chiral_restr0.047768
X-RAY DIFFRACTIONf_plane_restr0.006892
X-RAY DIFFRACTIONf_dihedral_angle_d11.6811751
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2794X-RAY DIFFRACTION5.999TORSIONAL
12B2794X-RAY DIFFRACTION5.999TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8853-1.91780.31571250.25992371249691
1.9178-1.95270.30781360.23322591272799
1.9527-1.99030.31061350.22882568270399
1.9903-2.03090.24781370.205525932730100
2.0309-2.0750.21881370.19382609274699
2.075-2.12330.21321370.1822609274699
2.1233-2.17640.24471370.17912602273999
2.1764-2.23520.2371360.17732579271599
2.2352-2.3010.19771370.168225992736100
2.301-2.37530.22161390.157726412780100
2.3753-2.46020.21791380.159626172755100
2.4602-2.55870.19451360.15972596273299
2.5587-2.67510.20941380.16012616275499
2.6751-2.81610.22161380.161126202758100
2.8161-2.99250.21071380.16192619275799
2.9925-3.22350.21081370.15982606274399
3.2235-3.54770.18291370.14462605274299
3.5477-4.06080.17621390.13612633277299
4.0608-5.11480.13631380.11042622276099
5.1148-43.20580.14931410.1412661280299
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)
10.6686-0.1134-0.25181.7890.70592.3448-0.00110.09590.0231-0.180.0121-0.026-0.07980.0308-0.00690.1518-0.0146-0.00540.15240.00540.134511.00064.97836.7401
21.07710.29450.15831.6822-0.88353.42030.0094-0.07830.1010.15860.04240.023-0.3151-0.1257-0.04680.18890.0245-0.00510.1244-0.01180.1563.512314.18523.3511
30.5577-0.0972-0.11131.3403-0.3311.385-0.07050.15550.0686-0.24150.11430.157-0.0894-0.1305-0.03330.159-0.0214-0.03060.18170.01220.13690.92526.84386.4965
42.44830.7377-0.21621.1144-0.08792.9662-0.05240.2163-0.1922-0.25930.0888-0.14920.14640.2901-0.04290.24640.00260.04010.2139-0.03070.147515.8427-2.436-6.061
52.12310.76880.02991.8454-0.07970.8150.0456-0.0098-0.17730.018-0.004-0.1960.10440.0601-0.02470.13320.0128-0.01530.11470.00160.133318.2462-8.684422.4891
62.9053-0.94890.69821.4939-0.41361.37180.0019-0.1128-0.22920.07350.03140.0720.0912-0.0525-0.04850.1477-0.0298-0.00450.10250.02330.1328.1572-12.054928.07
72.14520.0132-0.21081.3550.38220.92020.0210.1063-0.016-0.12830.0736-0.5021-0.11860.233-0.09330.1481-0.01990.01610.2103-0.01810.302533.96740.628622.6095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 294 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 295 through 390 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 391 through 455 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 538 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 224 through 318 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 319 through 426 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 427 through 538 )B0

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