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

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Basic information

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


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity ...NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase 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
ADENOSINE / GUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYLMETHIONINE / RNA-directed RNA polymerase L / Large structural protein
Similarity search - Component
Biological speciesHUMAN METAPNEUMOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 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 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Jun 14, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)98,47517
Polymers95,3222
Non-polymers3,15315
Water6,882382
1
A: RNA-DIRECTED RNA POLYMERASE L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1928
Polymers47,6611
Non-polymers1,5317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-DIRECTED RNA POLYMERASE L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2849
Polymers47,6611
Non-polymers1,6238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.220, 83.610, 182.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 47661.152 Da / Num. of mol.: 2 / Fragment: UNP 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: Q6WB93, UniProt: Q91L20*PLUS

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Non-polymers , 6 types, 397 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 3.21 Å3/Da / Density % sol: 61.71 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.21→83.6 Å / Num. obs: 62253 / % possible obs: 99.9 % / Observed criterion σ(I): 1.4 / Redundancy: 13.2 % / Biso Wilson estimate: 65.53 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.4
Reflection shellResolution: 2.21→9.88 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.21→44.2 Å / Cor.coef. Fo:Fc: 0.9464 / Cor.coef. Fo:Fc free: 0.9502 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.144 / SU Rfree Cruickshank DPI: 0.143
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 3154 5.07 %RANDOM
Rwork0.1903 ---
obs0.1909 62253 99.9 %-
Displacement parametersBiso mean: 69.94 Å2
Baniso -1Baniso -2Baniso -3
1--4.97 Å20 Å20 Å2
2---8.545 Å20 Å2
3---13.515 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: LAST / Resolution: 2.21→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5943 0 200 382 6525
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086300HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.978526HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2262SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes139HARMONIC2
X-RAY DIFFRACTIONt_gen_planes958HARMONIC5
X-RAY DIFFRACTIONt_it6300HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion17.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion816SEMIHARMONIC5
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_contact7146SEMIHARMONIC4
LS refinement shellResolution: 2.21→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2515 219 4.82 %
Rwork0.2327 4322 -
all0.2336 4541 -
obs--99.9 %
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)
10.5582-0.0995-0.10511.46470.81331.926-0.0298-0.05140.02730.10830.0965-0.11790.07760.1697-0.0666-0.08260.08110.00410.0256-0.0001-0.0811-24.0854.8988-38.9759
22.19240.34630.06811.93321.07972.2475-0.08590.0482-0.0325-0.052-0.04660.14620.2046-0.02070.1326-0.0740.04650.0523-0.1124-0.0041-0.1448-34.5992-3.4888-52.1994
32.10680.217-0.76162.54590.60471.6570.04210.01050.258-0.02040.0953-0.5431-0.22490.3781-0.1374-0.2004-0.0050.00010.0292-0.0401-0.0696-15.408519.0837-39.2717
41.3013-0.29290.74880.32230.15692.505-0.04470.0601-0.1079-0.01910.0582-0.01720.01380.0539-0.0136-0.00230.05290.0091-0.0871-0.0008-0.0594-21.68437.4866-9.8881
51.46140.34560.45941.08660.08741.5456-0.0278-0.04170.02590.0311-0.0335-0.03-0.01110.13330.0613-0.10650.0413-0.0111-0.04780.0306-0.0966-18.781614.26154.3492
62.27280.08010.14492.0507-0.75471.93810.085-0.1288-0.52870.06240.03420.28760.4419-0.1512-0.1193-0.032-0.0167-0.0417-0.18510.0177-0.0312-40.1393-5.0532-2.71

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