[English] 日本語
Yorodumi
- PDB-4xrs: Heterodimeric complex of transcription factors MEIS1 and DLX3 on ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xrs
TitleHeterodimeric complex of transcription factors MEIS1 and DLX3 on specific DNA
Components
  • (Homeobox protein ...) x 2
  • DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')
  • DNA (5'-D(P*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*A)-3')
  • DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*TP*T)-3')
  • DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')
KeywordsTRANSCRIPTION / heterodimer / DNA
Function / homology
Function and homology information


hair follicle cell proliferation / cell growth involved in cardiac muscle cell development / odontoblast differentiation / negative regulation of myeloid cell differentiation / lens morphogenesis in camera-type eye / eye development / hair cell differentiation / embryonic pattern specification / definitive hemopoiesis / hair follicle morphogenesis ...hair follicle cell proliferation / cell growth involved in cardiac muscle cell development / odontoblast differentiation / negative regulation of myeloid cell differentiation / lens morphogenesis in camera-type eye / eye development / hair cell differentiation / embryonic pattern specification / definitive hemopoiesis / hair follicle morphogenesis / megakaryocyte development / odontogenesis of dentin-containing tooth / blood vessel development / hemopoiesis / negative regulation of neuron differentiation / BMP signaling pathway / epithelial cell differentiation / locomotory behavior / animal organ morphogenesis / brain development / placenta development / Wnt signaling pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Distal-less-like homeobox protein, N-terminal domain / Homeobox protein distal-less-like N terminal / : / Homeobox protein PKNOX/Meis, N-terminal / N-terminal of Homeobox Meis and PKNOX1 / : / Homeobox KN domain / Homeobox KN domain / Helix-turn-helix motif / Homeobox domain, metazoa ...Distal-less-like homeobox protein, N-terminal domain / Homeobox protein distal-less-like N terminal / : / Homeobox protein PKNOX/Meis, N-terminal / N-terminal of Homeobox Meis and PKNOX1 / : / Homeobox KN domain / Homeobox KN domain / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox protein Meis1 / Homeobox protein DLX-3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsJorma, A. / Yin, Y. / Nitta, K.R. / Dave, K. / Enge, M. / Kivioja, T. / Popov, A. / Morgunova, E. / Taipale, J.
CitationJournal: Nature / Year: 2015
Title: DNA-dependent formation of transcription factor pairs alters their binding specificity.
Authors: Jolma, A. / Yin, Y. / Nitta, K.R. / Dave, K. / Popov, A. / Taipale, M. / Enge, M. / Kivioja, T. / Morgunova, E. / Taipale, J.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: DNA (5'-D(P*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*A)-3')
D: DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')
E: DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*TP*T)-3')
L: DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')
A: Homeobox protein Meis1
B: Homeobox protein Meis1
G: Homeobox protein DLX-3
I: Homeobox protein DLX-3


Theoretical massNumber of molelcules
Total (without water)47,7178
Polymers47,7178
Non-polymers00
Water00
1
M: DNA (5'-D(P*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*A)-3')
L: DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')
A: Homeobox protein Meis1
G: Homeobox protein DLX-3


Theoretical massNumber of molelcules
Total (without water)23,4054
Polymers23,4054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-18 kcal/mol
Surface area14060 Å2
MethodPISA
2
D: DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')
E: DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*TP*T)-3')
B: Homeobox protein Meis1
I: Homeobox protein DLX-3


Theoretical massNumber of molelcules
Total (without water)24,3124
Polymers24,3124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-15 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.636, 69.845, 116.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA chain , 4 types, 4 molecules MDEL

#1: DNA chain DNA (5'-D(P*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*A)-3')


Mass: 4527.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')


Mass: 5130.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*TP*T)-3')


Mass: 5585.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')


Mass: 5281.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Homeobox protein ... , 2 types, 4 molecules ABGI

#5: Protein Homeobox protein Meis1


Mass: 6914.002 Da / Num. of mol.: 2 / Fragment: UNP residues 283-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEIS1 / Plasmid: PETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O00470
#6: Protein Homeobox protein DLX-3


Mass: 6681.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLX3 / Plasmid: PETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O60479

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 8000, TRIS, Magnesium chloride, buthanol / PH range: 7 - 8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2014
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.08
ReflectionResolution: 2.9→50 Å / Num. all: 46033 / Num. obs: 11191 / % possible obs: 90.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 109.76 Å2 / Rmerge(I) obs: 0.0608 / Net I/σ(I): 13.08
Reflection shellResolution: 2.964→3.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.0608 / Mean I/σ(I) obs: 0.63 / % possible all: 88.39

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXphenix.refine: 1.9_1692refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2A, 2DJN

3k2a

2djn


Resolution: 3.5→49.314 Å / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 45.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.3591 651 5.33 %random
Rwork0.3305 11570 --
obs0.3427 6829 88.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 232.96 Å2 / Biso mean: 136.3207 Å2 / Biso min: 82.43 Å2
Refinement stepCycle: final / Resolution: 3.5→49.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 1352 0 0 3247
Num. residues----292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073471
X-RAY DIFFRACTIONf_angle_d1.1794961
X-RAY DIFFRACTIONf_chiral_restr0.183550
X-RAY DIFFRACTIONf_plane_restr0.007398
X-RAY DIFFRACTIONf_dihedral_angle_d27.2141390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5029-3.85520.46851630.38232894305784
3.8552-4.41270.42721530.38192941309485
4.4127-5.55780.40491570.36742890304784
5.5578-44.77040.30861390.30222845298482

+
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