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- PDB-3gtq: Backtracked RNA polymerase II complex induced by damage -

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Basic information

Entry
Database: PDB / ID: 3gtq
TitleBacktracked RNA polymerase II complex induced by damage
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • DNA (5'-D(*CP*TP*AP*CP*CP*CP*AP*TP*AP*AP*CP*CP*AP*CP*AP*GP*GP*CP*TP*CP*CP*TP*CP*TP*CP*CP*AP*TP*C)-3')
  • RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*GP*AP*GP*C)-3')
KeywordsTRANSCRIPTION / TRANSFERASE/DNA-RNA HYBRID / TRANSFERASE / DNA-RNA HYBRID / Backtrack / DNA-directed RNA polymerase / DNA binding / Isopeptide bond / Magnesium / Metal binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Zinc-finger / DNA damage / DNA repair / TRANSFERASE-DNA-RNA HYBRID COMPLEX
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / RNA polymerase II transcribes snRNA genes / Formation of the Early Elongation Complex / RNA Polymerase I Promoter Escape ...RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / RNA polymerase II transcribes snRNA genes / Formation of the Early Elongation Complex / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Promoter Escape / RNA polymerase II activity / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Estrogen-dependent gene expression / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / tRNA transcription by RNA polymerase III / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription initiation from RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / transcription by RNA polymerase II / DNA-directed RNA polymerase / transcription, RNA-templated / cytoplasmic stress granule / ribosome biogenesis / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase alpha subunit dimerisation domain / DCoH-like / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / Enzyme I; Chain A, domain 2 / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 ...Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase alpha subunit dimerisation domain / DCoH-like / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / Enzyme I; Chain A, domain 2 / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / 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 / N-terminal domain of TfIIb - #10 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 6 / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger TFIIS-type signature. / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases N / 8 kDa subunit / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase, Rpb5, N-terminal / RNA polymerase subunit 8 / RNA polymerase Rpb8 / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / : / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RPB5-like RNA polymerase subunit superfamily / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerases L / 13 to 16 Kd subunits signature. / : / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase Rpb5, C-terminal domain / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerases K / 14 to 18 Kd subunits signature. / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Gyrase A; domain 2 / Homeodomain-like / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb6 / Single Sheet / RNA polymerase Rpb2, domain 2 superfamily / : / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 2
Similarity search - Domain/homology
RNA (> 10) / RNA / DNA (> 10) / DNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...RNA (> 10) / RNA / DNA (> 10) / DNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsWang, D. / Bushnell, D.A. / Huang, X. / Westover, K.D. / Levitt, M. / Kornberg, R.D.
CitationJournal: Science / Year: 2009
Title: Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
Authors: Wang, D. / Bushnell, D.A. / Huang, X. / Westover, K.D. / Levitt, M. / Kornberg, R.D.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
R: RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*GP*AP*GP*C)-3')
T: DNA (5'-D(*CP*TP*AP*CP*CP*CP*AP*TP*AP*AP*CP*CP*AP*CP*AP*GP*GP*CP*TP*CP*CP*TP*CP*TP*CP*CP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,74320
Polymers482,22012
Non-polymers5238
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62540 Å2
ΔGint-306.3 kcal/mol
Surface area140500 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)168.186, 221.581, 192.800
Angle α, β, γ (deg.)90.00, 101.81, 90.00
Int Tables number5
Space group name H-MC121
DetailsASYMMETRIC UNIT IS THE BIOLOGICAL UNIT

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Components

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DNA-directed RNA polymerase II subunit ... , 5 types, 5 molecules ABCIK

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit B1 / RNA polymerase II subunit 1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit B1 / RNA polymerase II subunit 1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerase II largest subunit / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / Polymerase / RNA polymerase II subunit 2 / DNA-directed RNA polymerase II 140 kDa polypeptide / B150


Mass: 138937.297 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerase II 140 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / RNA polymerase II subunit 3 / DNA-directed RNA polymerase II 45 kDa ...RNA polymerase II subunit B3 / RNA polymerase II subunit 3 / DNA-directed RNA polymerase II 45 kDa polypeptide / B44.5


Mass: 35330.457 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerase II 45 kDa polypeptide / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P16370
#7: Protein DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / B12.6


Mass: 14308.161 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerase II subunit 9 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P27999
#9: Protein DNA-directed RNA polymerase II subunit RPB11 / Polymerase / RNA polymerase II subunit B11 / DNA-directed RNA polymerase II 13.6 kDa polypeptide / B13.6


Mass: 13633.493 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerase II 13.6 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#4: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerases I / II / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerases I / II / and III 27 kDa polypeptide / ABC27


Mass: 25117.094 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20434
#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 23 kDa polypeptide / ABC23


Mass: 17931.834 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20435
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / II / and III 14.5 ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / II / and III 14.5 kDa polypeptide / ABC14.5 / ABC14.4


Mass: 16525.363 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20436
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerases I / II / and III 8.3 ...RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerases I / II / and III 8.3 kDa polypeptide / ABC10-beta / ABC8


Mass: 8290.732 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerases I/II/III subunit 10 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P22139
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40422

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RNA chain / DNA chain / Non-polymers , 3 types, 10 molecules RT

#11: RNA chain RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*GP*AP*GP*C)-3')


Mass: 3914.424 Da / Num. of mol.: 1 / Fragment: RNA strand / Source method: obtained synthetically / Details: Synthetic RNA
#12: DNA chain DNA (5'-D(*CP*TP*AP*CP*CP*CP*AP*TP*AP*AP*CP*CP*AP*CP*AP*GP*GP*CP*TP*CP*CP*TP*CP*TP*CP*CP*AP*TP*C)-3')


