[English] 日本語
Yorodumi
- PDB-3rkq: NKX2.5 Homeodomain dimer bound to ANF-242 DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rkq
TitleNKX2.5 Homeodomain dimer bound to ANF-242 DNA
Components
  • (ANF-242 DNA) x 2
  • Homeobox protein Nkx-2.5
KeywordsTRANSCRIPTION/DNA / Helix-turn-Helix / DNA binding / Nucleus / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Nkx-2.5 complex / Purkinje myocyte differentiation / right ventricular cardiac muscle tissue morphogenesis / septum secundum development / proepicardium development / pulmonary myocardium development / cardiac ventricle formation / apoptotic process involved in heart morphogenesis / atrioventricular node cell fate commitment / bundle of His development ...Nkx-2.5 complex / Purkinje myocyte differentiation / right ventricular cardiac muscle tissue morphogenesis / septum secundum development / proepicardium development / pulmonary myocardium development / cardiac ventricle formation / apoptotic process involved in heart morphogenesis / atrioventricular node cell fate commitment / bundle of His development / atrial cardiac muscle cell development / ventricular cardiac myofibril assembly / atrioventricular node cell development / embryonic heart tube left/right pattern formation / positive regulation of cardioblast differentiation / atrial cardiac muscle tissue development / positive regulation of heart contraction / atrioventricular node development / ventricular cardiac muscle cell development / regulation of cardiac muscle cell proliferation / atrial septum morphogenesis / Physiological factors / negative regulation of myotube differentiation / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / pharyngeal system development / positive regulation of sodium ion transport / negative regulation of epithelial cell apoptotic process / outflow tract septum morphogenesis / cardiac muscle tissue morphogenesis / ventricular trabecula myocardium morphogenesis / heart trabecula formation / adult heart development / embryonic heart tube development / aortic valve morphogenesis / cardiac muscle cell development / Cardiogenesis / cardiac muscle cell proliferation / epithelial cell apoptotic process / negative regulation of cardiac muscle cell apoptotic process / DNA-binding transcription activator activity / ventricular septum morphogenesis / heart looping / cardiac septum morphogenesis / thyroid gland development / hemopoiesis / regulation of cardiac muscle contraction / regulation of cardiac conduction / positive regulation of transcription initiation by RNA polymerase II / vasculogenesis / heart morphogenesis / cardiac muscle contraction / spleen development / epithelial cell differentiation / positive regulation of neuron differentiation / epithelial cell proliferation / positive regulation of epithelial cell proliferation / protein-DNA complex / negative regulation of canonical Wnt signaling pathway / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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 ...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 Nkx-2.5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGenis, C. / Scone, P. / Kasahara, H. / Nam, H.-J.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal structure of the human NKX2.5 homeodomain in complex with DNA target.
Authors: Pradhan, L. / Genis, C. / Scone, P. / Weinberg, E.O. / Kasahara, H. / Nam, H.J.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Homeobox protein Nkx-2.5
B: Homeobox protein Nkx-2.5
C: ANF-242 DNA
D: ANF-242 DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9345
Polymers25,9104
Non-polymers241
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-33 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.450, 71.450, 94.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Homeobox protein Nkx-2.5 / Cardiac-specific homeobox / Homeobox protein CSX / Homeobox protein NK-2 homolog E


Mass: 7129.262 Da / Num. of mol.: 2 / Fragment: Homeodomain, UNP residues 138-194 / Mutation: C193S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NKX2-5, CSX, NKX2.5, NKX2E / Production host: Escherichia coli (E. coli) / References: UniProt: P52952
#2: DNA chain ANF-242 DNA


Mass: 5916.819 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain ANF-242 DNA


Mass: 5734.727 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM Tris pH 7.0, 5mM MgCl2, 15% polyethylene glycol monomethyl ether 550 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 30032 / Num. obs: 29800 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.7→1.76 Å / % possible all: 99.5

-
Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30.94 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 103 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1266 4.2 %Random
Rwork0.2109 28272 --
obs-29538 98.4 %-
Solvent computationBsol: 40.8257 Å2
Displacement parametersBiso max: 50.87 Å2 / Biso mean: 22.9407 Å2 / Biso min: 3.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.227 Å20 Å20 Å2
2---1.227 Å20 Å2
3---2.453 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 773 1 170 1942
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0231.5
X-RAY DIFFRACTIONc_scbond_it1.7842
X-RAY DIFFRACTIONc_mcangle_it1.5722
X-RAY DIFFRACTIONc_scangle_it2.6552.5

+
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://pdbjlvh1.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