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- PDB-3kj2: Mcl-1 in complex with Bim BH3 mutant F4aE -

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Basic information

Entry
Database: PDB / ID: 3kj2
TitleMcl-1 in complex with Bim BH3 mutant F4aE
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 / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / 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 / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / tube formation / positive regulation of T cell apoptotic process / regulation of organ growth / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / cellular response to glucocorticoid stimulus / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / BH domain binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / BH3 domain binding / positive regulation of IRE1-mediated unfolded protein response / 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 / response to cytokine / kidney development / positive regulation of protein-containing complex assembly / : / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / channel activity / spermatogenesis / microtubule binding / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / protein kinase binding / apoptotic process / 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, 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-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
ACETATE ION / Bcl-2-like protein 11 / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.351 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 1.2Nov 1, 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 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)21,0407
Polymers20,7192
Non-polymers3215
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-112 kcal/mol
Surface area9040 Å2
MethodPISA
2
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bcl-2-like protein 11
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bcl-2-like protein 11
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bcl-2-like protein 11
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,16028
Polymers82,8788
Non-polymers1,28320
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area14720 Å2
ΔGint-606 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.456, 71.487, 119.435
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-5-

HOH

21A-31-

HOH

31A-33-

HOH

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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 172-322)
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: 2782.075 Da / Num. of mol.: 1 / Fragment: BH3 region of Bim (UNP 1-21) / Mutation: F17E
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Imidazole, 0.2 M Zinc Acetate, 2% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 2, 2008
RadiationMonochromator: VarimaxHR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 9519 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.083 / Χ2: 1.083 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.435.60.4499251.02599.8
2.43-2.538.70.4219430.969100
2.53-2.659.90.3519380.997100
2.65-2.79100.2749400.993100
2.79-2.9610.10.2049421.007100
2.96-3.1910.10.1349271.019100
3.19-3.5110.10.0919581.079100
3.51-4.0210.10.0679601.205100
4.02-5.06100.0469631.161100
5.06-509.50.0410231.31599

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.351→24.289 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.32 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 448 4.71 %
Rwork0.208 --
obs0.21 9515 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 150.56 Å2 / Biso mean: 44.313 Å2 / Biso min: 14.78 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.351→24.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 8 64 1481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021437
X-RAY DIFFRACTIONf_angle_d0.5491931
X-RAY DIFFRACTIONf_chiral_restr0.041210
X-RAY DIFFRACTIONf_plane_restr0.001250
X-RAY DIFFRACTIONf_dihedral_angle_d13.794537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.351-2.690.2761480.22929543102
2.69-3.3880.2381530.20230033156
3.388-24.2910.2341470.19831103257
Refinement TLS params.Method: refined / Origin x: 3.5994 Å / Origin y: 20.3008 Å / Origin z: 42.3212 Å
111213212223313233
T0.0998 Å20.0065 Å20.0124 Å2-0.0522 Å2-0.0133 Å2--0.144 Å2
L1.6991 °2-0.5589 °20.271 °2-0.239 °20.0492 °2--0.7566 °2
S-0.0164 Å °-0.0662 Å °-0.0307 Å °0.0739 Å °0.0128 Å °0.0189 Å °0.0414 Å °-0.0348 Å °0.011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA172 - 322
2X-RAY DIFFRACTION1allB1 - 22
3X-RAY DIFFRACTION1allB - A1 - 4
4X-RAY DIFFRACTION1allA1 - 70
5X-RAY DIFFRACTION1allA1428

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