[English] 日本語
Yorodumi
- PDB-9mx9: Crystal structure of the DNA binding domain of FLI1 (F362A) in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mx9
TitleCrystal structure of the DNA binding domain of FLI1 (F362A) in complex with a DNA containing two contiguous GGAA sites
Components
  • DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*GP*AP*AP*GP*TP*G)-3')
  • Friend leukemia integration 1 transcription factor
KeywordsDNA BINDING PROTEIN/DNA / Ewing sarcoma / transcription factor / oncogenesis / bone tumor / drug target / deregulation / DNA BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


hemostasis / blood circulation / megakaryocyte development / animal organ morphogenesis / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding ...hemostasis / blood circulation / megakaryocyte development / animal organ morphogenesis / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Friend leukemia integration 1 transcription factor, pointed domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain ...Friend leukemia integration 1 transcription factor, pointed domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Friend leukemia integration 1 transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHou, C. / Tsodikov, O.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA243529 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structure and cooperative formation of a FLI1 filament on contiguous GGAA DNA sites.
Authors: Hou, C. / Tsodikov, O.V.
History
DepositionJan 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Friend leukemia integration 1 transcription factor
D: Friend leukemia integration 1 transcription factor
E: DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*GP*AP*AP*GP*TP*G)-3')
F: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8029
Polymers42,6014
Non-polymers2005
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.000, 119.000, 95.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein Friend leukemia integration 1 transcription factor / Proto-oncogene Fli-1 / Transcription factor ERGB


Mass: 16710.762 Da / Num. of mol.: 2 / Fragment: DNA-binding domain (residues 259-399) / Mutation: F362A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLI1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01543
#2: DNA chain DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*GP*AP*AP*GP*TP*G)-3')


Mass: 4708.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')


Mass: 4471.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate, pH 6.5, 18% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 11403 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.102 / Net I/σ(I): 24.3
Reflection shellResolution: 2.55→2.59 Å / Num. unique obs: 550 / CC1/2: 0.867

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5JVT

5jvt


Resolution: 2.55→37.66 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.143 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.511 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24965 599 5.3 %RANDOM
Rwork0.20628 ---
obs0.20855 10793 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.264 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å2-0 Å2
2---1.55 Å2-0 Å2
3---3.11 Å2
Refinement stepCycle: 1 / Resolution: 2.55→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 608 5 3 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122218
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181758
X-RAY DIFFRACTIONr_angle_refined_deg1.181.4863119
X-RAY DIFFRACTIONr_angle_other_deg1.2141.8694054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57421.64891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19315270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2351512
X-RAY DIFFRACTIONr_chiral_restr0.0580.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02552
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5485.383730
X-RAY DIFFRACTIONr_mcbond_other2.5395.379729
X-RAY DIFFRACTIONr_mcangle_it4.3258.062909
X-RAY DIFFRACTIONr_mcangle_other4.3228.067910
X-RAY DIFFRACTIONr_scbond_it2.5625.0761487
X-RAY DIFFRACTIONr_scbond_other2.5635.0761486
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2537.5562209
X-RAY DIFFRACTIONr_long_range_B_refined6.22152.3392688
X-RAY DIFFRACTIONr_long_range_B_other6.15852.2952687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.554→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 44 -
Rwork0.336 767 -
obs--99.88 %

+
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