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Basic information

Entry
Database: PDB / ID: 1uvi
TitleThe structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 6nt RNA
Components
  • 5'-R(*UP*UP*UP*UP*CP*CP)-3'
  • RNA-directed RNA polymerase
KeywordsPOLYMERASE / POLYMERASE-COMPLEX / RNA-DEPENDENT RNA POLYMERASE COMPLEX WITH 6NT RNA OLIGONUCLEOTIDE / TRANSCRIPTION / STRUCTURAL PROTEIN
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
: / RNA / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesPseudomonas phage phi6 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSalgado, P.S. / Makeyev, E.V. / Butcher, S. / Bamford, D. / Stuart, D.I. / Grimes, J.M.
CitationJournal: Structure / Year: 2004
Title: The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase.
Authors: Salgado, P.S. / Makeyev, E.V. / Butcher, S.J. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
History
DepositionJan 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_ec / _entity.src_method / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.4Dec 13, 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
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_asym_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_asym_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

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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
D: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
E: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
F: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,2459
Polymers230,0806
Non-polymers1653
Water7,530418
1
A: RNA-directed RNA polymerase
D: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7483
Polymers76,6932
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RNA-directed RNA polymerase
E: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7483
Polymers76,6932
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: RNA-directed RNA polymerase
F: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7483
Polymers76,6932
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.130, 93.711, 140.741
Angle α, β, γ (deg.)90.00, 101.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.12605, -0.73008, -0.67164), (-0.78933, -0.48391, 0.37787), (-0.60089, 0.48252, -0.63727)76.28954, 16.94423, 79.51358
2given(0.12605, -0.73008, -0.67164), (-0.78933, -0.48391, 0.37787), (-0.60089, 0.48252, -0.63727)76.28954, 16.94423, 79.51358
3given(-0.16141, -0.75668, 0.63355), (0.77481, -0.49478, -0.39353), (0.61124, 0.42736, 0.66614)-59.38855, 6.76792, -27.90308
4given(-0.16141, -0.75668, 0.63355), (0.77481, -0.49478, -0.39353), (0.61124, 0.42736, 0.66614)-59.38855, 6.76792, -27.90308
DetailsTHE POLYMERASE IS A MONOMER IN SOLUTION, BUT SINCEIT IS IN COMPLEX WITH RNA IN THIS ENTRY, THE OLIGOMERIS ANNOTATED AS A DIMER

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Components

#1: Protein RNA-directed RNA polymerase / Protein P2


Mass: 74903.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phi6 (virus) / Gene: P2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11124, RNA-directed RNA polymerase
#2: RNA chain 5'-R(*UP*UP*UP*UP*CP*CP)-3'


Mass: 1790.069 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: COMMERCIALLY SUPPLIED BY OSWELL LTD / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: P2 IS ONE OF THE 4 STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID, WHICH IS RESPONSIBLE ...FUNCTION: P2 IS ONE OF THE 4 STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID, WHICH IS RESPONSIBLE FOR GENOMIC REPLICATION AND TRANSCRIPTION.

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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 Å3/Da / Density % sol: 59 %
Crystal growpH: 7.3
Details: 100MM HEPES PH7.3, 13% PEG 20000, 2MM MNCL2, 2% EG, 0.036MG PROTEIN INCUBATED WITH 0.006MM 6NT RNA, pH 7.30
Crystal grow
*PLUS
Method: other
Details: Butcher, S.J., (2000) Acta Crystallogr.,Sect.D, D56, 1473.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
210 %PEG80001reservoir
30.1 MMES1reservoirpH6.7

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 142476 / % possible obs: 97.8 % / Observed criterion σ(I): 1.6 / Redundancy: 11 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 13.3
Reflection shellResolution: 2.13→2.15 Å / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.6 / % possible all: 83.7
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. obs: 142686 / Num. measured all: 1522219 / Rmerge(I) obs: 0.126
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 83.7 % / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HHS

1hhs


Resolution: 2.15→19.93 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2609497.07 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: 6NT RNA OLIGO WAS CRYSTALLIZED ONLY 4NT (5'-UUCC-3') WERE TRACEABLE IN ED MAPS BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 7208 5.1 %RANDOM
Rwork0.23 ---
obs0.23 142476 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43 Å2 / ksol: 0.38218 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å20 Å2-3.29 Å2
2--11.24 Å20 Å2
3----8.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-20 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.15→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15795 231 3 418 16447
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.583
X-RAY DIFFRACTIONc_mcangle_it3.414
X-RAY DIFFRACTIONc_scbond_it4.234
X-RAY DIFFRACTIONc_scangle_it5.545
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 1102 5.2 %
Rwork0.318 20033 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

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