[English] 日本語
Yorodumi
- PDB-5w65: RNA polymerase I Initial Transcribing Complex State 2 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5w65
TitleRNA polymerase I Initial Transcribing Complex State 2
Descriptor(DNA-directed RNA polymerase I subunit ...) x 7
(DNA-directed RNA polymerases I and III subunit ...) x 2
(DNA-directed RNA polymerases I/II/III subunit ...) x 5
(RNA polymerase I-specific transcription initiation factor ...) x 3
KeywordsTRANSCRIPTION / RNA Polymerase I Core Factor Transcription
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
MethodElectron microscopy (4.3 Å resolution / Particle / Single particle)
AuthorsHan, Y. / He, Y.
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.
Yan Han / Chunli Yan / Thi Hoang Duong Nguyen / Ashleigh J Jackobel / Ivaylo Ivanov / Bruce A Knutson / Yuan He

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 16, 2017 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Sep 20, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization
1.2Nov 8, 2017Structure modelDerived calculationspdbx_struct_assembly_pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase I subunit RPA190
B: DNA-directed RNA polymerase I subunit RPA135
C: DNA-directed RNA polymerases I and III subunit RPAC1
D: DNA-directed RNA polymerase I subunit RPA14
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase I subunit RPA43
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase I subunit RPA12
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerases I and III subunit RPAC2
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: DNA-directed RNA polymerase I subunit RPA49
N: DNA-directed RNA polymerase I subunit RPA34
O: RNA polymerase I-specific transcription initiation factor RRN6
P: RNA polymerase I-specific transcription initiation factor RRN7
Q: RNA polymerase I-specific transcription initiation factor RRN11
R: RNA
S: non-template strand DNA
T: template strand DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)846,27627
Polyers845,81820
Non-polymers4587
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)115320
ΔGint (kcal/M)-663
Surface area (Å2)241990

-
Components

+
DNA-directed RNA polymerase I subunit ... , 7 types, 7 molecules ABDGIMN

#1: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA190 / DNA-directed RNA polymerase I 190 kDa polypeptide / A190 / DNA-directed RNA polymerase I largest subunit


Mass: 186676.969 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P10964, EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#2: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA135 / DNA-directed RNA polymerase I 135 kDa polypeptide / A135 / DNA-directed RNA polymerase I polypeptide 2 / RNA polymerase I subunit 2


Mass: 135910.328 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P22138, EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#4: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA14 / A14 / DNA-directed RNA polymerase I 14 kDa polypeptide


Mass: 14599.128 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P50106

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#7: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA43 / A43 / DNA-directed DNA-dependent RNA polymerase 36 kDa polypeptide


Mass: 36264.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P46669

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#9: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA12 / A12 / A12.2 / DNA-directed RNA polymerase I 13.7 kDa polypeptide


Mass: 13676.566 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P32529

Cellular component

Molecular function

Biological process

  • mRNA cleavage (GO: 0006379)
  • negative regulation of transcription from RNA polymerase II promoter (GO: 0000122)
  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase I transcription (GO: 0006363)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#13: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA49 / A49 / DNA-directed RNA polymerase I 49 kDa polypeptide


Mass: 46721.707 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q01080

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription elongation from RNA polymerase I promoter (GO: 0006362)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#14: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA34 / A34 / DNA-directed DNA-dependent RNA polymerase 34.5 kDa polypeptide / A34.5


Mass: 26933.518 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P47006

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription elongation from RNA polymerase I promoter (GO: 0006362)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)

+
DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK

#3: Polypeptide(L)DNA-directed RNA polymerases I and III subunit RPAC1 / RNA polymerases I and III subunit AC1 / C37 / DNA-directed RNA polymerases I and III 40 kDa polypeptide / C40


Mass: 37732.613 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P07703

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)DNA-directed RNA polymerases I and III subunit RPAC2 / RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerases I and III 16 kDa polypeptide / RPA19


Mass: 16167.860 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P28000

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)

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

#5: Polypeptide(L)DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P20434

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#6: Polypeptide(L)DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P20435

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#8: Polypeptide(L)DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P20436

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#10: Polypeptide(L)DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P22139

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#12: Polypeptide(L)DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P40422

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)

+
RNA polymerase I-specific transcription initiation factor ... , 3 types, 3 molecules OPQ

#15: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN6


Mass: 100690.188 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P32786

Cellular component

Molecular function

  • RNA polymerase I regulatory region DNA binding (GO: 0001013)
  • RNA polymerase I transcription factor binding (GO: 0001179)
  • transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting (GO: 0001187)

Biological process

  • transcription initiation from RNA polymerase I promoter (GO: 0006361)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#16: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN7


Mass: 60435.195 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P40992

Cellular component

Molecular function

  • metal ion binding (GO: 0046872)
  • RNA polymerase I CORE element sequence-specific DNA binding (GO: 0001164)
  • TBP-class protein binding (GO: 0017025)
  • transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting (GO: 0001187)

Biological process

  • transcription initiation from RNA polymerase I promoter (GO: 0006361)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#17: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN11


Mass: 59334.262 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q04712

Cellular component

Molecular function

  • RNA polymerase I CORE element sequence-specific DNA binding (GO: 0001164)
  • TBP-class protein binding (GO: 0017025)
  • transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting (GO: 0001187)

Biological process

  • transcription initiation from RNA polymerase I promoter (GO: 0006361)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)

+
DNA chain , 2 types, 2 molecules ST

#19: DNA chainnon-template strand DNA


Mass: 16803.787 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae S288c
#20: DNA chaintemplate strand DNA


Mass: 16360.488 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae S288c

+
RNA chain / Non-polymers , 2 types, 8 molecules R

#18: RNA chainRNA


Mass: 1915.213 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae S288c
#21: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Formula: Zn

+
Details

Sequence detailsDUE TO LOW RESOLUTION THE SEQUENCE CORRESPONDING TO UNK SEGMENT COULD NOT BE MODELED

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: RNA Polymerase I Initial Transcribing Complex State 2 / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20
Source: MULTIPLE SOURCES
Molecular weightValue: 0.9 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil S7/2
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 / Calibrated defocus min: 1500 nm / Calibrated defocus max: 4500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 56.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

-
Processing

EM software
IDNameVersionCategoryImaging IDImage processing IDDetailsFitting ID
2Leginon3.1IMAGE ACQUISITION1
4Gctf0.5CTF CORRECTION1
7NAMD2.8MODEL FITTINGMDFF flexible fitting1
8Chimera1.11.2MODEL FITTINGrigid body fitting1
10Coot0.8.8MODEL REFINEMENT1
11PHENIX1.10.1MODEL REFINEMENT1
12RELION2.0INITIAL EULER ASSIGNMENT1
13RELION2.0FINAL EULER ASSIGNMENT1
14RELION2.0CLASSIFICATION1
15RELION2.0RECONSTRUCTION1
CTF correctionDetails: CTF amplitude correction was performed following 3D auto refinement in relion.
Type: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 38340 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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. See below links for details.
  • 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

+
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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more