[English] 日本語
Yorodumi
- PDB-3zp5: Crystal structure of the DNA binding ETS domain of the human prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zp5
TitleCrystal structure of the DNA binding ETS domain of the human protein FEV in complex with DNA
Components
  • 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'
  • 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'
  • PROTEIN FEV
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


neuron fate specification / maternal behavior / neuron maturation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of gene expression ...neuron fate specification / maternal behavior / neuron maturation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNewman, J.A. / Cooper, C.D.O. / Krojer, T. / Shrestha, L. / Allerston, C.K. / Vollmar, M. / Arrowsmith, C.H. / Burgess-Brown, N. / Edwards, A. / von Delft, F. / Gileadi, O.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structures of the Ets Domains of Transcription Factors Etv1, Etv4, Etv5 and Fev: Determinants of DNA Binding and Redox Regulation by Disulfide Bond Formation.
Authors: Cooper, C.D.O. / Newman, J.A. / Aitkenhead, H. / Allerston, C.K. / Gileadi, O.
History
DepositionFeb 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN FEV
C: 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'
G: 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)17,9033
Polymers17,9033
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-17.5 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.224, 64.554, 110.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein PROTEIN FEV / FIFTH EWING VARIANT PROTEIN / PC12 ETS DOMAIN-CONTAINING TRANSCRIPTION FACTOR 1 / PC12 ETS FACTOR 1 / PET-1


Mass: 11813.431 Da / Num. of mol.: 1 / Fragment: ETS DOMAIN, RESIDUES 42-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q99581
#2: DNA chain 5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'


Mass: 2995.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'


Mass: 3094.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST TWO RESIDUES ARE FROM PURIFICATION TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 25% PEG 3350, 0.1M BIS TRIS PH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→110 Å / Num. obs: 12431 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 38.52 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YPR

2ypr


Resolution: 2→30.976 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 31.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 598 4.8 %
Rwork0.2097 --
obs0.2118 12387 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.75 Å2
Refinement stepCycle: LAST / Resolution: 2→30.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms745 404 0 36 1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021235
X-RAY DIFFRACTIONf_angle_d0.6961748
X-RAY DIFFRACTIONf_dihedral_angle_d21.76482
X-RAY DIFFRACTIONf_chiral_restr0.035179
X-RAY DIFFRACTIONf_plane_restr0.001156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.20140.33341530.29272895X-RAY DIFFRACTION100
2.2014-2.51980.28691490.26182927X-RAY DIFFRACTION100
2.5198-3.17420.29351440.24482957X-RAY DIFFRACTION100
3.1742-30.97970.22071520.17593010X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -11.1284 Å / Origin y: -7.6218 Å / Origin z: -15.7403 Å
111213212223313233
T0.5068 Å20.0268 Å2-0.0308 Å2-0.374 Å2-0.1032 Å2--0.3625 Å2
L3.7419 °2-0.7152 °2-3.8808 °2-2.3349 °21.9128 °2--9.2899 °2
S0.2216 Å °0.47 Å °-0.2159 Å °0.112 Å °-0.6011 Å °0.2148 Å °-0.5889 Å °-1.0711 Å °0.2112 Å °
Refinement TLS groupSelection details: ALL

+
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