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- PDB-4atk: MITF:E-box complex -

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Basic information

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


melanocyte apoptotic process / SUMOylation of transcription factors / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of DNA-templated transcription initiation / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling / camera-type eye development / pigmentation ...melanocyte apoptotic process / SUMOylation of transcription factors / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of DNA-templated transcription initiation / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling / camera-type eye development / pigmentation / E-box binding / cell fate commitment / osteoclast differentiation / negative regulation of cell migration / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / nucleoplasm / 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 domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. ...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 domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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: 2.95 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR
B: MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR
C: 5'-D(*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*T)-3'
D: 5'-D(*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)37,9834
Polymers37,9834
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-36.8 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.420, 45.090, 110.660
Angle α, β, γ (deg.)90.00, 136.47, 90.00
Int Tables number5
Space group name H-MC121

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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(*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*T)-3' / E-BOX SEQUENCE


Mass: 4898.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHETIC / Source: (synth.) MUS MUSCULUS (house mouse)
Sequence detailsISOFORM A2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.09 % / Description: NONE

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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: 0.488
ReflectionResolution: 2.95→55 Å / Num. obs: 10446 / % possible obs: 94.7 % / Observed criterion σ(I): 3.5 / Redundancy: 4.7 % / Biso Wilson estimate: 69 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 94.4

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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: 2.95→26.072 Å / σ(F): 0 / Phase error: 34.51 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2736 521 5.1 %
Rwork0.2534 --
obs0.2551 10312 92.69 %
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.048 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 75.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2536 Å20 Å21.0151 Å2
2---3.9941 Å20 Å2
3---4.2476 Å2
Refinement stepCycle: LAST / Resolution: 2.95→26.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 650 0 0 1653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091760
X-RAY DIFFRACTIONf_angle_d1.42500
X-RAY DIFFRACTIONf_dihedral_angle_d24.49740
X-RAY DIFFRACTIONf_chiral_restr0.078273
X-RAY DIFFRACTIONf_plane_restr0.006214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9573-3.2520.431110.50292341X-RAY DIFFRACTION86
3.252-3.71580.27791170.26032495X-RAY DIFFRACTION92
3.7158-4.65650.26531280.22262505X-RAY DIFFRACTION92
4.6565-14.66210.25441340.21192396X-RAY DIFFRACTION85
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)
14.47050.1151-3.85561.95520.30825.16480.1709-0.55770.29970.4212-0.1805-0.0719-0.7826-0.19050.28810.40810.0156-0.22670.3185-0.03990.226527.023914.470914.424
26.8399-0.2039-0.24620.21920.14120.0928-0.10410.5893-0.2026-0.8569-0.08330.82160.8809-1.41890.15290.7537-0.2339-0.23650.8180.03390.474623.11257.8334-6.4901
38.0357-2.6843-5.86481.4672.1984.72460.28150.3003-0.1908-0.0295-0.2244-0.2142-0.4117-0.11170.00060.17750.0345-0.10190.10240.08690.272639.74872.7895-5.1597
41.64391.0110.00220.8895-0.27731.32410.1742-0.4642-0.5051-0.0787-0.12910.10260.3191-0.3850.09990.1564-0.0675-0.05420.21410.06390.167821.9942-1.252810.1444
53.2622.17894.05485.33471.495.42260.0583-1.0318-0.15240.79790.3477-1.27520.08711.7694-0.04410.42570.023-0.20490.60290.04080.371744.71673.711613.889
62.54830.4128-0.59731.1282-0.53991.4904-0.1756-0.34380.06180.1091-0.1224-0.206-0.48320.35130.03650.2823-0.0032-0.19080.09860.03560.144939.782310.29474.437
71.5595-1.31261.10561.1558-1.18571.93520.2798-0.4267-0.22610.0825-0.0540.18590.4304-0.16510.17920.2509-0.0446-0.9360.8141-0.03560.281719.00635.2718.2257
81.8239-0.12460.31680.9921-0.63641.8708-0.1082-0.18390.078-0.06580.06070.142-0.3243-0.41030.00030.334-0.074-0.79150.7958-0.14680.196718.1397.725617.9625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 207:230)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 231:242)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 243:268)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 205:230)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 231:242)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 243:259)
7X-RAY DIFFRACTION7CHAIN C
8X-RAY DIFFRACTION8CHAIN D

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