Mass: 8679.603 Da / Num. of mol.: 1 / Fragment: DNA template strand / Source method: obtained synthetically / Details: Synthetic template DNA
#13: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsTHE DNA NON-TEMPLATE STRAND (LABELED AS ENTITY 13 IN THE RELATED ENTRIES) IS MISSING IN COORDINATES ...THE DNA NON-TEMPLATE STRAND (LABELED AS ENTITY 13 IN THE RELATED ENTRIES) IS MISSING IN COORDINATES DUE TO LACK OF ELECTRON DENSITY. THE ENTITY 13 IS A DNA (5'-D(*GP*TP*GP*GP*TP*TP*AP*TP*GP*GP*GP*TP*AP*G)-3')

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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: 3.61 Å3/Da / Density % sol: 65.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2HPO4/NaH2PO411
2Dioxane1,4-Dioxane11
3DTT11
4PEG 600011
5(NH4)2HPO4/NaH2PO412
6Dioxane1,4-Dioxane12
7DTT12
8PEG 600012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 66377 / % possible obs: 96.1 % / Redundancy: 2.7 % / Net I/σ(I): 10.2
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.5 / % possible all: 96.8

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R9T
Resolution: 3.8→50 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.821 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.896 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ENTIRE CHAIN N WHICH IS A DNA NON-TEMPLATE STRAND, REPORTED AS ENTITY 13 IN RELATED ENTRIES WITH THE SEQUENCE (DG)(DT)(DG)(DG)(DT)(DT) ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ENTIRE CHAIN N WHICH IS A DNA NON-TEMPLATE STRAND, REPORTED AS ENTITY 13 IN RELATED ENTRIES WITH THE SEQUENCE (DG)(DT)(DG)(DG)(DT)(DT)(DA)(DT)(DG)(DG)(DG)(DT)(DA)(DG), IS MISSING IN COORDINATES DUE TO LACK OF ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.3348 3287 5.1 %RANDOM
Rwork0.27056 ---
obs0.27378 61632 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.463 Å2
Baniso -1Baniso -2Baniso -3
1-6.09 Å20 Å2-8.48 Å2
2---7.55 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 3.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28140 477 8 0 28625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02229194
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.98939523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53553518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17824.0291333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.78155251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.60115222
X-RAY DIFFRACTIONr_chiral_restr0.1080.24447
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0221676
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2680.215249
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.219399
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.21084
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5661.517634
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.039228569
X-RAY DIFFRACTIONr_scbond_it0.875311560
X-RAY DIFFRACTIONr_scangle_it1.5754.510954
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.8→3.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 248 -
Rwork0.393 4443 -
obs--94.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.73380.74180.42540.9351-0.09770.96670.03960.11440.1130.11220.0181-0.1776-0.18080.2678-0.05770.0001-0.0003-0.00010-0.0001046.81686.388139.2181
20.4263-0.18810.19240.5716-0.07710.63080.0901-0.020.02430.12610.0646-0.11120.17140.1064-0.15470.0370.0375-0.1296-0.09840.0002-0.03726.5916-25.590969.1482
30.2744-0.02420.14760.2480.10560.51030.05440.02040.01280.0116-0.02090.01760.0282-0.0936-0.0335-0.1523-0.04310.0345-0.04150.0532-0.0912-10.59553.399843.7193
40.20260.01720.49642.7375-0.57931.3573-0.16860.1169-0.01790.58630.1432-0.2386-0.2974-0.01810.025500.00020.0001-0.00010.0002024.192229.245791.4818
52.1495-0.92291.13353.0169-0.73450.9168-0.1213-0.51310.28130.324-0.1173-0.49440.106-0.04940.23870.000200.000400.0001031.349411.431760.128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 154
2X-RAY DIFFRACTION1A161 - 186
3X-RAY DIFFRACTION1A199 - 346
4X-RAY DIFFRACTION1A1395 - 1445
5X-RAY DIFFRACTION1B1151 - 1224
6X-RAY DIFFRACTION2A809 - 1141
7X-RAY DIFFRACTION2A1275 - 1394
8X-RAY DIFFRACTION2E2 - 215
9X-RAY DIFFRACTION2F72 - 155
10X-RAY DIFFRACTION3A347 - 808
11X-RAY DIFFRACTION3B20 - 70
12X-RAY DIFFRACTION3B90 - 217
13X-RAY DIFFRACTION3C3 - 268
14X-RAY DIFFRACTION3B406 - 437
15X-RAY DIFFRACTION3B446 - 668
16X-RAY DIFFRACTION3B678 - 715
17X-RAY DIFFRACTION3B722 - 919
18X-RAY DIFFRACTION3B933 - 1150
19X-RAY DIFFRACTION3J1 - 65
20X-RAY DIFFRACTION3K1 - 114
21X-RAY DIFFRACTION3L25 - 70
22X-RAY DIFFRACTION3H2 - 63
23X-RAY DIFFRACTION3H76 - 146
24X-RAY DIFFRACTION3I40 - 120
25X-RAY DIFFRACTION4A1142 - 1176
26X-RAY DIFFRACTION4A1187 - 1272
27X-RAY DIFFRACTION4B218 - 335
28X-RAY DIFFRACTION4B345 - 405
29X-RAY DIFFRACTION4I2 - 39
30X-RAY DIFFRACTION5T1 - 28
31X-RAY DIFFRACTION5R1 - 12

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

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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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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Yorodumi

Thousand views of thousand structures

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  • 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

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