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- PDB-6eec: Mycobacterium tuberculosis RNAP promoter unwinding intermediate c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6eec | ||||||||||||||||||||||||||||||||
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Title | Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter captured by Corallopyronin | ||||||||||||||||||||||||||||||||
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![]() | TRANSCRIPTION/DNA / initiation / ![]() ![]() | ||||||||||||||||||||||||||||||||
Function / homology | RNA polymerase Rpb2, OB-fold / RNA polymerase-binding protein RbpA / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||
Specimen source | ![]() ![]() | ||||||||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||
![]() | Darst, S.A. / Campbell, E.A. / Boyaci Selcuk, H. / Chen, J. | ||||||||||||||||||||||||||||||||
![]() | Journal: Nature / Year: 2019 Title: Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding. ![]() | ||||||||||||||||||||||||||||||||
Validation Report | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||
Date | Deposition: Aug 13, 2018 / Release: Nov 21, 2018
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmcif format | ![]() ![]() |
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PDB format | ![]() ![]() |
PDBML Plus | ![]() |
Others | ![]() |
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Links
-Related structure data
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Assembly
Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein/peptide | ![]() Mass: 37745.328 Da / Num. of mol.: 2 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | | ![]() Mass: 130070.797 Da / Num. of mol.: 1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #3: Protein/peptide | | ![]() Mass: 148202.219 Da / Num. of mol.: 1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #4: Protein/peptide | | ![]() Mass: 11776.996 Da / Num. of mol.: 1 / Source: (gene. exp.) ![]() ![]() Gene: rpoZ, ERS007672_03979, ERS007703_04032, ERS007720_04749, ERS027652_00548, ERS027654_02543, ERS027656_03959, ERS124361_02246 Production host: ![]() ![]() ![]() References: UniProt: A0A0T9N9K3, ![]() |
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-Protein/peptide , 1 types, 1 molecules F
#5: Protein/peptide | Mass: 58169.477 Da / Num. of mol.: 1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-RNA polymerase-binding ... , 2 types, 2 molecules JM
#6: Protein/peptide | Mass: 12993.695 Da / Num. of mol.: 1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#9: Protein/peptide | Mass: 17933.361 Da / Num. of mol.: 1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules OP
#7: DNA chain | Mass: 27907.809 Da / Num. of mol.: 1 / Source: (synth.) ![]() ![]() |
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#8: DNA chain | Mass: 27618.625 Da / Num. of mol.: 1 / Source: (synth.) ![]() ![]() |
-Non-polymers , 3 types, 4 molecules 




#10: Chemical | ChemComp-C0L / | ||
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#11: Chemical | #12: Chemical | ChemComp-MG / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / Reconstruction method: ![]() |
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Sample preparation
Component | Name: Mycobacterium tuberculosis RNAP open promoter complex / Type: COMPLEX / Entity ID: 1,Source (natural) | Organism: | ![]() ![]() Source (recombinant) | Organism: | ![]() ![]() ![]() Buffer solution | pH: 8 | Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied | ![]() ![]() Specimen support | Details: unspecified | Vitrification | ![]() Cryogen name: ETHANE | |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Microscope model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 69.9 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.55 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 246409 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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