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- PDB-3pk1: Crystal structure of Mcl-1 in complex with the BaxBH3 domain -

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Basic information

Entry
Database: PDB / ID: 3pk1
TitleCrystal structure of Mcl-1 in complex with the BaxBH3 domain
Components
  • Apoptosis regulator BAX
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOPTOSIS/APOPTOSIS REGULATOR / Bcl-2 family fold / Regulation of apoptosis / Bax / mitochondria / APOPTOSIS-APOPTOSIS REGULATOR complex
Function / homology
Function and homology information


T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / B cell homeostatic proliferation / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / regulation of nitrogen utilization / cell fate determination / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / channel activity / positive regulation of epithelial cell apoptotic process / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / hypothalamus development / thymocyte apoptotic process / pore complex / BH3 domain binding / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / germ cell development / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / negative regulation of apoptotic signaling pathway / protein transmembrane transporter activity / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of anoikis / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / ectopic germ cell programmed cell death / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / ovarian follicle development / extrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / negative regulation of autophagy / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / response to cytokine / apoptotic signaling pathway / response to gamma radiation / positive regulation of protein-containing complex assembly
Similarity search - Function
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 ...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
: / Apoptosis regulator BAX / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.486 Å
AuthorsCzabotar, P.E. / Colman, P.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Mutation to Bax beyond the BH3 domain disrupts interactions with pro-survival proteins and promotes apoptosis
Authors: Czabotar, P.E. / Lee, E.F. / Thompson, G.V. / Wardak, A.Z. / Fairlie, W.D. / Colman, P.M.
History
DepositionNov 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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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: Apoptosis regulator BAX
C: Induced myeloid leukemia cell differentiation protein Mcl-1
D: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,25422
Polymers50,2314
Non-polymers2,02318
Water88349
1
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,24012
Polymers25,1152
Non-polymers1,12410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-17 kcal/mol
Surface area9050 Å2
MethodPISA
2
C: Induced myeloid leukemia cell differentiation protein Mcl-1
D: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,01510
Polymers25,1152
Non-polymers8998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-17 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.923, 81.469, 57.927
Angle α, β, γ (deg.)90.00, 124.23, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLYGLYchain A and (resseq 173:192 or resseq 205:321 )AA173 - 19236 - 55
121THRTHRVALVALchain A and (resseq 173:192 or resseq 205:321 )AA205 - 32168 - 184
211SERSERGLYGLYchain C and (resseq 173:192 or resseq 205:321 )CC173 - 19236 - 55
221THRTHRVALVALchain C and (resseq 173:192 or resseq 205:321 )CC205 - 32168 - 184
112ALAALAILEILEchain B and (resseq 54:80 )BB54 - 807 - 33
212ALAALAILEILEchain D and (resseq 54:80 )DD54 - 807 - 33

NCS ensembles :
ID
1
2

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Components

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


Mass: 21278.070 Da / Num. of mol.: 2 / Fragment: Mcl-1 Bcl-2 like region, UNP residues 174-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07820
#2: Protein/peptide Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 3837.381 Da / Num. of mol.: 2 / Fragment: BH3 domain, UNP residues 48-81 / Source method: obtained synthetically / Details: Synthesized peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07812
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.9 Å3/Da / Density % sol: 35.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M Sodium Acetate, 0.1M Hepes, 25mM Cadmium Sulfate, 5mM TCEP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 26, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
Reflection twinOperator: h+2*l,-k,-l / Fraction: 0.154
ReflectionResolution: 2.486→50 Å / Num. all: 13250 / Num. obs: 13065 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 17.13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.5-2.594.90.6412.351237194.1
2.59-2.695.20.5872.821273196.8
2.69-2.825.50.4873.691308198.7
2.82-2.965.90.1414.91317199.7
2.96-3.1560.3136.71302199.7
3.15-3.3960.18610.881331199.5
3.39-3.736.10.11316.371303199.8
3.73-4.2760.0724.11341199.8
4.27-5.386.10.05131.891321199.8
5.38-505.80.03641.471332197.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NL9

2nl9


Resolution: 2.486→20.136 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 1.34 / Phase error: 42.4 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 671 5.14 %Random
Rwork0.212 ---
obs0.2135 13062 98.2 %-
all-13733 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.211 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 162.63 Å2 / Biso min: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.5445 Å20 Å223.7726 Å2
2---11.0388 Å20 Å2
3---1.4943 Å2
Refinement stepCycle: LAST / Resolution: 2.486→20.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 18 49 2740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082707
X-RAY DIFFRACTIONf_angle_d1.1013627
X-RAY DIFFRACTIONf_dihedral_angle_d16.41027
X-RAY DIFFRACTIONf_chiral_restr0.067413
X-RAY DIFFRACTIONf_plane_restr0.003457
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1114X-RAY DIFFRACTIONPOSITIONAL0.061
12C1114X-RAY DIFFRACTIONPOSITIONAL0.061
21B213X-RAY DIFFRACTIONPOSITIONAL0.027
22D213X-RAY DIFFRACTIONPOSITIONAL0.027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4887-2.73840.35831520.31342959X-RAY DIFFRACTION90
2.7384-3.1330.33791490.27763137X-RAY DIFFRACTION95
3.133-3.94110.22981680.20863127X-RAY DIFFRACTION95
3.9411-18.6250.20541830.1713168X-RAY DIFFRACTION94
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)
1-0.23680.0926-0.17441.09780.24431.39520.0125-0.1189-0.018-0.0857-0.17440.1829-0.0898-0.008600.35470.0314-0.0030.3451-0.00470.421617.2162-45.8321-2.5905
20.0689-0.01990.20310.0135-0.13050.26370.11930.004-0.23610.2739-0.0961-0.50320.2869-0.05570.00020.3402-0.00060.02750.3886-0.00260.31322.6665-52.50939.2911
30.72810.0888-1.25640.94040.62710.45390.12330.1068-0.11560.048-0.09370.2441-0.1697-0.00600.36440.0173-0.02890.3655-0.02440.3593.3922-21.889818.5031
40.1743-0.0986-0.16840.0172-0.06130.0659-0.16820.1755-0.01230.67280.0438-0.1774-0.1453-0.1747-00.4078-0.02520.02050.3949-0.02720.39116.4056-15.373818.9866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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