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

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Basic information

Entry
Database: PDB / ID: 4ucy
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 / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTP binding / ATP binding / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile.
Similarity search - Domain/homology
Biological speciesHUMAN METAPNEUMOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.83 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. / 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
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)95,6456
Polymers95,3222
Non-polymers3234
Water1,54986
1
A: RNA-DIRECTED RNA POLYMERASE L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8233
Polymers47,6611
Non-polymers1612
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)47,8233
Polymers47,6611
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.230, 82.160, 183.120
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.15 % / 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: 2.83→82.16 Å / Num. obs: 28922 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 104.33 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13

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Processing

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

Resolution: 2.83→61.15 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.9301 / SU R Cruickshank DPI: 0.751 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.764 / SU Rfree Blow DPI: 0.288 / SU Rfree Cruickshank DPI: 0.292
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 1378 4.77 %RANDOM
Rwork0.1955 ---
obs0.1967 28861 99.87 %-
Displacement parametersBiso mean: 96.81 Å2
Baniso -1Baniso -2Baniso -3
1--4.6008 Å20 Å20 Å2
2---20.5003 Å20 Å2
3---25.1011 Å2
Refine analyzeLuzzati coordinate error obs: 0.454 Å
Refinement stepCycle: LAST / Resolution: 2.83→61.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6260 0 12 86 6358
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086402HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.048639HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2289SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes905HARMONIC5
X-RAY DIFFRACTIONt_it6402HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion20.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion836SEMIHARMONIC5
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_contact7085SEMIHARMONIC4
LS refinement shellResolution: 2.83→2.94 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2972 145 4.89 %
Rwork0.2571 2818 -
all0.259 2963 -
obs--99.87 %

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