[English] 日本語
Yorodumi
- PDB-4ati: MITF:M-box complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ati
TitleMITF:M-box complex
Components
  • 5'-D(*AP*GP*GP*GP*TP*CP*AP*TP*GP*TP*GP*CP*TP*AP*AP*C)-3'
  • 5'-D(*GP*TP*TP*AP*GP*CP*AP*CP*AP*TP*GP*AP*CP*CP*CP*T)-3'
  • MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR
KeywordsDNA-BINDING PROTEIN/DNA / DNA-BINDING PROTEIN-DNA COMPLEX / MELANOMA
Function / homology
Function and homology information


melanocyte apoptotic process / SUMOylation of transcription factors / positive regulation of DNA-templated transcription initiation / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling / camera-type eye development / pigmentation / E-box binding / cell fate commitment ...melanocyte apoptotic process / SUMOylation of transcription factors / positive regulation of DNA-templated transcription initiation / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling / camera-type eye development / pigmentation / E-box binding / cell fate commitment / negative regulation of cell migration / osteoclast differentiation / Wnt signaling pathway / regulation of cell population proliferation / regulation of gene expression / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / lysosomal membrane / DNA-templated transcription / chromatin binding / positive regulation of gene expression / 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 / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleus / cytoplasm
Similarity search - Function
MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain ...MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Microphthalmia-associated transcription factor
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPogenberg, V. / Deineko, V. / Wilmanns, M.
CitationJournal: Genes Dev. / Year: 2012
Title: Restricted Leucine Zipper Dimerization and Specificity of DNA Recognition of the Melanocyte Master Regulator Mitf
Authors: Pogenberg, V. / Hogmundsdottir, M. / Bergsteinsdottir, K. / Schepsky, A. / Phung, B. / Deineko, V. / Milewski, M. / Steingrimsson, E. / Wilmanns, M.
History
DepositionMay 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Dec 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: MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR
B: MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR
C: 5'-D(*GP*TP*TP*AP*GP*CP*AP*CP*AP*TP*GP*AP*CP*CP*CP*T)-3'
D: 5'-D(*AP*GP*GP*GP*TP*CP*AP*TP*GP*TP*GP*CP*TP*AP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)37,9834
Polymers37,9834
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-37.4 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.990, 104.260, 44.900
Angle α, β, γ (deg.)90.00, 112.15, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR / MITF


Mass: 14093.230 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 180-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q08874
#2: DNA chain 5'-D(*GP*TP*TP*AP*GP*CP*AP*CP*AP*TP*GP*AP*CP*CP*CP*T)-3' / E-BOX SEQUENCE


Mass: 4858.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse)
#3: DNA chain 5'-D(*AP*GP*GP*GP*TP*CP*AP*TP*GP*TP*GP*CP*TP*AP*AP*C)-3' / E-BOX SEQUENCE


Mass: 4938.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsISOFORM A2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 68 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9535
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
Reflection twinOperator: -H-2L, -K, L / Fraction: 0.499
ReflectionResolution: 2.6→55 Å / Num. obs: 15081 / % possible obs: 96.6 % / Observed criterion σ(I): 2.5 / Redundancy: 3.5 % / Biso Wilson estimate: 75.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ATH

4ath


Resolution: 2.6→37.869 Å / σ(F): 0 / Phase error: 31.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2737 759 5 %
Rwork0.2274 --
obs0.2302 15081 96.39 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.769 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 79.3 Å2
Baniso -1Baniso -2Baniso -3
1-11.2707 Å20 Å22.6111 Å2
2---23.8887 Å20 Å2
3---12.618 Å2
Refinement stepCycle: LAST / Resolution: 2.6→37.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 650 0 14 1728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011801
X-RAY DIFFRACTIONf_angle_d1.3612548
X-RAY DIFFRACTIONf_dihedral_angle_d23.465750
X-RAY DIFFRACTIONf_chiral_restr0.073281
X-RAY DIFFRACTIONf_plane_restr0.007217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6003-2.79940.6141680.56792811X-RAY DIFFRACTION92
2.7994-3.0780.44221570.38862928X-RAY DIFFRACTION94
3.078-3.51630.28381550.23422929X-RAY DIFFRACTION95
3.5163-4.40390.20741340.18472988X-RAY DIFFRACTION95
4.4039-13.39380.23961370.17942643X-RAY DIFFRACTION84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.56140.3147-0.46026.3161-0.46521.8664-0.0786-0.439-0.11960.54490.1131-1.5309-0.00790.5379-0.03310.69660.1246-0.46990.5947-0.15640.915420.6636-19.139218.8272
23.7832-0.0483-0.60866.6668-1.68175.76750.5038-0.3055-0.42160.7042-0.2993-1.69410.56010.7433-0.25330.57860.0133-0.43780.7567-0.21870.933520.1371-19.711921.167
34.46053.11240.4687.44780.69412.3740.6517-0.1887-0.02971.269-0.0614-0.2610.5255-0.1022-0.45240.4335-0.0379-0.00560.66910.05660.116.4925-20.72721.4517
40.0137-0.143-0.08561.65020.18022.86950.49960.29770.1164-0.622-0.34150.16450.5423-0.7411-0.10410.33910.06320.04890.76540.06770.213-7.1124-22.04925.0651
52.5714-0.9874-1.92034.43821.22351.49160.1661-0.26060.4385-0.22740.2131-1.36960.25310.0895-0.26240.2908-0.00580.00080.65340.0130.50917.6208-23.893110.2746
66.0947-1.80633.02561.59920.4383.2274-0.1447-0.29020.71120.1113-0.24910.0236-0.7472-0.62570.13210.51980.08720.07720.70290.05920.21341.176-5.95549.484
71.46660.43360.93541.39230.27480.60090.30740.3520.2092-0.0295-0.17060.36750.1381-0.1697-0.03270.2937-0.07590.03230.8054-0.03260.15-13.9217-18.046710.7308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN C
2X-RAY DIFFRACTION2CHAIN D
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 209:242)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 243:269)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 203:229)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 230:242)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 243:274)

+
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