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- PDB-2rod: Solution Structure of MCL-1 Complexed with NoxaA -

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Basic information

Entry
Database: PDB / ID: 2rod
TitleSolution Structure of MCL-1 Complexed with NoxaA
Components
  • Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
  • Noxa
KeywordsAPOPTOSIS / Mcl-1 / NoxaA / BH3-only / Bcl-2 / Cytoplasm / Developmental protein / Differentiation / Membrane / Mitochondrion / Nucleus / Phosphoprotein / Transmembrane / Ubl conjugation
Function / homology
Function and homology information


Activation of NOXA and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of establishment of protein localization to mitochondrion / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / fibroblast apoptotic process / positive regulation of DNA damage response, signal transduction by p53 class mediator / Bcl-2 family protein complex / apoptotic mitochondrial changes / T cell homeostasis ...Activation of NOXA and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of establishment of protein localization to mitochondrion / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / fibroblast apoptotic process / positive regulation of DNA damage response, signal transduction by p53 class mediator / Bcl-2 family protein complex / apoptotic mitochondrial changes / T cell homeostasis / BH3 domain binding / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of anoikis / 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 X-ray / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / response to UV / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / negative regulation of autophagy / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / regulation of apoptotic process / cell differentiation / positive regulation of apoptotic process / mitochondrial matrix / protein heterodimerization activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / 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 detailsStructure of BH3 domain of the BH3-only protein NoxaA bound to Mcl-1
AuthorsDay, C.L. / Smits, C. / Fan, F.C. / Lee, E.F. / Fairlie, W.D. / Hinds, M.G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the BH3 Domains from the p53-Inducible BH3-Only Proteins Noxa and Puma in Complex with Mcl-1
Authors: Day, C.L. / Smits, C. / Fan, F.C. / Lee, E.F. / Fairlie, W.D. / Hinds, M.G.
History
DepositionMar 17, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
B: Noxa


Theoretical massNumber of molelcules
Total (without water)21,3012
Polymers21,3012
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 least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Induced myeloid leukemia cell differentiation protein Mcl-1 homolog / Bcl-2-related protein EAT/mcl1 / Mcl-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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P97287
#2: Protein/peptide Noxa / NoxaA


Mass: 3040.490 Da / Num. of mol.: 1 / Fragment: residues 17-42
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Noxa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q9JM54

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of BH3 domain of the BH3-only protein NoxaA bound to Mcl-1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D HNHA
1423D 1H-15N NOESY
1523D 1H-13C NOESY
1623D HNHA
NMR detailsText: standard 3D heteronuclear NMR methods were used for resonance assignment

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM [U-100% 13C; U-100% 15N] Mcl-1; 0.5mM NoxaA; 95% H2O/5% D2O95% H2O/5% D2O
20.5mM Mcl-1; 0.5mM [U-100% 13C; U-100% 15N] NoxaA; 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMcl-1[U-100% 13C; U-100% 15N]1
0.5 mMNoxaA1
0.5 mMMcl-12
0.5 mMNoxaA[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 120 mM / pH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
XEASY1.3Bartels et al.peak picking
XEASY1.3Bartels et al.chemical shift assignment
XEASY1.3Bartels et al.data analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: The structures were calculated based on a total of 3355 constraints. 2662 are NOE derived and 184 of these are intermolecular. A total of 325 dihedral angle constraints were used and 184 hydrogen bonds.
NMR constraintsNOE constraints total: 2662 / NOE intraresidue total count: 849 / NOE long range total count: 725 / NOE medium range total count: 545 / NOE sequential total count: 543 / Hydrogen bond constraints total count: 184 / Protein phi angle constraints total count: 175 / Protein psi angle constraints total count: 150
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 256 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.2 Å
NMR ensemble rmsDistance rms dev: 0.01 Å / Distance rms dev error: 0.0009 Å

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