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- PDB-5hzb: Crystal structure of GII.10 P domain in complex with 2-fucosyllac... -

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Basic information

Entry
Database: PDB / ID: 5hzb
TitleCrystal structure of GII.10 P domain in complex with 2-fucosyllactose (2'FL)
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / Norovirus capsid / P domain / HMO / human milk / 2-fucosyllactose / Virus
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / 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 ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / 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 GII.10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.553 Å
AuthorsHansman, G.S. / Koromyslova, A.D. / Singh, B.K.S.
CitationJournal: J.Virol. / Year: 2016
Title: Structural Basis for Norovirus Inhibition by Human Milk Oligosaccharides.
Authors: Weichert, S. / Koromyslova, A. / Singh, B.K. / Hansman, S. / Jennewein, S. / Schroten, H. / Hansman, G.S.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: 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 / 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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7507
Polymers69,0132
Non-polymers7375
Water12,953719
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint8 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.680, 78.900, 71.070
Angle α, β, γ (deg.)90.000, 102.290, 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 / Capsid


Mass: 34506.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.10 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5F4T5
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Sodium Nitrate, Bis-Tris Propane, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.55→42.81 Å / Num. obs: 94121 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 16.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rsym value: 0.04 / Net I/σ(I): 15.47
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.55-1.650.2822.59193.9
1.65-1.760.1824.22196.6
1.76-1.90.1176.76193.6
1.9-2.080.0811.14180.9
2.08-2.330.05416.49188.9
2.33-2.690.03523.18195.7
2.69-3.290.02332.28195.7
3.29-4.640.01843.87189.8
4.64-44.0520.01546.67195.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.43 Å42.81 Å
Translation5.43 Å42.81 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3onu

