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- PDB-4ud0: X-ray structure and activities of an essential Mononegavirales L-... -

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Basic information

Entry
Database: PDB / ID: 4ud0
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
S-ADENOSYL-L-HOMOCYSTEINE / Large structural protein
Similarity search - Component
Biological speciesHUMAN METAPNEUMOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,1754
Polymers47,6291
Non-polymers5463
Water36020
1
B: RNA-DIRECTED RNA POLYMERASE L
hetero molecules

B: RNA-DIRECTED RNA POLYMERASE L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3508
Polymers95,2582
Non-polymers1,0926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_375y-2,x+2,-z1
Buried area2030 Å2
ΔGint-48.9 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.610, 75.610, 187.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 47629.090 Da / Num. of mol.: 1 / Fragment: METHYLTRANSFERASE DOMAIN, RESIDUES 1600-2005 / Mutation: YES
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.26 Å3/Da / Density % sol: 62.23 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorDate: May 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→62.65 Å / Num. obs: 10856 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 35.1 % / Biso Wilson estimate: 152.68 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→62.65 Å / Cor.coef. Fo:Fc: 0.9239 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.377
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 522 4.83 %RANDOM
Rwork0.1994 ---
obs0.2009 10817 99.74 %-
Displacement parametersBiso mean: 144.59 Å2
Baniso -1Baniso -2Baniso -3
1--18.4594 Å20 Å20 Å2
2---18.4594 Å20 Å2
3---36.9189 Å2
Refine analyzeLuzzati coordinate error obs: 0.77 Å
Refinement stepCycle: LAST / Resolution: 3.2→62.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 32 20 2892
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082935HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043962HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1043SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes425HARMONIC5
X-RAY DIFFRACTIONt_it2935HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion21.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion385SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle6HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3365SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.58 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2727 135 4.49 %
Rwork0.2465 2870 -
all0.2476 3005 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: -119.9282 Å / Origin y: 25.7664 Å / Origin z: 20.0235 Å
111213212223313233
T-0.6203 Å20.1621 Å2-0.2018 Å2--0.2684 Å2-0.0881 Å2---0.2076 Å2
L-0.8818 °20.2491 °2-0.6197 °2-1.7825 °2-2.0051 °2--1.1862 °2
S-0.0306 Å °-0.0044 Å °0.2223 Å °0.2612 Å °0.0501 Å °-0.3611 Å °-0.0933 Å °0.3627 Å °-0.0195 Å °
Refinement TLS groupSelection details: { B|* }

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