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- PDB-6b6i: 2.4A resolution structure of human Norovirus GII.4 protease -

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Basic information

Entry
Database: PDB / ID: 6b6i
Title2.4A resolution structure of human Norovirus GII.4 protease
Components3C-like protease
KeywordsVIRAL PROTEIN / Protease / 3C-like protease / viral protease / GII.4 / Minerva
Function / homology
Function and homology information


calicivirin / RNA-protein covalent cross-linking / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding
Similarity search - Function
Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases ...Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesNorovirus GII.4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsMuzzarelli, K.M. / Kuiper, B.D. / Spellmon, N.S. / Hackett, J. / Brunzelle, J.S. / Kovari, I.A. / Amblard, F. / Yang, Z. / Schinazi, R.F. / Kovari, L.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Wayne State University United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural and Antiviral Studies of the Human Norovirus GII.4 Protease.
Authors: Muzzarelli, K.M. / Kuiper, B. / Spellmon, N. / Brunzelle, J. / Hackett, J. / Amblard, F. / Zhou, S. / Liu, P. / Kovari, I.A. / Yang, Z. / Schinazi, R.F. / Kovari, L.C.
History
DepositionOct 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: 3C-like protease
B: 3C-like protease
C: 3C-like protease
D: 3C-like protease
E: 3C-like protease
F: 3C-like protease
G: 3C-like protease
H: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)153,9378
Polymers153,9378
Non-polymers00
Water1,838102
1
A: 3C-like protease
B: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)38,4842
Polymers38,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-10 kcal/mol
Surface area16200 Å2
MethodPISA
2
C: 3C-like protease
D: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)38,4842
Polymers38,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-9 kcal/mol
Surface area15970 Å2
MethodPISA
3
E: 3C-like protease
F: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)38,4842
Polymers38,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-10 kcal/mol
Surface area16140 Å2
MethodPISA
4
G: 3C-like protease
H: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)38,4842
Polymers38,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-10 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.940, 112.940, 153.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
3C-like protease /


Mass: 19242.172 Da / Num. of mol.: 8 / Fragment: UNP residues 982-1162 / Mutation: C139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A076EGG6, UniProt: A0A0K2E2J2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, Lithium Sulfate, Tris, MES, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.44→52.99 Å / Num. obs: 81454 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.4
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.355 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6060 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IPH

2iph


Resolution: 2.44→51.123 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.16
RfactorNum. reflection% reflection
Rfree0.222 3994 4.91 %
Rwork0.1796 --
obs0.1816 81400 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.44→51.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10514 0 0 102 10616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810777
X-RAY DIFFRACTIONf_angle_d1.20714599
X-RAY DIFFRACTIONf_dihedral_angle_d13.573912
X-RAY DIFFRACTIONf_chiral_restr0.0461637
X-RAY DIFFRACTIONf_plane_restr0.0051874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.46870.33781220.30392675X-RAY DIFFRACTION100
2.4687-2.49880.31171060.29562734X-RAY DIFFRACTION100
2.4988-2.53050.35751160.29622663X-RAY DIFFRACTION100
2.5305-2.56380.31261410.27862720X-RAY DIFFRACTION100
2.5638-2.59890.33961600.27922592X-RAY DIFFRACTION100
2.5989-2.6360.34311360.26612663X-RAY DIFFRACTION100
2.636-2.67530.27951360.24662718X-RAY DIFFRACTION100
2.6753-2.71710.31581480.23752603X-RAY DIFFRACTION100
2.7171-2.76170.27381400.23432714X-RAY DIFFRACTION100
2.7617-2.80930.27061520.23362592X-RAY DIFFRACTION100
2.8093-2.86040.2791330.23622693X-RAY DIFFRACTION100
2.8604-2.91540.27461260.22532695X-RAY DIFFRACTION100
2.9154-2.97490.23991160.23842722X-RAY DIFFRACTION100
2.9749-3.03960.29351420.23652635X-RAY DIFFRACTION100
3.0396-3.11030.30521520.23892685X-RAY DIFFRACTION100
3.1103-3.18810.27851600.22542594X-RAY DIFFRACTION100
3.1881-3.27420.25051760.20972640X-RAY DIFFRACTION100
3.2742-3.37060.28411280.19952711X-RAY DIFFRACTION100
3.3706-3.47930.23711300.19912652X-RAY DIFFRACTION100
3.4793-3.60370.25361620.18662658X-RAY DIFFRACTION100
3.6037-3.74790.23331440.18132676X-RAY DIFFRACTION100
3.7479-3.91840.23961200.17562683X-RAY DIFFRACTION100
3.9184-4.12490.19561880.15742597X-RAY DIFFRACTION100
4.1249-4.38320.1711540.14872659X-RAY DIFFRACTION100
4.3832-4.72140.15261260.12412698X-RAY DIFFRACTION100
4.7214-5.19620.16011300.12982662X-RAY DIFFRACTION100
5.1962-5.94710.19161200.15362712X-RAY DIFFRACTION100
5.9471-7.48890.1921280.15722677X-RAY DIFFRACTION100
7.4889-51.13450.1791020.15382683X-RAY DIFFRACTION100

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