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- PDB-4a8y: Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bac... -

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Basic information

Entry
Database: PDB / ID: 4a8y
TitleNon-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation
Components
  • 5'-D(*TP*TP*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3'
  • RNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / VIRAL POLYMERASE / TRANSFERASE
Function / homology
Function and homology information


RNA uridylyltransferase activity / virion component / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
Phage p2 RNA dependent RNA polymerase domain / Alpha-Beta Plaits - #1600 / Dihydrolipoamide Transferase / Dihydrolipoamide Transferase - #10 / Cystovirus, RNA-directed RNA polymerase, N-terminal / Cystovirus, RNA-directed RNA polymerase / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / Other non-globular / Globin-like ...Phage p2 RNA dependent RNA polymerase domain / Alpha-Beta Plaits - #1600 / Dihydrolipoamide Transferase / Dihydrolipoamide Transferase - #10 / Cystovirus, RNA-directed RNA polymerase, N-terminal / Cystovirus, RNA-directed RNA polymerase / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / Other non-globular / Globin-like / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHI6 (virus)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å
AuthorsWright, S. / Poranen, M.M. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
CitationJournal: J.Virol. / Year: 2012
Title: Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation.
Authors: Wright, S. / Poranen, M.M. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
History
DepositionNov 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: RNA-DIRECTED RNA POLYMERASE
B: RNA-DIRECTED RNA POLYMERASE
C: RNA-DIRECTED RNA POLYMERASE
F: 5'-D(*TP*TP*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3'
G: 5'-D(*TP*TP*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3'
H: 5'-D(*TP*TP*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,53111
Polymers237,9616
Non-polymers1,5705
Water00
1
A: RNA-DIRECTED RNA POLYMERASE
F: 5'-D(*TP*TP*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8524
Polymers79,3202
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-DIRECTED RNA POLYMERASE
G: 5'-D(*TP*TP*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8524
Polymers79,3202
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-10.4 kcal/mol
Surface area26280 Å2
MethodPISA
3
C: RNA-DIRECTED RNA POLYMERASE
H: 5'-D(*TP*TP*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8273
Polymers79,3202
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-13.2 kcal/mol
Surface area26400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.760, 89.290, 140.990
Angle α, β, γ (deg.)90.00, 101.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA-DIRECTED RNA POLYMERASE / PROTEIN P2 / P2 POLYMERASE


Mass: 75033.406 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI6 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P11124, RNA-directed RNA polymerase
#2: DNA chain 5'-D(*TP*TP*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3'


Mass: 4286.789 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 635 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 635 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, GLU 635 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 635 TO GLN ENGINEERED RESIDUE IN CHAIN C, GLU 635 TO GLN
Sequence detailsSYNTHETIC SEQUENCE FOR CHAIN F, G, AND H TO FORM A HAIRPIN WITH 4 BASE OVERHANG. THE MET 465 (ILE ...SYNTHETIC SEQUENCE FOR CHAIN F, G, AND H TO FORM A HAIRPIN WITH 4 BASE OVERHANG. THE MET 465 (ILE 457) CONFLICT IS OWING TO A SEQUENCE DIFFERENCE (CONFIRMED EXPERIMENTALLY) FROM THAT IN THE UNIPROT ENTRY.

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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: 2.74 Å3/Da / Density % sol: 55.08 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.4→68 Å / Num. obs: 30875 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 67.27 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10

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Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HHS

1hhs


Resolution: 3.41→67.61 Å / Cor.coef. Fo:Fc: 0.8511 / Cor.coef. Fo:Fc free: 0.8091 / Cross valid method: THROUGHOUT / σ(F): 0
Details: NUMBER OF RESTRAINT LIBRARIES USED: 8 REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ATP. NUMBER OF ATOMS WITH PROPER CCP4 ATOM ...Details: NUMBER OF RESTRAINT LIBRARIES USED: 8 REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ATP. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=15826. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=39. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 1545 5 %RANDOM
Rwork0.2177 ---
obs0.2196 30773 87 %-
Displacement parametersBiso mean: 119.24 Å2
Baniso -1Baniso -2Baniso -3
1-22.1189 Å20 Å25.078 Å2
2---68.0784 Å20 Å2
3---45.9595 Å2
Refine analyzeLuzzati coordinate error obs: 1.027 Å
Refinement stepCycle: LAST / Resolution: 3.41→67.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15610 216 41 0 15867
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00816271HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0522054HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5714SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes379HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2351HARMONIC5
X-RAY DIFFRACTIONt_it16271HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion18.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2012SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18513SEMIHARMONIC4
LS refinement shellResolution: 3.41→3.53 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.274 100 4.63 %
Rwork0.2465 2060 -
all0.2478 2160 -
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)
12.0630.73240.19680.52730.14231.84980.04920.27880.0721-0.08830.098-0.0184-0.0213-0.3607-0.1471-0.24740.0478-0.12850.3040.0496-0.36058.87251.614828.486
20.85250.37230.52980.69350.48531.5414-0.02410.3415-0.1610.09420.1893-0.08030.14940.4206-0.1652-0.16460.0774-0.12270.304-0.1179-0.361758.335821.037756.0906
31.7667-0.1753-1.92180.47090.74513.61690.32190.2897-0.0250.1063-0.21310.1121-0.4788-0.4003-0.1088-0.00020.1085-0.095-0.0161-0.0551-0.323-42.80193.5531-3.7602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESIDUES 1-664)
2X-RAY DIFFRACTION2(CHAIN B AND RESIDUES 1-664)
3X-RAY DIFFRACTION3(CHAIN C AND RESIDUES 1-664)

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