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- PDB-1iw7: Crystal structure of the RNA polymerase holoenzyme from Thermus t... -

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Basic information

Entry
Database: PDB / ID: 1iw7
TitleCrystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution
Components(RNA polymerase ...) x 5
KeywordsTRANSFERASE / RNA polymerase holoenzyme / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1410 / Ribonucleotide Reductase Protein R1; domain 1 - #90 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #280 / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / Molybdopterin biosynthesis moea protein, domain 2 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase Rpb1, domain 3 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1410 / Ribonucleotide Reductase Protein R1; domain 1 - #90 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #280 / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / Molybdopterin biosynthesis moea protein, domain 2 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase Rpb1, domain 3 / Molybdopterin biosynthesis moea protein, domain 2 / RNA polymerase Rpb1 funnel domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Enzyme I; Chain A, domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Wheat Germ Agglutinin (Isolectin 2); domain 1 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Gyrase A; domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Four Helix Bundle (Hemerythrin (Met), subunit A) / Beta Complex / Helix non-globular / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature.
Similarity search - Domain/homology
LEAD (II) ION / : / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: NATURE / Year: 2002
Title: Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution
Authors: Vassylyev, D.G. / Sekine, S. / Laptenko, O. / Lee, J. / Vassylyeva, M.N. / Borukhov, S. / Yokoyama, S.
History
DepositionApr 22, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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 polymerase alpha subunit
B: RNA polymerase alpha subunit
C: RNA polymerase beta subunit
D: RNA polymerase beta subunit
E: RNA polymerase omega subunit
F: RNA polymerase sigma-70 subunit
K: RNA polymerase alpha subunit
L: RNA polymerase alpha subunit
M: RNA polymerase beta subunit
N: RNA polymerase beta subunit
O: RNA polymerase omega subunit
P: RNA polymerase sigma-70 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)865,888501
Polymers853,27112
Non-polymers12,617489
Water98,6505476
1
A: RNA polymerase alpha subunit
B: RNA polymerase alpha subunit
C: RNA polymerase beta subunit
D: RNA polymerase beta subunit
E: RNA polymerase omega subunit
F: RNA polymerase sigma-70 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)433,369268
Polymers426,6356
Non-polymers6,734262
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: RNA polymerase alpha subunit
L: RNA polymerase alpha subunit
M: RNA polymerase beta subunit
N: RNA polymerase beta subunit
O: RNA polymerase omega subunit
P: RNA polymerase sigma-70 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)432,519233
Polymers426,6356
Non-polymers5,883227
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)236.350, 236.350, 249.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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RNA polymerase ... , 5 types, 12 molecules ABKLCMDNEOFP

#1: Protein
RNA polymerase alpha subunit


Mass: 35056.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase
#2: Protein RNA polymerase beta subunit


Mass: 125436.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q8RQE9*PLUS, DNA-directed RNA polymerase
#3: Protein RNA polymerase beta subunit


Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q8RQE8*PLUS, DNA-directed RNA polymerase
#4: Protein RNA polymerase omega subunit


Mass: 11521.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q8RQE7*PLUS, DNA-directed RNA polymerase
#5: Protein RNA polymerase sigma-70 subunit


Mass: 48568.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: GenBank: 4239959, UniProt: Q5SKW1*PLUS, DNA-directed RNA polymerase

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Non-polymers , 3 types, 5965 molecules

#6: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 485 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pb
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5476 / Source method: isolated from a natural source / Formula: H2O

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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: 4.71 Å3/Da / Density % sol: 73.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Mg formate, PEG400, Spermidine, TRIS HCl, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
213 mMmagnesium formate1reservoir
35 %PEG4001reservoir
42 mMdithiothreitol1reservoir
520 mMMES1reservoirpH5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 25, 2001
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 1449705 / Num. obs: 1362723 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.5 / % possible all: 89.2
Reflection
*PLUS
Num. obs: 452740 / % possible obs: 94.6 % / Num. measured all: 1362723 / Rmerge(I) obs: 0.133
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 89.2 % / Rmerge(I) obs: 0.37

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I6V

1i6v


Resolution: 2.6→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Merohedral twinning (-h,-k,l). Twinning fraction - 0.5.
RfactorNum. reflectionSelection details
Rfree0.274 20891 THIN SHELS
Rwork0.228 --
all0.232 478583 -
obs0.232 427116 -
Displacement parametersBiso mean: 58.9 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53564 0 489 5476 59529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2.08
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_dihedral_angle_d25.05
LS refinement shellResolution: 2.6→2.7 Å / Rfactor Rfree: 0.322 / Rfactor Rwork: 0.303
Refinement
*PLUS
% reflection Rfree: 4 % / Rfactor all: 0.232 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.05
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18
LS refinement shell
*PLUS
Rfactor Rfree: 0.322 / Rfactor Rwork: 0.303

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