3onu


Resolution: 1.553→42.808 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.2 / Phase error: 18.97
RfactorNum. reflection% reflection
Rfree0.1953 7571 4.98 %
Rwork0.1636 --
obs0.1652 94095 75.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.91 Å2 / Biso mean: 22.5959 Å2 / Biso min: 9.26 Å2
Refinement stepCycle: final / Resolution: 1.553→42.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4765 0 49 719 5533
Biso mean--29.41 32.75 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075003
X-RAY DIFFRACTIONf_angle_d1.0896861
X-RAY DIFFRACTIONf_chiral_restr0.046776
X-RAY DIFFRACTIONf_plane_restr0.006903
X-RAY DIFFRACTIONf_dihedral_angle_d11.6211796
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2762X-RAY DIFFRACTION4.167TORSIONAL
12B2762X-RAY DIFFRACTION4.167TORSIONAL
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 (%)
1.5532-1.57090.2512270.2594290451767
1.5709-1.58930.25692410.23644927516876
1.5893-1.60870.23192420.22434590483272
1.6087-1.62910.24382610.22044860512177
1.6291-1.65050.2522640.20915063532779
1.6505-1.67310.21162560.19594951520779
1.6731-1.6970.22212630.18845076533979
1.697-1.72240.23092560.19554963521978
1.7224-1.74930.21212710.18575061533279
1.7493-1.7780.1922650.17115131539680
1.778-1.80860.21252760.16985046532281
1.8086-1.84150.17722700.16165124539480
1.8415-1.87690.19992560.18364881513775
1.8769-1.91530.32111840.25263467365155
1.9153-1.95690.24951740.24223496367055
1.9569-2.00240.22192370.18154608484572
2.0024-2.05250.21722480.18184635488372
2.0525-2.1080.23712070.18383841404861
2.108-2.170.18672560.17015023527979
2.17-2.24010.20072480.1844694494274
2.2401-2.32010.20962140.18234285449967
2.3201-2.4130.21422650.15315291555683
2.413-2.52280.20212760.15835295557183
2.5228-2.65580.18132800.1635098537880
2.6558-2.82220.19082610.17074742500375
2.8222-3.040.19172760.15475288556483
3.04-3.34580.20442840.15645320560484
3.3458-3.82970.18792450.14244953519877
3.8297-4.8240.14652740.11935097537180
4.824-42.82460.15312940.1345455574986
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)
10.2571-0.0690.04640.0575-0.02130.7446-0.040.04970.0149-0.0077-0.03340.0157-0.11610.0786-0.00060.1467-0.0118-0.01330.10390.00260.12458.52148.810211.2471
20.4185-0.0202-0.0670.2188-0.20840.4025-0.02990.00880.03550.01390.0180.0329-0.1174-0.0684-00.1490.0085-0.00570.1025-0.00340.11781.26999.041817.1073
30.36830.027-0.05840.2852-0.11320.2594-0.02790.0662-0.0962-0.07190.0084-0.02180.02560.1050.04410.1474-0.0140.03680.2009-0.01860.112615.857-2.4309-5.7041
40.01640.0245-0.01620.0219-0.0046-0.0053-0.01350.35130.3356-0.08470.0310.09260.01750.23340.00120.16130.01930.03840.3290.00960.205233.7285-0.386810.686
50.0181-0.01760.00110.0073-0.00440.0119-0.0511-0.05230.0136-0.0528-0.0122-0.0216-0.0884-0.0132-00.140.006-0.00210.11990.00530.130922.00761.918421.0789
60.01310.0092-0.0181-0.0138-0.00190.00760.0506-0.0620.06990.00490.0420.0230.00480.020300.105-0.00930.01720.1404-0.00930.13621.94423.210627.2548
70.01160.0039-0.00950.0119-0.02180.01160.0833-0.1556-0.10740.0331-0.0473-0.07180.10260.1699-00.15270.0139-0.02910.2372-0.00360.176829.4112-7.641436.3279
80.00050.02280.0052-0.0070.0210.02890.05370.0755-0.1232-0.03520.0238-0.01550.04050.1029-00.130.02770.00620.1527-0.01810.168923.6585-11.116918.2591
90.0657-0.00190.04430.05630.01770.10820.0992-0.1498-0.15970.0438-0.05850.09240.03670.00550.01610.1311-0.0397-0.02030.12370.01530.21981.3027-14.884528.5622
100.23180.0905-0.15840.0427-0.04680.32250.13210.1026-0.27750.06530.03870.07440.2577-0.13150.03840.2175-0.0003-0.0540.1493-0.02920.2515.9954-19.164721.1177
110.0297-0.03950.00920.0894-0.00090.14590.18120.0694-0.1499-0.11470.04720.00470.10160.06140.03440.19680.0322-0.04740.1063-0.02410.216617.3638-20.451220.9971
120.0419-0.0441-0.0340.0528-0.04550.0563-0.0301-0.0007-0.0986-0.00480.04010.03110.00880.02180.00010.12660.006-0.00380.11390.00890.13654.5341-8.648725.6888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 327 )A225 - 327
2X-RAY DIFFRACTION2chain 'A' and (resid 328 through 455 )A328 - 455
3X-RAY DIFFRACTION3chain 'A' and (resid 456 through 538 )A456 - 538
4X-RAY DIFFRACTION4chain 'B' and (resid 224 through 233 )B224 - 233
5X-RAY DIFFRACTION5chain 'B' and (resid 234 through 241 )B234 - 241
6X-RAY DIFFRACTION6chain 'B' and (resid 242 through 251 )B242 - 251
7X-RAY DIFFRACTION7chain 'B' and (resid 252 through 261 )B252 - 261
8X-RAY DIFFRACTION8chain 'B' and (resid 262 through 282 )B262 - 282
9X-RAY DIFFRACTION9chain 'B' and (resid 283 through 301 )B283 - 301
10X-RAY DIFFRACTION10chain 'B' and (resid 302 through 317 )B302 - 317
11X-RAY DIFFRACTION11chain 'B' and (resid 318 through 327 )B318 - 327
12X-RAY DIFFRACTION12chain 'B' and (resid 328 through 343 )B328 - 343

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