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- PDB-2nla: Crystal structure of the Mcl-1:mNoxaB BH3 complex -

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Basic information

Entry
Database: PDB / ID: 2nla
TitleCrystal structure of the Mcl-1:mNoxaB BH3 complex
Components
  • FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
  • Phorbol-12-myristate-13-acetate-induced protein 1
KeywordsAPOPTOSIS / Bcl-2 / Mcl-1 / Noxa
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 / BH domain binding / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity ...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 / BH domain binding / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / 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 / protein transmembrane transporter activity / 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 / Signaling by ALK fusions and activated point mutants / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / 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 / Induced myeloid leukemia cell differentiation protein Mcl-1 / Phorbol-12-myristate-13-acetate-induced protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCzabotar, P.E. / 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. / Fairlie, W.D. / Hinds, M.G. / Colman, P.M.
History
DepositionOct 19, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 14, 2017Group: Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / pdbx_entity_src_syn
Item: _entity.src_method
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Dec 27, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
B: Phorbol-12-myristate-13-acetate-induced protein 1


Theoretical massNumber of molelcules
Total (without water)20,8302
Polymers20,8302
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-10 kcal/mol
Surface area9110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.381, 85.381, 46.916
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog


Mass: 17816.135 Da / Num. of mol.: 1 / Fragment: residues 171-208 and residues 209-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens
Genus: Rattus, Homo / Species: , / Strain: , / Gene: Mcl1 / Plasmid: pGEX-6P3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P97287, UniProt: Q07820
#2: Protein/peptide Phorbol-12-myristate-13-acetate-induced protein 1 / Protein Noxa


Mass: 3013.519 Da / Num. of mol.: 1 / Fragment: BH3 (UNP residues 68-93) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9JM54
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG 4K, 4% isopropanol, 5% dioxane, 0.1M tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9715 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2005 / Details: monochrometer
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochrometer
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9715 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 4938 / % possible obs: 99.9 % / Redundancy: 9 % / Rmerge(I) obs: 0.068 / Χ2: 1.383 / Net I/σ(I): 13.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.646 / Num. unique all: 476 / Χ2: 0.941 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERV. 1.3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→73.92 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.873 / SU B: 55.937 / SU ML: 0.472 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CHAIN D REFERS TO THE NOXA PEPTIDE WHICH IS COVALENTLY LINKED TO MCL-1 THROUGH CYS 286 OF MCL-1 AND CYS 75 OF NOXA. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 230 4.7 %RANDOM
Rwork0.207 ---
obs0.211 4699 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20.68 Å20 Å2
2--1.36 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.8→73.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 0 31 1406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221395
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9511874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5715169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21322.95871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.40715264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5161517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021044
X-RAY DIFFRACTIONr_nbd_refined0.2420.2717
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2947
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.29
X-RAY DIFFRACTIONr_mcbond_it0.4251.5875
X-RAY DIFFRACTIONr_mcangle_it0.70521353
X-RAY DIFFRACTIONr_scbond_it0.9493590
X-RAY DIFFRACTIONr_scangle_it1.5614.5521
LS refinement shellResolution: 2.798→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 18 -
Rwork0.413 344 -
obs-362 98.91 %
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)
17.3458-0.5017-0.61555.72160.08510.5334-0.0137-0.46160.776-0.15520.1268-0.0328-0.9296-0.6959-0.1132-0.35860.0610.031-0.3017-0.0586-0.323-26.60623.2318-7.1963
220.4622-9.66523.559220.42760.30257.76550.57581.2816-0.6782-1.8879-0.06371.5006-0.11880.0764-0.5121-0.1677-0.01080.0187-0.1562-0.1316-0.4211-18.725320.71814.2364
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA175 - 3215 - 151
22BB73 - 936 - 26

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