[English] 日本語
Yorodumi
- PDB-8zh9: The structure of ELK1-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zh9
TitleThe structure of ELK1-DNA complex
Components
  • DNA (5'-D(*AP*AP*AP*TP*TP*TP*CP*CP*GP*GP*AP*CP*TP*GP*GP*T)-3')
  • DNA (5'-D(*AP*CP*CP*AP*GP*TP*CP*CP*GP*GP*AP*AP*AP*TP*TP*T)-3')
  • ETS transcription factor ELK1
KeywordsDNA BINDING PROTEIN/DNA / Complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / ETS transcription factor ELK1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, G. / Sun, L.T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271314 China
National Natural Science Foundation of China (NSFC)32102504 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Host genetic variation governs PCV2 susceptibility through CXCL13 and ELK1-mediated immune regulation.
Authors: Liu, G. / Gao, Y. / Cheng, Y. / Wang, W. / Li, X. / Wu, Y. / Gao, F. / Zhou, Z.W. / Sun, Y. / Jiang, Y. / Yang, N. / Shu, Y. / Sun, L.
History
DepositionMay 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*CP*AP*GP*TP*CP*CP*GP*GP*AP*AP*AP*TP*TP*T)-3')
B: DNA (5'-D(*AP*AP*AP*TP*TP*TP*CP*CP*GP*GP*AP*CP*TP*GP*GP*T)-3')
C: ETS transcription factor ELK1


Theoretical massNumber of molelcules
Total (without water)20,8633
Polymers20,8633
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, ELK1 can be pulled down by DNA., gel filtration, There was a shift of ELK1 co-injected with DNA from the position of free ELK1 or DNA in size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-28 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.318, 62.345, 99.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: DNA chain DNA (5'-D(*AP*CP*CP*AP*GP*TP*CP*CP*GP*GP*AP*AP*AP*TP*TP*T)-3')


Mass: 4882.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Sus scrofa (pig)
#2: DNA chain DNA (5'-D(*AP*AP*AP*TP*TP*TP*CP*CP*GP*GP*AP*CP*TP*GP*GP*T)-3')


Mass: 4913.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Sus scrofa (pig)
#3: Protein ETS transcription factor ELK1


Mass: 11067.706 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ELK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4X1T8E2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.05 M TRIS hydrochloride pH 8.5, 0.2 M Ammonium chloride, 0.01 M Calcium chloride dihydrate, 30% w/v Polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 8912 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 39.15 Å2 / CC1/2: 0.958 / Net I/σ(I): 10.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 840 / CC1/2: 0.817 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DUX

1dux


Resolution: 2.4→29.73 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245 413 4.97 %
Rwork0.1931 7901 -
obs0.1957 8314 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 650 0 36 1412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091471
X-RAY DIFFRACTIONf_angle_d1.00562119
X-RAY DIFFRACTIONf_chiral_restr0.0499229
X-RAY DIFFRACTIONf_plane_restr0.0118156
X-RAY DIFFRACTIONf_dihedral_angle_d31.231410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.750.28931170.24032506X-RAY DIFFRACTION94.42
2.75-3.460.2311460.2082628X-RAY DIFFRACTION98.82
3.46-29.730.2421500.17382767X-RAY DIFFRACTION98.58
Refinement TLS params.Method: refined / Origin x: 5.19009567119 Å / Origin y: -5.68901637343 Å / Origin z: 18.8724260794 Å
111213212223313233
T0.177643055417 Å20.0196055660215 Å2-0.00515664494488 Å2-0.217152824203 Å20.0800260849453 Å2--0.2417526308 Å2
L3.30944080063 °20.219563869771 °2-1.40354926244 °2-4.08087266264 °20.57177136306 °2--3.50767536354 °2
S0.0834475306294 Å °0.117953981112 Å °0.181743026049 Å °0.0961283876177 Å °0.158513238445 Å °0.0483223115185 Å °-0.221710241953 Å °0.213566262228 Å °-0.199981301012 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