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- PDB-4c7n: Crystal Structure of the synthetic peptide iM10 in complex with t... -

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Basic information

Entry
Database: PDB / ID: 4c7n
TitleCrystal Structure of the synthetic peptide iM10 in complex with the coiled-coil region of MITF
Components
  • MICROPHTHALMIA ASSOCIATED TRANSCRIPTION FACTOR
  • SYNTHETIC ALPHA-HELIX, IM10
KeywordsTRANSCRIPTION / 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 RNA biosynthetic process / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / regulation of osteoclast differentiation / melanocyte differentiation / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence ...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 RNA biosynthetic process / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / regulation of osteoclast differentiation / melanocyte differentiation / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / bone remodeling / Regulation of MITF-M-dependent genes involved in apoptosis / camera-type eye development / E-box binding / Regulation of MITF-M-dependent genes involved in pigmentation / SUMOylation of transcription factors / cell fate commitment / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / 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 / nucleoplasm / nucleus / cytosol / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 ...MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Microphthalmia-associated transcription factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsWohlwend, D. / Gerhardt, S. / Kuekenshoener, T. / Einsle, O.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Improving Coiled Coil Stability While Maintaining Specificity by a Bacterial Hitchhiker Selection System.
Authors: Kukenshoner, T. / Wohlwend, D. / Niemoller, J. / Dondapati, P. / Speck, J. / Adeniran, A.V. / Nieth, A. / Gerhardt, S. / Einsle, O. / Muller, K.M. / Arndt, K.M.
History
DepositionSep 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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: SYNTHETIC ALPHA-HELIX, IM10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3948
Polymers12,1912
Non-polymers1,2046
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-102.6 kcal/mol
Surface area7890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.701, 33.265, 61.125
Angle α, β, γ (deg.)90.00, 94.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MICROPHTHALMIA ASSOCIATED TRANSCRIPTION FACTOR


Mass: 6102.989 Da / Num. of mol.: 1 / Fragment: COILED-COIL REGION, RESIDUES 357-403 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O75030
#2: Protein SYNTHETIC ALPHA-HELIX, IM10


Mass: 6087.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN 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

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

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.6 % / Description: NONE
Crystal growpH: 7 / Details: 3.5 M NAFORMATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00799
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2013
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00799 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.25312 266 4.7 %RANDOM
Rwork0.22755 ---
obs0.22872 5428 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å2-0.68 Å2
2--0 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→60.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 6 49 888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019839
X-RAY DIFFRACTIONr_bond_other_d0.0020.02853
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9451116
X-RAY DIFFRACTIONr_angle_other_deg0.73431941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.934596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76223.70454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.16615181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3821513
X-RAY DIFFRACTIONr_chiral_restr0.0640.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
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_it1.2142.092390
X-RAY DIFFRACTIONr_mcbond_other1.1952.087389
X-RAY DIFFRACTIONr_mcangle_it1.8093.109484
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8552.466449
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 29 -
Rwork0.251 409 -
obs--100 %
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)
11.1931-0.92635.09111.505-5.616537.86-0.10930.16480.0895-0.0586-0.039-0.1071-0.28150.31290.14820.0385-0.0286-0.00740.03660.00690.084118.821814.121976.0408
21.46520.46282.64631.67784.578329.2477-0.04230.159-0.0879-0.03770.00380.08890.309-0.57310.03850.0151-0.02490.00160.05690.00170.072112.357413.798176.4947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 48
2X-RAY DIFFRACTION2B1 - 51

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