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- PDB-6gy9: Fucose-functionalized precision glycomacromolecules targeting hum... -

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Basic information

Entry
Database: PDB / ID: 6gy9
TitleFucose-functionalized precision glycomacromolecules targeting human norovirus capsid protein
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Norovirus / GII.10 / P domain / fucose / triazol
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
Chem-KBA / Capsid protein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsRuoff, K. / Kilic, T. / Hansman, G.S.
CitationJournal: Biomacromolecules / Year: 2018
Title: Fucose-Functionalized Precision Glycomacromolecules Targeting Human Norovirus Capsid Protein.
Authors: Bucher, K.S. / Yan, H. / Creutznacher, R. / Ruoff, K. / Mallagaray, A. / Grafmuller, A. / Dirks, J.S. / Kilic, T. / Weickert, S. / Rubailo, A. / Drescher, M. / Schmidt, S. / Hansman, G. / ...Authors: Bucher, K.S. / Yan, H. / Creutznacher, R. / Ruoff, K. / Mallagaray, A. / Grafmuller, A. / Dirks, J.S. / Kilic, T. / Weickert, S. / Rubailo, A. / Drescher, M. / Schmidt, S. / Hansman, G. / Peters, T. / Uetrecht, C. / Hartmann, L.
History
DepositionJun 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)69,2856
Polymers68,8392
Non-polymers4454
Water5,350297
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-6 kcal/mol
Surface area24180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.280, 80.370, 71.510
Angle α, β, γ (deg.)90.00, 101.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein


Mass: 34419.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5F4T5
#2: Sugar ChemComp-KBA / 2-(1H-1,2,3-triazol-1-yl)ethyl 6-deoxy-alpha-L-galactopyranoside / (2~{S},3~{S},4~{R},5~{S},6~{R})-2-methyl-6-[2-(1,2,3-triazol-1-yl)ethoxy]oxane-3,4,5-triol / 2-(1H-1,2,3-triazol-1-yl)ethyl 6-deoxy-alpha-L-galactoside / 2-(1H-1,2,3-triazol-1-yl)ethyl 6-deoxy-L-galactoside / 2-(1H-1,2,3-triazol-1-yl)ethyl 6-deoxy-galactoside


Type: L-saccharide / Mass: 259.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium nitrate, 0.1 M bis-tris propane (pH7.5), 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.83→35.02 Å / Num. obs: 61315 / % possible obs: 93.55 % / Redundancy: 2.7 % / Biso Wilson estimate: 25.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0411 / Rpim(I) all: 0.02932 / Rrim(I) all: 0.05075 / Net I/σ(I): 15.92
Reflection shellResolution: 1.83→1.89 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.5186 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 6006 / CC1/2: 0.867 / Rpim(I) all: 0.3773 / Rrim(I) all: 0.6452 / % possible all: 92.57

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSVERSION Jun 1, 2017data reduction
XSCALEVERSION Jun 1, 2017data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONU

3onu


Resolution: 1.83→34.17 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.45
RfactorNum. reflection% reflection
Rfree0.2324 3044 5 %
Rwork0.2004 --
obs0.202 60920 93.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4649 0 30 297 4976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074820
X-RAY DIFFRACTIONf_angle_d0.8036608
X-RAY DIFFRACTIONf_dihedral_angle_d2.6293334
X-RAY DIFFRACTIONf_chiral_restr0.056747
X-RAY DIFFRACTIONf_plane_restr0.006867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.85570.37781300.33862483X-RAY DIFFRACTION89
1.8557-1.88620.34471420.29872696X-RAY DIFFRACTION96
1.8862-1.91870.35851370.352596X-RAY DIFFRACTION95
1.9187-1.95360.48461290.45452497X-RAY DIFFRACTION88
1.9536-1.99110.29581390.25622637X-RAY DIFFRACTION95
1.9911-2.03180.27771430.20962706X-RAY DIFFRACTION97
2.0318-2.07590.23251430.20382727X-RAY DIFFRACTION97
2.0759-2.12420.26091430.20262711X-RAY DIFFRACTION96
2.1242-2.17730.24251400.2042666X-RAY DIFFRACTION96
2.1773-2.23620.22891430.21752701X-RAY DIFFRACTION96
2.2362-2.3020.40421250.31862373X-RAY DIFFRACTION85
2.302-2.37630.22141400.20882656X-RAY DIFFRACTION94
2.3763-2.46120.21441390.1932657X-RAY DIFFRACTION95
2.4612-2.55970.21231420.1922699X-RAY DIFFRACTION96
2.5597-2.67620.24491430.19842699X-RAY DIFFRACTION96
2.6762-2.81720.23991390.20972656X-RAY DIFFRACTION94
2.8172-2.99360.21991390.20352644X-RAY DIFFRACTION94
2.9936-3.22460.23511380.19622608X-RAY DIFFRACTION93
3.2246-3.54880.23521400.19922665X-RAY DIFFRACTION95
3.5488-4.06170.21221370.17422608X-RAY DIFFRACTION92
4.0617-5.11480.15681370.13462595X-RAY DIFFRACTION91
5.1148-34.170.1771360.15892596X-RAY DIFFRACTION90
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)
10.8002-0.1979-0.11770.84170.20042.2017-0.05280.02410.0769-0.004-0.0502-0.0262-0.26480.11450.09430.2626-0.0246-0.04960.1990.02030.23878.93919.919211.1813
21.013-0.04650.00170.9125-0.30071.6688-0.05140.00950.10730.05290.01130.0408-0.2904-0.06040.03530.23390.0057-0.02910.16580.00620.20111.357910.362917.2802
33.22361.21750.32042.35050.29444.0411-0.08750.3352-0.1639-0.27990.0704-0.15570.0960.2430.03120.23670.01340.02220.2601-0.00360.192715.9057-1.5781-5.678
42.23580.05470.33290.7534-0.12250.4490.15230.0321-0.2671-0.0691-0.0520.03640.15320.0576-0.11680.25480.0081-0.0450.2141-0.00040.248518.8993-8.30422.7219
52.0451-0.30470.71180.423-0.31141.05170.0805-0.1402-0.4607-0.01050.05720.12240.1338-0.1172-0.14540.1992-0.028-0.03820.17450.04960.27496.5821-10.721829.881
62.5978-0.3974-0.44040.99150.32211.39610.10090.06090.1228-0.06970.0043-0.2573-0.02520.3231-0.11450.20260.00430.0010.2571-0.00130.248733.68831.370224.1538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 327 )
2X-RAY DIFFRACTION2chain 'A' and (resid 328 through 455 )
3X-RAY DIFFRACTION3chain 'A' and (resid 456 through 538 )
4X-RAY DIFFRACTION4chain 'B' and (resid 225 through 327 )
5X-RAY DIFFRACTION5chain 'B' and (resid 328 through 426 )
6X-RAY DIFFRACTION6chain 'B' and (resid 427 through 538 )

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