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- PDB-6nu9: Crystal Structure of a Zinc-Binding Non-Structural Protein from t... -

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Basic information

Entry
Database: PDB / ID: 6nu9
TitleCrystal Structure of a Zinc-Binding Non-Structural Protein from the Hepatitis E Virus
ComponentsZinc-Binding Non-Structural Protein
KeywordsVIRAL PROTEIN / HEV / Non-Structural Protein / Zinc-Binding
Function / homology
Function and homology information


mRNA methyltransferase activity / RNA processing / cysteine-type peptidase activity / helicase activity / viral protein processing / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding
Similarity search - Function
Hepatitis E virus, cysteine peptidase / Hepatitis E virus, hinge domain / Hepatitis E cysteine protease / Protein of unknown function (DUF3729) / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase ...Hepatitis E virus, cysteine peptidase / Hepatitis E virus, hinge domain / Hepatitis E cysteine protease / Protein of unknown function (DUF3729) / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NITRITE ION / Methyltransferase
Similarity search - Component
Biological speciesHepatitis E virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.761 Å
AuthorsProudfoot, A. / Bussiere, D.
CitationJournal: J.Virol. / Year: 2019
Title: First Crystal Structure of a Nonstructural Hepatitis E Viral Protein Identifies a Putative Novel Zinc-Binding Protein.
Authors: Proudfoot, A. / Hyrina, A. / Holdorf, M. / Frank, A.O. / Bussiere, D.
History
DepositionJan 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 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 / _citation_author.identifier_ORCID
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc-Binding Non-Structural Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6414
Polymers19,4381
Non-polymers2043
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-36 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.399, 64.399, 158.901
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-202-

NO2

21A-202-

NO2

31A-464-

HOH

41A-519-

HOH

51A-601-

HOH

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Components

#1: Protein Zinc-Binding Non-Structural Protein


Mass: 19437.670 Da / Num. of mol.: 1 / Fragment: UNP residues 510-691
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q89444
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 18% w/v PEG3350, 180 mM lithium nitrate, 10 mM nickel chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 300K / Detector: PIXEL / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.761→52.624 Å / Num. obs: 20137 / % possible obs: 99.9 % / Redundancy: 33.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.038 / Net I/σ(I): 13.4
Reflection shellResolution: 1.76→1.82 Å / Rmerge(I) obs: 1.028 / Num. unique obs: 1960 / CC1/2: 0.339 / Rpim(I) all: 0.334

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHENIX1.14_3260phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 1.761→52.624 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.59
RfactorNum. reflection% reflection
Rfree0.2691 952 4.73 %
Rwork0.2369 --
obs0.2385 20136 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.58 Å2 / Biso mean: 17.817 Å2 / Biso min: 2.57 Å2
Refinement stepCycle: final / Resolution: 1.761→52.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 10 339 1588
Biso mean--36.64 29.37 -
Num. residues----168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.761-1.85390.36731160.368226732789
1.8539-1.970.33131340.297826712805
1.97-2.12210.29221310.271326812812
2.1221-2.33570.29771360.247927062842
2.3357-2.67370.28921380.242527242862
2.6737-3.36850.23711260.20627832909
3.3685-52.64740.22661710.185629463117
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)
10.60470.49080.48832.0401-0.84062.3141-0.1307-0.0324-0.02450.13070.12310.11270.093-0.39110.0710.02640.07140.07390.1299-0.0319-0.00410.250416.099477.3104
21.4869-0.2059-0.30241.07330.10892.0734-0.17380.07850.150.06140.09240.0535-0.2201-0.14070.0440.04230.13320.01320.0208-0.08590.02516.737618.361279.1289
31.8442-0.79650.89930.9566-0.78720.6977-0.0586-0.10930.26360.09220.0417-0.0359-0.1403-0.01420.06290.12970.0784-0.03770.1494-0.02660.080410.692823.531584.3165
45.2126-0.3508-2.45242.04730.40283.38770.22940.24340.2176-0.42090.0061-0.5282-0.21190.2269-0.27440.23810.0081-0.04620.0758-0.11150.28885.228434.509274.1594
51.50790.0482-1.7311.5736-0.16973.3829-0.08690.02820.15610.0575-0.02480.086-0.1933-0.29620.07590.10140.0679-0.01570.1754-0.03650.0757-6.751530.307677.6972
61.3252-1.16250.80293.2532-0.93332.16320.0209-0.0241-0.14270.1420.13280.35140.029-0.4516-0.1330.06340.0204-0.01240.1087-0.01470.0696-7.040120.01176.9812
70.47030.0557-0.67371.1538-0.04190.978-0.1339-0.0205-0.21510.31130.04140.10680.1829-0.02850.02990.07050.0388-0.00110.089-0.00680.05460.201412.806777.8217
83.7064-0.01841.15541.70490.22122.8467-0.13340.27230.3434-0.2130.1351-0.2347-0.21250.32790.02230.0842-0.0525-0.00010.1481-0.10720.151917.734819.782570.0745
95.7350.4359-1.24944.44551.11533.5933-0.0410.3870.3412-0.32660.1077-0.0901-0.4913-0.0164-0.04010.0738-0.027-0.07250.0449-0.04760.142210.327725.692370.5676
100.5137-0.5934-0.53891.8843-0.74482.10890.0426-0.19230.50130.24060.0482-0.7059-0.35160.4476-0.10770.13780.0164-0.01770.1702-0.10530.27258.143426.393178.3217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 28 )A7 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 60 )A29 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 70 )A61 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 85 )A71 - 85
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 98 )A86 - 98
6X-RAY DIFFRACTION6chain 'A' and (resid 99 through 116 )A99 - 116
7X-RAY DIFFRACTION7chain 'A' and (resid 117 through 134 )A117 - 134
8X-RAY DIFFRACTION8chain 'A' and (resid 135 through 153 )A135 - 153
9X-RAY DIFFRACTION9chain 'A' and (resid 154 through 168 )A154 - 168
10X-RAY DIFFRACTION10chain 'A' and (resid 169 through 182 )A169 - 182

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