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- PDB-2jm6: Solution structure of MCL-1 complexed with NOXAB -

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Basic information

Entry
Database: PDB / ID: 2jm6
TitleSolution structure of MCL-1 complexed with NOXAB
Components
  • Myeloid cell leukemia-1 protein Mcl-1 homolog
  • Noxa
KeywordsAPOPTOSIS / MCL-1 / BCL-2 / HELICAL BUNDLE / BH3-ONLY
Function / homology
Function and homology information


Activation of NOXA and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / BH domain binding / channel activity / fibroblast apoptotic process / mitochondrial fusion ...Activation of NOXA and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / BH domain binding / channel activity / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / T cell homeostasis / BH3 domain binding / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of anoikis / response to X-ray / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to UV / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / activation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / regulation of apoptotic process / mitochondrial outer membrane / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Phorbol-12-myristate-13-acetate-induced protein 1 / Phorbol-12-myristate-13-acetate-induced / 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 ...Phorbol-12-myristate-13-acetate-induced protein 1 / Phorbol-12-myristate-13-acetate-induced / 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 / Phorbol-12-myristate-13-acetate-induced protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsMCL-1/NOXAB complex
AuthorsCzabotar, P.E. / Lee, E.F. / van Delft, M.F. / Day, C.L. / Smith, B.J. / Huang, D.C.S. / Fairlie, W.D. / Hinds, M.G. / Colman, P.M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural insights into the degradation of Mcl-1 induced by BH3 domains
Authors: Czabotar, P.E. / Lee, E.F. / van Delft, M.F. / Day, C.L. / Smith, B.J. / Huang, D.C.S. / Fairlie, W.D. / Hinds, M.G. / Colman, P.M.
History
DepositionOct 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Noxa
B: Myeloid cell leukemia-1 protein Mcl-1 homolog


Theoretical massNumber of molelcules
Total (without water)21,4052
Polymers21,4052
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 / 256lowest energy, least restraint violations, structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Noxa


Mass: 3144.715 Da / Num. of mol.: 1 / Fragment: residues 68-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pmaip1, Noxa / Plasmid: PET-31b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9JM54
#2: Protein Myeloid cell leukemia-1 protein Mcl-1 homolog / Bcl-2-related protein EAT/mcl1 / Induced myeloid leukemia cell differentiation protein


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: Mcl1 / Plasmid: PGEX6P-3 / 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 / Details: MCL-1/NOXAB complex
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY
1323D 1H-13C NOESY
1423D 1H-15N NOESY
1533D HNHA
1633D HNHA
1733D HNHB
1823D HNHB
1913D HNCA
11023D HNCA
11113D (H)CCH-TOCSY
11223D (H)CCH-TOCSY
11313D HNCO
11423D HNCO
NMR detailsText: The structure was determined using standard 3D heteronuclear methods

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C, U-99% 15N] MCL_1, 0.5 mM NOXAB, 95% H2O, 5% D2O95% H2O/5% D2O
20.5 mM MCL-1, 0.5 mM [U-100% 13C, U-100% 15N] NOXAB, 95% H2O, 5% D2O95% H2O/5% D2O
30.5 mM [U-15N] MCL-1, 0.5 mM NOXAB, 95% H2O, 5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMCL_1[U-99% 13C; U-99% 15N]1
0.5 mMNOXABnatural abundance1
0.5 mMMCL-1natural abundance2
0.5 mMNOXAB[U-100% 13C; U-100% 15N]2
0.5 mMMCL-1[U-15N]3
0.5 mMNOXABnatural abundance3
Sample conditionsIonic strength: 120 / 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 AVBrukerAV5001
Bruker DRXBrukerDRX6002
Bruker AVBrukerAV8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3BRUKER BIOSPINcollection
TopSpin1.3BRUKER BIOSPINstructure solution
XEASY1.3.13Bartels et al.structure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: lowest energy, least restraint violations, structures with acceptable covalent geometry
Conformers calculated total number: 256 / Conformers submitted total number: 20

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