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- PDB-9ugp: Crystal structure of MCL-1 in complex with HRK BH3 -

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Basic information

Entry
Database: PDB / ID: 9ugp
TitleCrystal structure of MCL-1 in complex with HRK BH3
Components
  • Activator of apoptosis harakiri
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOPTOSIS / BCL-2 family / mitochondrial apoptosis / BH3 Mimetics
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / positive regulation of release of cytochrome c from mitochondria / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / positive regulation of release of cytochrome c from mitochondria / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / negative regulation of autophagy / release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / positive regulation of neuron apoptotic process / channel activity / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Activator of apoptosis harakiri / Activator of apoptosis harakiri / Apoptosis regulator, Mcl-1 / 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 ...Activator of apoptosis harakiri / Activator of apoptosis harakiri / Apoptosis regulator, Mcl-1 / 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
Similarity search - Domain/homology
Activator of apoptosis harakiri / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsWei, H. / Wang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82470176, 82273496 and 31900880 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural analysis of apoptotic MCL1-HRK complex.
Authors: Wang, J. / Jiang, L. / Wei, H.
History
DepositionApr 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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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: Activator of apoptosis harakiri


Theoretical massNumber of molelcules
Total (without water)20,4852
Polymers20,4852
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-14 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.044, 53.997, 68.344
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-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 17669.154 Da / Num. of mol.: 1
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 Activator of apoptosis harakiri / BH3-interacting domain-containing protein 3 / Neuronal death protein DP5


Mass: 2816.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00198
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS pH 6.5, 25%(w/v) polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.39→42.37 Å / Num. obs: 55736 / % possible obs: 88.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.3
Reflection shellResolution: 1.392→1.454 Å / Num. unique obs: 1509 / CC1/2: 0.335

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→25.11 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1966 3692 6.63 %
Rwork0.1711 --
obs0.1728 55711 86.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→25.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 0 176 1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.086
X-RAY DIFFRACTIONf_dihedral_angle_d3.984187
X-RAY DIFFRACTIONf_chiral_restr0.09211
X-RAY DIFFRACTIONf_plane_restr0.01239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.410.3456340.2906497X-RAY DIFFRACTION21
1.41-1.430.3219530.3117739X-RAY DIFFRACTION32
1.43-1.450.29867961X-RAY DIFFRACTION41
1.45-1.470.2608911166X-RAY DIFFRACTION51
1.47-1.490.2525980.251400X-RAY DIFFRACTION60
1.5-1.520.31071120.27571659X-RAY DIFFRACTION72
1.52-1.550.31841390.27111988X-RAY DIFFRACTION85
1.55-1.570.30161490.26742124X-RAY DIFFRACTION93
1.57-1.60.24541600.22892281X-RAY DIFFRACTION97
1.6-1.640.23851630.2172323X-RAY DIFFRACTION99
1.64-1.670.20391600.19732298X-RAY DIFFRACTION100
1.67-1.710.20421660.19182292X-RAY DIFFRACTION99
1.71-1.750.21031660.18292297X-RAY DIFFRACTION100
1.75-1.80.20731650.18822322X-RAY DIFFRACTION100
1.8-1.850.20561630.18242316X-RAY DIFFRACTION100
1.85-1.910.23211620.18982277X-RAY DIFFRACTION100
1.91-1.980.2231690.17162312X-RAY DIFFRACTION100
1.98-2.060.21531630.15732336X-RAY DIFFRACTION100
2.06-2.160.17351640.14972292X-RAY DIFFRACTION100
2.16-2.270.18571620.15262324X-RAY DIFFRACTION100
2.27-2.410.19411640.16322293X-RAY DIFFRACTION100
2.41-2.60.18581670.15792309X-RAY DIFFRACTION100
2.6-2.860.17511610.16982320X-RAY DIFFRACTION100
2.86-3.270.19811640.16622304X-RAY DIFFRACTION100
3.27-4.120.17651620.15112299X-RAY DIFFRACTION99
4.12-25.110.17861680.15882290X-RAY DIFFRACTION99
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)
11.3515-0.6212-0.21594.55810.64821.0208-0.0399-0.23720.1715-0.02060.1905-0.4652-0.02320.2786-0.170.1593-0.00920.0010.2081-0.04210.21629.9391-2.78875.6007
21.47540.25420.17742.3080.52942.6539-0.00410.08040.5876-0.22390.201-0.6792-0.39790.4977-0.15390.2292-0.07660.03510.2228-0.01030.30616.20626.391-1.8914
32.2167-0.38680.91862.4332-1.93855.0348-0.0617-0.46380.45460.4091-0.1022-0.1917-0.5554-0.00880.0780.23820.0111-0.02720.2425-0.06520.2877-7.92179.468213.8355
42.15020.5129-0.55241.55220.93341.97180.0436-0.35320.03160.1551-0.0007-0.14650.07330.0527-0.03360.14770.0032-0.01850.1726-0.00170.1595-4.06390.36419.6916
52.06060.19560.29085.18493.03413.6673-0.1228-0.5978-0.00670.32760.1795-0.07650.14530.2757-0.08570.18150.0193-0.01250.2745-0.01850.19743.9231-2.061613.1881
62.8181-0.88310.71583.4808-0.29941.8160.11290.4313-0.1537-0.293-0.0624-0.01520.0070.1987-0.0640.15530.00630.01540.1926-0.01540.13421.0876-6.2665-6.4967
71.3540.1957-0.1810.79290.06068.2391-0.09910.12810.0751-0.0053-0.01060.0754-0.0998-0.51770.09550.16470.011-0.0080.17190.00360.1362-12.52971.90460.3965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 169 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 223 )
3X-RAY DIFFRACTION3chain 'A' and (resid 224 through 239 )
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 281 )
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 301 )
6X-RAY DIFFRACTION6chain 'A' and (resid 302 through 322 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 51 )

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