[English] 日本語
Yorodumi
- PDB-9bcu: Cryo-EM structure of Thermococcus kodakarensis FttA-dependent tra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bcu
TitleCryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 nt RNA
Components
  • (DNA-directed RNA polymerase subunit ...) x 11
  • (Transcription elongation factor ...) x 2
  • RNA (29-MER)
  • Transcription termination factor FttA
  • non-template strand DNA
  • template strand DNA
KeywordsTRANSCRIPTION / RNA polymerase / pre-termination complex / FttA / archaea
Function / homology
Function and homology information


exonuclease activity / transcription elongation-coupled chromatin remodeling / transcription initiation at RNA polymerase III promoter / RNA polymerase II activity / translation elongation factor activity / DNA-directed RNA polymerase complex / RNA endonuclease activity / regulation of DNA-templated transcription elongation / DNA-templated transcription termination / ribonucleoside binding ...exonuclease activity / transcription elongation-coupled chromatin remodeling / transcription initiation at RNA polymerase III promoter / RNA polymerase II activity / translation elongation factor activity / DNA-directed RNA polymerase complex / RNA endonuclease activity / regulation of DNA-templated transcription elongation / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / Hydrolases; Acting on ester bonds / protein dimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
: / Transcription termination factor CPSF1, archaea / KH domain, archaeal / KH domain / Archaeal transcription elongation factor Spt4 / Transcription elongation factor Spt5, archaeal / Archaeal transcription elongation factor Spt4 superfamily / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 ...: / Transcription termination factor CPSF1, archaea / KH domain, archaeal / KH domain / Archaeal transcription elongation factor Spt4 / Transcription elongation factor Spt5, archaeal / Archaeal transcription elongation factor Spt4 superfamily / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / DNA-directed RNA polymerase, subunit E/RPC8 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / S1 domain profile. / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / K Homology domain / K homology RNA-binding domain / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo11 ...DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo11 / Transcription termination factor FttA / Transcription elongation factor Spt5 / DNA-directed RNA polymerase subunit Rpo7 / Transcription elongation factor Spt4 / DNA-directed RNA polymerase subunit Rpo10
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsYou, L. / Ebright, R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural basis of archaeal FttA-dependent transcription termination
Authors: You, L. / Ebright, R.H.
History
DepositionApr 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit A'
B: DNA-directed RNA polymerase subunit B
C: DNA-directed RNA polymerase subunit A"
D: DNA-directed RNA polymerase subunit D
E: DNA-directed RNA polymerase subunit E
F: DNA-directed RNA polymerase subunit F
H: DNA-directed RNA polymerase subunit H
K: DNA-directed RNA polymerase subunit K
L: DNA-directed RNA polymerase subunit L
N: DNA-directed RNA polymerase subunit N
P: DNA-directed RNA polymerase subunit P
G: Transcription elongation factor Spt5
I: Transcription elongation factor Spt4
J: Transcription termination factor FttA
M: Transcription termination factor FttA
5: non-template strand DNA
6: template strand DNA
7: RNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)591,60327
Polymers591,05518
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
DNA-directed RNA polymerase subunit ... , 11 types, 11 molecules ABCDEFHKLNP

#1: Protein DNA-directed RNA polymerase subunit A' / DNA-directed RNA polymerase subunit Rpo1N


Mass: 103038.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE33
#2: Protein DNA-directed RNA polymerase subunit B


Mass: 127468.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE32
#3: Protein DNA-directed RNA polymerase subunit A" / DNA-directed RNA polymerase subunit Rpo1C


Mass: 43727.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE34, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit D


Mass: 29657.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea)
#5: Protein DNA-directed RNA polymerase subunit E / DNA-directed RNA polymerase subunit Rpo7


Mass: 21893.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JIY4
#6: Protein DNA-directed RNA polymerase subunit F


Mass: 14519.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea)
#7: Protein DNA-directed RNA polymerase subunit H / DNA-directed RNA polymerase subunit Rpo5


Mass: 9522.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE31, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit K


Mass: 6583.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea)
#9: Protein DNA-directed RNA polymerase subunit L / DNA-directed RNA polymerase subunit Rpo11


Mass: 11013.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE88, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase subunit N / DNA-directed RNA polymerase subunit Rpo10


Mass: 7601.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJC9, DNA-directed RNA polymerase
#11: Protein/peptide DNA-directed RNA polymerase subunit P / DNA-directed RNA polymerase subunit Rpo12


Mass: 5553.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDM8, DNA-directed RNA polymerase

-
Transcription elongation factor ... , 2 types, 2 molecules GI

#12: Protein Transcription elongation factor Spt5


Mass: 16776.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: spt5 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q5JH33
#13: Protein Transcription elongation factor Spt4


Mass: 8561.870 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: spt4, TK1698 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q5JIY5

-
DNA chain , 2 types, 2 molecules 56

#15: DNA chain non-template strand DNA


Mass: 11096.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain template strand DNA


Mass: 11060.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein / RNA chain , 2 types, 3 molecules JM7

#14: Protein Transcription termination factor FttA / Cleavage and polyadenylation specficity factor subunit homolog


Mass: 73473.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK1428 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q5JH24
#17: RNA chain RNA (29-MER)


Mass: 16032.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 2 types, 9 molecules

#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#19: Chemical
ChemComp-ZN / ZINC ION


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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: FttA-dependent transcription termination complex containing 52 nt RNA
Type: COMPLEX / Entity ID: #1-#17 / Source: RECOMBINANT
Molecular weightValue: 0.556 MDa / Experimental value: NO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta2
Buffer solutionpH: 7.5
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48.33 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

-
Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 977159
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137835 / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 68.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00240679
ELECTRON MICROSCOPYf_angle_d0.468855312
ELECTRON MICROSCOPYf_chiral_restr0.04166205
ELECTRON MICROSCOPYf_plane_restr0.0046916
ELECTRON MICROSCOPYf_dihedral_angle_d9.9916117

+
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://pdbjlvh1.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