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- PDB-1wsx: Solution structure of MCL-1 -

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Basic information

Entry
Database: PDB / ID: 1wsx
TitleSolution structure of MCL-1
Componentsmyeloid cell leukemia sequence 1
KeywordsAPOPTOSIS / helical bundle / Bcl-2 / BH3 / Mcl-1
Function / homology
Function and homology information


BH domain binding / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy ...BH domain binding / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / mitochondrial outer membrane / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions ...Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, distance geometry, simulated annealing
AuthorsDay, C.L. / Chen, L. / Richardson, S.J. / Harrison, P.J. / Huang, D.C. / Hinds, M.G.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Solution Structure of Prosurvival Mcl-1 and Characterization of Its Binding by Proapoptotic BH3-only Ligands
Authors: Day, C.L. / Chen, L. / Richardson, S.J. / Harrison, P.J. / Huang, D.C. / Hinds, M.G.
History
DepositionNov 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: myeloid cell leukemia sequence 1


Theoretical massNumber of molelcules
Total (without water)18,2611
Polymers18,2611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 256structures with the lowest energy, structures with the least restraint violations, structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein myeloid cell leukemia sequence 1 / Myeloid Cell Leukemia-1


Mass: 18260.670 Da / Num. of mol.: 1 / Fragment: residues 152-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: mcl-1 / Plasmid: PLASMID / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P97287

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
1213D 15N-separated NOESY
2313D 13C-separated NOESY
NMR detailsText: the structure was determined using standard 3D heteronuclar NMR techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM U-15N Mcl-150mM Sodium Phoshate; 70mM Sodium Chloride; 0.04% Sodium Azide; 95% H2O, 5% D2O
21mM U-13C,15N Mcl-150mM Sodium Phoshate; 70mM Sodium Chloride; 0.04% Sodium Azide; 95% H2O, 5% D2O
Sample conditionsIonic strength: 120mM / pH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVBrukerAV5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker AGcollection
XEASY1.3.13Bartels, C., Xia, T.H., Billeter, M., Guntert, P., and Wuthrich, K.data analysis
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.structure solution
XPLOR-NIH2C.D.SCHWIETERS,J.J.KUSZEWSKI,N.TJANDRA,G.M.CLORErefinement
RefinementMethod: torsion angle dynamics, distance geometry, simulated annealing
Software ordinal: 1
Details: The structures are based on a total of 3974 constaints, 3507 are NOE-derived distance constraints, 335 dihedral angle restraints and 66 hydrogen bond constraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy, structures with the least restraint violations, structures with acceptable covalent geometry
Conformers calculated total number: 256 / Conformers submitted total number: 20

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