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

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Basic information

Entry
Database: PDB / ID: 4ucj
TitleX-ray structure and activities of an essential Mononegavirales L- protein domain
ComponentsRNA-DIRECTED RNA POLYMERASE L
KeywordsTRANSFERASE / HUMAN METAPNEUMOVIRUS / 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
RNA-directed RNA polymerase L / Large structural protein
Similarity search - Component
Biological speciesHUMAN METAPNEUMOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 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 1.0Nov 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 1.2Oct 23, 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 / 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 / _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
A: RNA-DIRECTED RNA POLYMERASE L
B: RNA-DIRECTED RNA POLYMERASE L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,03010
Polymers95,3222
Non-polymers7078
Water1,02757
1
A: RNA-DIRECTED RNA POLYMERASE L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0155
Polymers47,6611
Non-polymers3544
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)48,0155
Polymers47,6611
Non-polymers3544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.100, 84.530, 181.220
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, 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
#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.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.3 Å3/Da / Density % sol: 62.71 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.26→42.26 Å / Num. obs: 20356 / % possible obs: 99.9 % / Observed criterion σ(I): 1.4 / Redundancy: 12.8 % / Biso Wilson estimate: 134.4 Å2 / Rmerge(I) obs: 0.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.26→42.26 Å / Cor.coef. Fo:Fc: 0.9178 / Cor.coef. Fo:Fc free: 0.8954 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.387
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1042 5.13 %RANDOM
Rwork0.1859 ---
obs0.1876 20304 99.92 %-
Displacement parametersBiso mean: 113.16 Å2
Baniso -1Baniso -2Baniso -3
1--21.2555 Å20 Å20 Å2
2---14.9723 Å20 Å2
3---36.2278 Å2
Refine analyzeLuzzati coordinate error obs: 0.753 Å
Refinement stepCycle: LAST / Resolution: 3.26→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6014 0 32 57 6103
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086169HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.988321HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2199SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes868HARMONIC5
X-RAY DIFFRACTIONt_it6169HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.12
X-RAY DIFFRACTIONt_other_torsion19.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion799SEMIHARMONIC5
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_contact6758SEMIHARMONIC4
LS refinement shellResolution: 3.26→3.44 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3111 145 5.02 %
Rwork0.2534 2743 -
all0.2562 2888 -
obs--99.92 %
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)
11.9270.42380.03172.8263-1.28971.766-0.13940.0364-0.00760.15940.11990.2662-0.2143-0.37340.0195-0.15850.1445-0.0238-0.035-0.02950.053327.6414-5.5535-45.4296
22.13380.5324-0.97511.62-0.17051.4770.0861-0.09120.18340.1129-0.08360.0037-0.191-0.1029-0.00250.2020.12960.02040.0405-0.08210.199825.7517-7.72160.687

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