- PDB-4c7n: Crystal Structure of the synthetic peptide iM10 in complex with t... -
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Basic information
Entry
Database: PDB / ID: 4c7n
Title
Crystal Structure of the synthetic peptide iM10 in complex with the coiled-coil region of MITF
Components
MICROPHTHALMIA ASSOCIATED TRANSCRIPTION FACTOR
SYNTHETIC ALPHA-HELIX, IM10
Keywords
TRANSCRIPTION / COILED-COIL / PROTEIN ENGINEERING
Function / homology
Function and homology information
melanocyte apoptotic process / Regulation of MITF-M dependent genes involved in invasion / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / positive regulation of DNA-templated transcription initiation / Regulation of MITF-M dependent genes involved in metabolism / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / regulation of RNA biosynthetic process / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling ...melanocyte apoptotic process / Regulation of MITF-M dependent genes involved in invasion / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / positive regulation of DNA-templated transcription initiation / Regulation of MITF-M dependent genes involved in metabolism / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / regulation of RNA biosynthetic process / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling / E-box binding / Regulation of MITF-M-dependent genes involved in apoptosis / camera-type eye development / Regulation of MITF-M-dependent genes involved in pigmentation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cell fate commitment / SUMOylation of transcription factors / Transcriptional and post-translational regulation of MITF-M expression and activity / osteoclast differentiation / negative regulation of cell migration / DNA-binding transcription repressor activity, RNA polymerase II-specific / Wnt signaling pathway / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / lysosomal membrane / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / negative regulation of apoptotic process / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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. ...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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence details
CHAIN A CORRESPONDS TO ISOFORM 9 OF 075030. ALA1, SER2, ALA50, PRO51 ARE THE CAP RESIDUES FROM THE ...CHAIN A CORRESPONDS TO ISOFORM 9 OF 075030. ALA1, SER2, ALA50, PRO51 ARE THE CAP RESIDUES FROM THE CHEMICAL SYNTHESIS.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2 Å3/Da / Density % sol: 38.6 % / Description: NONE
Resolution: 1.95→60.92 Å / Num. obs: 7041 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.6
Reflection shell
Resolution: 1.95→2.18 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 6.6 / % possible all: 99.7
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Processing
Software
Name
Version
Classification
REFMAC
5.7.0032
refinement
XDS
datareduction
Aimless
datascaling
autoSHARP
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.1→60.92 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.888 / SU B: 7.424 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. DISORDERED REGIONS WERE NOT MODELED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25312
266
4.7 %
RANDOM
Rwork
0.22755
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obs
0.22872
5428
99.89 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK