[English] 日本語
Yorodumi
- PDB-7f2f: The complex of DNA with the C-terminal domain of TYE7 from Saccha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f2f
TitleThe complex of DNA with the C-terminal domain of TYE7 from Saccharomyces cerevisiae.
Components
  • DNA (5'-D(*CP*AP*GP*AP*TP*CP*AP*TP*GP*TP*GP*TP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*CP*AP*CP*AP*CP*AP*TP*GP*AP*TP*CP*T)-3')
  • Serine-rich protein TYE7
KeywordsTRANSCRIPTION / Glycolysis / bHLH transcription factor
Function / homology
Function and homology information


DNA-binding transcription activator activity / positive regulation of glycolytic process / transcription elongation by RNA polymerase II / sequence-specific DNA binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor TYE7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsGui, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of the complex of DNA with the C-terminal domain of TYE7 from Saccharomyces cerevisiae.
Authors: Gui, W. / Xue, L. / Yue, J. / Kuang, Z. / Jin, Y. / Niu, L.
History
DepositionJun 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine-rich protein TYE7
B: Serine-rich protein TYE7
E: DNA (5'-D(*CP*AP*GP*AP*TP*CP*AP*TP*GP*TP*GP*TP*GP*CP*C)-3')
H: DNA (5'-D(*GP*GP*GP*CP*AP*CP*AP*CP*AP*TP*GP*AP*TP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)40,8954
Polymers40,8954
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-63 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.025, 73.025, 181.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11H-1-

DG

-
Components

#1: Protein Serine-rich protein TYE7 / Basic-helix-loop-helix protein SGC1


Mass: 15858.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TYE7, SGC1, YOR344C, O6233 / Production host: Escherichia coli (E. coli) / References: UniProt: P33122
#2: DNA chain DNA (5'-D(*CP*AP*GP*AP*TP*CP*AP*TP*GP*TP*GP*TP*GP*CP*C)-3')


Mass: 4584.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*GP*CP*AP*CP*AP*CP*AP*TP*GP*AP*TP*CP*T)-3')


Mass: 4593.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH7.5, 10% w/v PEG 8000, 11% v/v ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.55→67.76 Å / Num. obs: 16802 / % possible obs: 99.9 % / Redundancy: 17.9 % / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 33.15
Reflection shellResolution: 2.55→2.59 Å / Mean I/σ(I) obs: 2.05 / Num. unique obs: 818 / CC1/2: 0.876 / CC star: 0.967

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AM9

1am9


Resolution: 2.55→67.76 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.87 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 838 5 %RANDOM
Rwork0.2459 ---
obs0.2478 15898 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 190.25 Å2 / Biso mean: 70.705 Å2 / Biso min: 28.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å2-0 Å2-0 Å2
2--2.31 Å2-0 Å2
3----4.62 Å2
Refinement stepCycle: final / Resolution: 2.55→67.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 593 0 0 2137
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0172274
X-RAY DIFFRACTIONr_bond_other_d0.0030.021935
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.6973189
X-RAY DIFFRACTIONr_angle_other_deg1.22734466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3125184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.762584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77315331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9161512
X-RAY DIFFRACTIONr_chiral_restr0.1250.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022124
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02516
LS refinement shellResolution: 2.551→2.617 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.524 68 -
Rwork0.434 1089 -
all-1157 -
obs--96.82 %

+
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://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