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- PDB-3kj0: Mcl-1 in complex with Bim BH3 mutant I2dY -

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Basic information

Entry
Database: PDB / ID: 3kj0
TitleMcl-1 in complex with Bim BH3 mutant I2dY
Components
  • Bcl-2-like protein 11
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOPTOSIS / bcl-2 / bh3 / protein-peptide complex / Alternative splicing / Cytoplasm / Developmental protein / Differentiation / Isopeptide bond / Membrane / Mitochondrion / Nucleus / Phosphoprotein / Polymorphism / Transmembrane / Ubl conjugation
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / meiosis I / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / mammary gland development / cell fate determination / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / cellular response to glucocorticoid stimulus / mitochondrial fusion / channel activity / Bcl-2 family protein complex / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / BH3 domain binding / T cell homeostasis / odontogenesis of dentin-containing tooth / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / negative regulation of autophagy / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / kidney development / response to cytokine / positive regulation of protein-containing complex assembly / Signaling by ALK fusions and activated point mutants / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / microtubule binding / spermatogenesis / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein kinase binding / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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
Bcl-2-like protein 11 / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFire, E. / Grant, R.A. / Keating, A.E.
CitationJournal: Protein Sci. / Year: 2010
Title: Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes.
Authors: Fire, E. / Gulla, S.V. / Grant, R.A. / Keating, A.E.
History
DepositionNov 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 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
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2393
Polymers21,1172
Non-polymers1221
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-10 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.381, 52.943, 69.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT / Bcl-2-like protein 3 / Bcl2-L-3


Mass: 17937.359 Da / Num. of mol.: 1 / Fragment: (UNP 172-326)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L3, mcl-1, MCL1 / Plasmid: pSV282 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q07820
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 3179.463 Da / Num. of mol.: 1 / Fragment: BH3 region of BIM (UNP 1-23) / Mutation: I6Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L11, BIM / Plasmid: pSV282 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O43521
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.777568 Å3/Da / Density % sol: 30.804321 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris, 45% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2007
RadiationMonochromator: crystal monochronomater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 16362 / % possible obs: 96.3 % / Redundancy: 7.9 % / Biso Wilson estimate: 18.51 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.339 / % possible all: 68.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_129refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.138 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.21 / σ(F): 1.37 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 777 4.76 %
Rwork0.1853 --
obs0.1872 16317 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.31 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 22.464 Å2
Baniso -1Baniso -2Baniso -3
1--3.054 Å20 Å20 Å2
2--3.047 Å20 Å2
3---0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 8 139 1633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031521
X-RAY DIFFRACTIONf_angle_d0.6432047
X-RAY DIFFRACTIONf_dihedral_angle_d13.305572
X-RAY DIFFRACTIONf_chiral_restr0.048217
X-RAY DIFFRACTIONf_plane_restr0.003266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7004-1.80690.26861070.22292064X-RAY DIFFRACTION79
1.8069-1.94640.23811270.19652628X-RAY DIFFRACTION99
1.9464-2.14220.22971390.18142656X-RAY DIFFRACTION100
2.1422-2.4520.25171420.17992640X-RAY DIFFRACTION100
2.452-3.08870.23631130.18132741X-RAY DIFFRACTION100
3.0887-29.14240.19771490.17962811X-RAY DIFFRACTION100

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