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- PDB-1uvn: The structural basis for RNA specificity and Ca2 inhibition of an... -

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Basic information

Entry
Database: PDB / ID: 1uvn
TitleThe structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 ca2+ inhibition complex
Components
  • 5'-R(*UP*UP*UP*UP*CP*CP)-3'
  • RNA-directed RNA polymerase
KeywordsPOLYMERASE / RNA-DEPENDENT RNA POLYMERASE CA INHIBITION COMPLEX WITH 6NT RNA OLIGONUCLEOTIDE / GTP / MN / TRANSCRIPTION
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
GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesPseudomonas phage phi6 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 26, 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 / _entity_name_com.name / _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: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
C: RNA-directed RNA polymerase
D: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
E: RNA-directed RNA polymerase
F: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,62421
Polymers230,0806
Non-polymers3,54415
Water2,756153
1
A: RNA-directed RNA polymerase
B: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8757
Polymers76,6932
Non-polymers1,1815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: RNA-directed RNA polymerase
D: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8757
Polymers76,6932
Non-polymers1,1815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: RNA-directed RNA polymerase
F: 5'-R(*UP*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8757
Polymers76,6932
Non-polymers1,1815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.504, 92.134, 140.755
Angle α, β, γ (deg.)90.00, 101.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))
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

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Protein / RNA chain , 2 types, 6 molecules ACEBDF

#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)

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Non-polymers , 4 types, 168 molecules

#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsP2 IS ONE OF THE STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID, RESPONSIBLE FOR GENOMIC ...P2 IS ONE OF THE STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID, 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: 2.92 Å3/Da / Density % sol: 57.86 % / Description: DATA COLLECTED AT MN K EDGE
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. SOAKING: 25MM CACL2 AND 40-60MM GTP (LITHIUM SALT), pH 7.30
Crystal grow
*PLUS
Temperature: 293 K / pH: 6.7 / Method: vapor diffusion, sitting drop
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: ESRF / Beamline: BM14 / Wavelength: 1.894
DetectorDate: Apr 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.894 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 51586 / % possible obs: 96.9 % / Observed criterion σ(I): 1.5 / Redundancy: 17 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 11.9
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 1.6 / % possible all: 78.4
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. measured all: 880290 / Rmerge(I) obs: 0.151
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 78.4 % / 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: 3→19.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1522098.25 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2575 5 %RANDOM
Rwork0.234 ---
obs0.234 51384 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48 Å2 / ksol: 0.331938 e/Å3
Displacement parametersBiso mean: 62 Å2
Baniso -1Baniso -2Baniso -3
1--6.84 Å20 Å2-4.47 Å2
2--30.97 Å20 Å2
3----24.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.46 Å
Luzzati d res low-20 Å
Luzzati sigma a0.67 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 3→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15795 231 201 153 16380
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.833
X-RAY DIFFRACTIONc_mcangle_it4.574
X-RAY DIFFRACTIONc_scbond_it4.674
X-RAY DIFFRACTIONc_scangle_it7.045
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.449 338 4.7 %
Rwork0.426 6901 -
obs--82.3 %
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 DIFFRACTION4GTP
Refinement
*PLUS
Highest resolution: 3 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_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.23

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