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- PDB-2pqk: X-ray crystal structure of human Mcl-1 in complex with Bim BH3 -

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Basic information

Entry
Database: PDB / ID: 2pqk
TitleX-ray crystal structure of human Mcl-1 in complex with Bim BH3
Components
  • Bim BH3 peptide
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOPTOSIS / Bcl-2 family / BH3 domain
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / protein transmembrane transporter activity / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / protein transmembrane transporter activity / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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
Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBare, 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
DepositionMay 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 10, 2013Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software

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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: Bim BH3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5426
Polymers21,3232
Non-polymers2194
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-79 kcal/mol
Surface area8620 Å2
MethodPISA
2
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bim BH3 peptide
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bim BH3 peptide
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bim BH3 peptide
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bim BH3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,16924
Polymers85,2938
Non-polymers87716
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 area13510 Å2
ΔGint-434 kcal/mol
Surface area30180 Å2
MethodPISA
3
A: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules

B: Bim BH3 peptide
hetero molecules

B: Bim BH3 peptide
hetero molecules

B: Bim BH3 peptide
hetero molecules

B: Bim BH3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,16924
Polymers85,2938
Non-polymers87716
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
crystal symmetry operation5_455x-1/2,y+1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Buried area7650 Å2
ΔGint-455 kcal/mol
Surface area36040 Å2
MethodPISA
4
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bim BH3 peptide
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bim BH3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,08512
Polymers42,6464
Non-polymers4388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6010 Å2
ΔGint-206 kcal/mol
Surface area15830 Å2
MethodPISA
5
A: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules

B: Bim BH3 peptide
hetero molecules

B: Bim BH3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,08512
Polymers42,6464
Non-polymers4388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Buried area3080 Å2
ΔGint-216 kcal/mol
Surface area18760 Å2
MethodPISA
6
A: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules

B: Bim BH3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5426
Polymers21,3232
Non-polymers2194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Buried area960 Å2
ΔGint-91 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.087, 71.846, 118.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1-

HOH

21A-62-

HOH

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Components

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


Mass: 17937.359 Da / Num. of mol.: 1 / Fragment: residues 172-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q07820
#2: Protein/peptide Bim BH3 peptide


Mass: 3385.771 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide, the sequence naturally occurs in Homo sapiens (Human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M zinc acetate, 0.1M imidazole, 20% PEG 3350, pH 7.0, 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 / Wavelength: 0.98166
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98166 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 15 / Number: 199904 / Rmerge(I) obs: 0.059 / Χ2: 1.39 / D res high: 2.03 Å / D res low: 50 Å / Num. obs: 27631 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.375098.110.0361.5797.2
3.474.3710010.0471.6597.3
3.033.4710010.051.6757.5
2.763.0310010.0611.5087.6
2.562.7610010.0841.397.6
2.412.5610010.1011.097.7
2.292.4110010.1311.0137.6
2.192.2910010.2481.7127.4
2.12.1999.810.2380.9597.1
2.032.197.710.3671.2475.3
ReflectionResolution: 2→34.6 Å / Num. obs: 15537 / % possible obs: 99 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.062 / Χ2: 1.469 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.075.60.33514650.711195.5
2.07-2.156.60.23715040.792198
2.15-2.2570.18215540.953199.7
2.25-2.377.20.13815340.9051100
2.37-2.527.30.11415591.1011100
2.52-2.717.30.09215581.2251100
2.71-2.997.20.07615711.5251100
2.99-3.427.20.06615752.1931100
3.42-4.3170.05215892.671100
4.31-506.60.0416282.356196.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→34.6 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.721 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 776 5 %RANDOM
Rwork0.194 ---
obs0.196 15537 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.035 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.86 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 4 118 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221382
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.9341863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.325167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17923.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43715246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9671514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021042
X-RAY DIFFRACTIONr_nbd_refined0.210.2698
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2110
X-RAY DIFFRACTIONr_metal_ion_refined0.2790.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.218
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1030.24
X-RAY DIFFRACTIONr_mcbond_it0.6461.5833
X-RAY DIFFRACTIONr_mcangle_it1.21121337
X-RAY DIFFRACTIONr_scbond_it1.9413573
X-RAY DIFFRACTIONr_scangle_it3.1174.5526
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 38 -
Rwork0.204 964 -
obs-1002 87.97 %
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)
12.73480.06680.29892.01480.18831.88230.0674-0.1775-0.31190.38380.0046-0.01950.2710.0076-0.072-0.00580.0086-0.0092-0.0748-0.0023-0.04812.638919.796242.9922
24.4472-0.10191.36962.71022.97339.13120.0256-0.04460.05250.13080.0493-0.46690.33550.1153-0.0749-0.09640.0340.0141-0.0551-0.0285-0.031712.409426.090735.1058
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA172 - 3213 - 152
22BB0 - 224 - 26

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