[English] 日本語
Yorodumi
- PDB-1uvl: The structural basis for RNA specificity and Ca2 inhibition of an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uvl
TitleThe structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 5nt RNA. Conformation B
Components
  • 5'-R(*UP*UP*UP*CP*CP)-3'
  • RNA-directed RNA polymerase
KeywordsTRANSFERASE / POLYMERASE / OLIGONUCLEOTIDE POLYMERASE / TRANSCRIPTION / STRUCTURAL PROTEIN
Function / homology
Function and homology information


RNA uridylyltransferase activity / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / 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 (bacteriophage)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Feb 1, 2012Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Mar 7, 2018Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / database_PDB_caveat / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct / 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.src_method / _entity_name_com.name / _struct.title / _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 1.3Dec 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 / 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-directed RNA polymerase
B: 5'-R(*UP*UP*UP*CP*CP)-3'
C: RNA-directed RNA polymerase
D: 5'-R(*UP*UP*UP*CP*CP)-3'
E: RNA-directed RNA polymerase
F: 5'-R(*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,3269
Polymers229,1616
Non-polymers1653
Water00
1
A: RNA-directed RNA polymerase
B: 5'-R(*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4423
Polymers76,3872
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-18 kcal/mol
Surface area25350 Å2
MethodPISA
2
C: RNA-directed RNA polymerase
D: 5'-R(*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4423
Polymers76,3872
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-17.9 kcal/mol
Surface area25370 Å2
MethodPISA
3
E: RNA-directed RNA polymerase
F: 5'-R(*UP*UP*UP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4423
Polymers76,3872
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-17.8 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.946, 91.881, 140.762
Angle α, β, γ (deg.)90.00, 101.56, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
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
DetailsTHE POLYMERASE IS A MONOMER IN SOLUTION, BUT SINCE IT IS IN COMPLEX WITH RNA IN THIS ENTRY, THE OLIGOMER IS ANNOTATED AS A DIMER

-
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 (bacteriophage) / Gene: P2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11124, RNA-directed RNA polymerase
#2: RNA chain 5'-R(*UP*UP*UP*CP*CP)-3'


Mass: 1483.904 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growpH: 7.3
Details: 100MM HEPES PH7.3, 13% PEG 20000, 2MM MNCL2, 2% EG 0.036MG PROTEIN INCUBATED WITH 0.006MM 5NT RNA, 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

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977
DetectorDate: Oct 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 176845 / % possible obs: 99.2 % / Observed criterion σ(I): 1.8 / Redundancy: 12 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.9
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 1.8 / % possible all: 93.5
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. obs: 176955 / Num. measured all: 2110477 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 93.5 % / Mean I/σ(I) obs: 1.8

-
Processing

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

1hhs


Resolution: 2→19.82 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2563207.42 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.299 8877 5 %RANDOM
Rwork0.281 ---
obs0.281 176845 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35 Å2 / ksol: 0.363381 e/Å3
Displacement parametersBiso mean: 46.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.69 Å20 Å2-5.52 Å2
2--19.54 Å20 Å2
3----12.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.39 Å
Luzzati d res low-20 Å
Luzzati sigma a0.56 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15795 291 3 0 16089
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
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_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.34
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.883
X-RAY DIFFRACTIONc_mcangle_it3.874
X-RAY DIFFRACTIONc_scbond_it4.774
X-RAY DIFFRACTIONc_scangle_it6.375
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.469 1427 5.1 %
Rwork0.456 26769 -
obs--95.4 %
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 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_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.34

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more