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- PDB-6ld2: Zika NS5 polymerase domain -

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Basic information

Entry
Database: PDB / ID: 6ld2
TitleZika NS5 polymerase domain
ComponentsRNA-directed RNA polymerase NS5
KeywordsTRANSFERASE / Zika Polymerase NS5 RdRP RNA depdendant RNA polymerase
Function / homology
Function and homology information


response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding
Similarity search - Function
Photosystem II protein D1 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Chem-KY3 / Photosystem q(B) protein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsEl Sahili, A. / Lescar, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (Singapore)NRF2016-CRP001-063 Singapore
CitationJournal: J.Virol. / Year: 2020
Title: Non-nucleoside Inhibitors of Zika Virus RNA-Dependent RNA Polymerase.
Authors: Gharbi-Ayachi, A. / Santhanakrishnan, S. / Wong, Y.H. / Chan, K.W.K. / Tan, S.T. / Bates, R.W. / Vasudevan, S.G. / El Sahili, A. / Lescar, J.
History
DepositionNov 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: 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 / _citation_author.name
Revision 1.2Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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: RNA-directed RNA polymerase NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3054
Polymers74,9041
Non-polymers4013
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.94, 85.06, 69.74
Angle α, β, γ (deg.)90, 113.44, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA-directed RNA polymerase NS5 / NS5


Mass: 74904.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A024B7W1, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-KY3 / (1S,2S,4S,5R)-2,4-dimethoxy-5-thiophen-2-yl-cyclohexane-1-carboxylic acid


Mass: 270.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 10% PEG 6000, 0.2M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9538 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9538 Å / Relative weight: 1
ReflectionResolution: 1.4→55.65 Å / Num. obs: 132763 / % possible obs: 98.72 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.06
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.08589 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 13223 / CC1/2: 0.419

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TFR

5tfr


Resolution: 1.4→55.65 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.062 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.064 / SU Rfree Blow DPI: 0.066 / SU Rfree Cruickshank DPI: 0.064
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 6639 -RANDOM
Rwork0.202 ---
obs0.2032 132761 98.7 %-
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1-1.7186 Å20 Å2-0.7582 Å2
2--2.5438 Å20 Å2
3----4.2624 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.4→55.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 20 618 5275
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084851HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.916569HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1723SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes821HARMONIC5
X-RAY DIFFRACTIONt_it4851HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion596SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5035SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion15.42
LS refinement shellResolution: 1.4→1.45 Å
RfactorNum. reflection% reflection
Rfree0.3786 133 -
Rwork0.3789 --
obs--97.48 %

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