[English] 日本語
Yorodumi
- PDB-3tj1: Crystal Structure of RNA Polymerase I Transcription Initiation Fa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tj1
TitleCrystal Structure of RNA Polymerase I Transcription Initiation Factor Rrn3
ComponentsRNA polymerase I-specific transcription initiation factor RRN3
KeywordsTRANSCRIPTION / HEAT repeat / Transcription Factor / Nucleus
Function / homology
Function and homology information


RNA polymerase I core binding / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase I promoter / nucleolus / nucleus
Similarity search - Function
RNA polymerase I specific transcription initiation factor RRN3 / RNA polymerase I specific transcription initiation factor RRN3
Similarity search - Domain/homology
RNA polymerase I-specific transcription initiation factor RRN3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsBlattner, C. / Jennebach, S. / Herzog, F. / Mayer, A. / Cheung, A.C.M. / Witte, G. / Lorenzen, K. / Hopfner, K.-P. / Heck, A.J.R. / Aebersold, R. / Cramer, P.
CitationJournal: Genes Dev. / Year: 2011
Title: Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth.
Authors: Blattner, C. / Jennebach, S. / Herzog, F. / Mayer, A. / Cheung, A.C. / Witte, G. / Lorenzen, K. / Hopfner, K.P. / Heck, A.J. / Aebersold, R. / Cramer, P.
History
DepositionAug 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Jan 24, 2018Group: Data collection / Structure summary / Category: audit_author / diffrn / Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA polymerase I-specific transcription initiation factor RRN3
B: RNA polymerase I-specific transcription initiation factor RRN3


Theoretical massNumber of molelcules
Total (without water)149,6642
Polymers149,6642
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-10 kcal/mol
Surface area41720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.770, 101.770, 162.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RNA polymerase I-specific transcription initiation factor RRN3


Mass: 74831.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRN3, YKL125W / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P36070
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG 3350, 250 mM sodium-potassium-tartrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0086, 1.0094, 1.0129
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2008
RadiationMonochromator: Liquid nitrogen cooled channel-cut silicon monochromator Si(111)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00861
21.00941
31.01291
ReflectionResolution: 2.85→50 Å / Num. all: 38079 / Num. obs: 38054 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.85→2.92 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
SHARPphasing
BUSTER2.11.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.85→48.55 Å / Cor.coef. Fo:Fc: 0.9308 / Cor.coef. Fo:Fc free: 0.9165 / SU R Cruickshank DPI: 0.701 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1900 4.99 %RANDOM
Rwork0.2082 ---
obs0.2099 38054 99.96 %-
all-38079 --
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.8169 Å20 Å20 Å2
2---23.5086 Å20 Å2
3---15.6916 Å2
Refine analyzeLuzzati coordinate error obs: 0.436 Å
Refinement stepCycle: LAST / Resolution: 2.85→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7972 0 0 103 8075
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018152HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1311017HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2891SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes208HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1145HARMONIC5
X-RAY DIFFRACTIONt_it8152HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion20.59
X-RAY DIFFRACTIONt_chiral_improper_torsion1072SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact9979SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.93 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2524 136 4.68 %
Rwork0.2416 2771 -
all0.2421 2907 -
obs--99.96 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6201-0.23241.39130.2875-0.3823.1169-0.1462-0.2317-0.0014-0.03980.12790.1204-0.225-0.65560.0183-0.16230.0723-0.00520.17870.007-0.163128.934229.9838110.55
20.71880.67011.57660.26810.82812.8058-0.08170.25250.0089-0.00640.1298-0.1003-0.07050.7183-0.0481-0.12920.0360.00220.2856-0.0314-0.141477.678830.4171132.529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A46 - 617
2X-RAY DIFFRACTION2{ B|* }B46 - 617

+
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