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- PDB-4ath: MITF apo structure -

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Basic information

Entry
Database: PDB / ID: 4ath
TitleMITF apo structure
ComponentsMICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR
KeywordsDNA BINDING PROTEIN / TRANSCRIPTION FACTOR / MELANOMA
Function / homology
Function and homology information


SUMOylation of transcription factors / Regulation of MITF-M-dependent genes involved in apoptosis / melanocyte apoptotic process / 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 ...SUMOylation of transcription factors / Regulation of MITF-M-dependent genes involved in apoptosis / melanocyte apoptotic process / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / lysosomal membrane / 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
Microphthalmia-associated transcription factor
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsPogenberg, V. / Milewski, M. / 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 1.2Jul 17, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4667
Polymers19,9862
Non-polymers4805
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-81.8 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.375, 39.891, 55.160
Angle α, β, γ (deg.)90.00, 117.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MICROPHTHALMIA-ASSOCIATED TRANSCRIPTION FACTOR / MITF


Mass: 9993.066 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 217-296
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsISOFORM A2 SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 52.89 % / Description: NONE
Crystal growDetails: 1.5 M AMMONIUM SULFATE AND 150 MM SODIUM ACETATE (PH 5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.965
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Details: MULTILAYER MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.95→45 Å / Num. obs: 14742 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.2
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.2 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.95→49.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.492 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22778 733 5 %RANDOM
Rwork0.19399 ---
obs0.19566 13993 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.966 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å22.2 Å2
2---0.55 Å20 Å2
3---2.56 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 25 153 1507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211443
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9681942
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2585175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86123.2181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75815298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1561521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2201
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5861.5837
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08921346
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0333606
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3164.5591
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 54 -
Rwork0.295 887 -
obs--83.13 %
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)
14.64-0.4839-0.69230.99230.72061.3982-0.00710.7093-0.3807-0.1749-0.0393-0.15220.34910.220.04650.34710.0780.03980.34590.04770.216750.170133.2246-24.949
21.9689-0.1198-0.41380.11080.0750.30570.12710.59230.9494-0.13290.0243-0.1078-0.2270.042-0.15140.34-0.02040.01070.45740.21670.550447.286248.7783-24.6934
35.49250.2291-1.20432.427-0.30323.27410.09720.08210.5601-0.13760.0314-0.0928-0.11780.1556-0.12860.1310.027-0.01910.13550.04540.211945.296543.4263-13.9358
410.06750.7956-2.11430.24490.06681.00660.0031-0.31230.47320.05830.03690.1034-0.11390.0395-0.04010.19690.03350.00510.17770.00180.237526.764741.2781-3.8945
58.88260.2839-0.19181.7892-0.06811.9361-0.094-0.3420.00170.04440.02270.030.0870.05530.07130.15240.00240.0150.06130.00630.16521.85936.05140.1379
65.84821.5302-0.60292.37-1.172.35750.06820.44920.4762-0.3848-0.0396-0.5904-0.14840.5979-0.02860.3078-0.02090.12550.245-0.04950.421459.850438.6369-15.3389
72.4441-0.5246-0.11631.35530.08251.25160.05960.1558-0.1653-0.0891-0.01290.05050.14870.0466-0.04660.15090.0032-0.00410.1185-0.02340.119745.112730.3138-12.938
87.8874-2.5071-2.42690.87130.76610.85130.13160.43290.0532-0.1462-0.0988-0.06570.0396-0.0258-0.03290.2190.01350.00160.17420.00270.185720.156942.2475-11.5684
98.5505-1.089-2.07463.69630.6284.5769-0.0013-0.23310.1390.2160.0210.2695-0.0067-0.2062-0.01970.1282-0.0101-0.02660.024500.1261-3.184345.71370.8487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A216 - 229
2X-RAY DIFFRACTION2A230 - 242
3X-RAY DIFFRACTION3A243 - 259
4X-RAY DIFFRACTION4A260 - 271
5X-RAY DIFFRACTION5A272 - 295
6X-RAY DIFFRACTION6B214 - 225
7X-RAY DIFFRACTION7B226 - 259
8X-RAY DIFFRACTION8B260 - 276
9X-RAY DIFFRACTION9B277 - 295

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