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- PDB-4ucz: X-ray structure and activities of an essential Mononegavirales L-... -

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Basic information

Entry
Database: PDB / ID: 4ucz
TitleX-ray structure and activities of an essential Mononegavirales L- protein domain
ComponentsRNA-DIRECTED RNA POLYMERASE L
KeywordsTRANSFERASE / CAPPING / L PROTEIN / ROSSMANN / TRIPHOSPHATASE
Function / homology
Function and homology information


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTP binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile.
Similarity search - Domain/homology
GUANOSINE / GUANOSINE-5'-TRIPHOSPHATE / Large structural protein
Similarity search - Component
Biological speciesHUMAN METAPNEUMOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsPaesen, G.C. / Collet, A. / Sallamand, C. / Debart, F. / Vasseur, J.J. / Canard, B. / Decroly, E. / Grimes, J.M.
CitationJournal: Nat.Commun. / Year: 2015
Title: X-Ray Structure and Activities of an Essential Mononegavirales L-Protein Domain.
Authors: Paesen, G.C. / Collet, A. / Sallamand, C. / Debart, F. / Vasseur, J.J. / Canard, B. / Decroly, E. / Grimes, J.M.
History
DepositionDec 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-DIRECTED RNA POLYMERASE L
B: RNA-DIRECTED RNA POLYMERASE L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2606
Polymers95,3222
Non-polymers9374
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-7.6 kcal/mol
Surface area35620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.800, 83.710, 182.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-DIRECTED RNA POLYMERASE L / LARGE STRUCTURAL PROTEIN


Mass: 47661.152 Da / Num. of mol.: 2 / Fragment: METHYLTRANSFERASE DOMAIN, RESIDUES 1600-2005
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN METAPNEUMOVIRUS / Plasmid: POPIN_E / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q91L20
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.07 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.99→78.8 Å / Num. obs: 25194 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.5 % / Biso Wilson estimate: 109.18 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 45.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→76.1 Å / Cor.coef. Fo:Fc: 0.9286 / Cor.coef. Fo:Fc free: 0.9177 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.353
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1182 4.76 %RANDOM
Rwork0.1973 ---
obs0.1992 24839 98.78 %-
Displacement parametersBiso mean: 99.64 Å2
Baniso -1Baniso -2Baniso -3
1--19.8651 Å20 Å20 Å2
2---3.9573 Å20 Å2
3---23.8224 Å2
Refine analyzeLuzzati coordinate error obs: 0.468 Å
Refinement stepCycle: LAST / Resolution: 2.99→76.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6142 0 54 80 6276
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086343HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.018575HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2273SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes146HARMONIC2
X-RAY DIFFRACTIONt_gen_planes922HARMONIC5
X-RAY DIFFRACTIONt_it6343HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion18.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion827SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance8HARMONIC1
X-RAY DIFFRACTIONt_utility_angle12HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7067SEMIHARMONIC4
LS refinement shellResolution: 2.99→3.12 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3692 141 4.8 %
Rwork0.2622 2797 -
all0.2674 2938 -
obs--98.78 %

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