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- PDB-5w89: Crystal structure of human Mcl-1 in complex with modified Bim BH3... -

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Basic information

Entry
Database: PDB / ID: 5w89
TitleCrystal structure of human Mcl-1 in complex with modified Bim BH3 peptide SAH-MS1-18
Components
  • Induced myeloid leukemia cell differentiation protein Mcl-1
  • modified Bim BH3 peptide SAH-MS1-18
KeywordsPEPTIDE BINDING PROTEIN / Stapled peptide / BCL-2 family / BH3 domain / apoptosis
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH domain binding / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH domain binding / 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 / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / 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 / Resolution: 1.42 Å
AuthorsRezaei Araghi, R. / Jenson, J.M. / Grant, R.A. / Keating, A.E.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Iterative optimization yields Mcl-1-targeting stapled peptides with selective cytotoxicity to Mcl-1-dependent cancer cells.
Authors: Rezaei Araghi, R. / Bird, G.H. / Ryan, J.A. / Jenson, J.M. / Godes, M. / Pritz, J.R. / Grant, R.A. / Letai, A. / Walensky, L.D. / Keating, A.E.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry / _struct_conn_type.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: modified Bim BH3 peptide SAH-MS1-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8784
Polymers19,7482
Non-polymers1312
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-46 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.390, 43.390, 163.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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: 17249.705 Da / Num. of mol.: 1 / Fragment: UNP residues 172-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q07820
#2: Protein/peptide modified Bim BH3 peptide SAH-MS1-18


Mass: 2497.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.95 Å3/Da / Density % sol: 36.85 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Reservior: 25% PEG 3350, 50mM Tris pH 9.0, 0.2 M Ammonium acetate; Protein: 408 uM in 20 mM TRis , 10 mM TCEP, 5mM Zn2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.42→19.405 Å / Num. obs: 30358 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 17.304 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.085 / Χ2: 1.147 / Net I/σ(I): 15.97 / Num. measured all: 525289 / Scaling rejects: 920
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.42-1.4617.2331.3261.8538189221622160.7281.367100
1.46-1.517.3510.9932.6237686217221720.7841.024100
1.5-1.5416.8160.7823.434977208120800.8360.806100
1.54-1.5917.9480.6334.3236381202720270.9130.652100
1.59-1.6417.6070.4715.9135020198919890.9490.486100
1.64-1.716.6530.4046.7932140193219300.9530.41799.9
1.7-1.7617.2350.3258.4131764185318430.9730.33599.5
1.76-1.8318.3990.24711.6933027179617950.9860.25499.9
1.83-1.9118.1590.214.431198172017180.9880.20699.9
1.91-2.0117.5550.16317.9228861165116440.9940.16899.6
2.01-2.1217.6720.12822.1427921158915800.9950.13299.4
2.12-2.2517.0770.1125.4825393149814870.9970.11399.3
2.25-2.415.4870.09927.1621605142013950.9960.10398.2
2.4-2.5917.4590.08731.4422871132813100.9980.08998.6
2.59-2.8417.9680.07733.8621759122812110.9980.07998.6
2.84-3.1817.3290.0735.8919027112210980.9980.07297.9
3.18-3.6717.3020.06338.911709410149880.9990.06497.4
3.67-4.4915.8680.05638.49130918628250.9980.05795.7
4.49-6.3517.0020.05239.57112897026640.9990.05494.6
6.35-19.40515.5740.05338.8359964293850.9990.05589.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.42→19.405 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.78
RfactorNum. reflection% reflection
Rfree0.1855 1518 5 %
Rwork0.142 --
obs0.1442 30358 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.79 Å2 / Biso mean: 31.5563 Å2 / Biso min: 9.64 Å2
Refinement stepCycle: final / Resolution: 1.42→19.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 2 124 1443
Biso mean--23.16 39.88 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081355
X-RAY DIFFRACTIONf_angle_d0.8651826
X-RAY DIFFRACTIONf_chiral_restr0.058200
X-RAY DIFFRACTIONf_plane_restr0.005233
X-RAY DIFFRACTIONf_dihedral_angle_d24.07511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.42-1.46580.25651350.174725652700100
1.4658-1.51820.23461360.151325842720100
1.5182-1.5790.23131360.152425912727100
1.579-1.65080.17341360.126125892725100
1.6508-1.73780.19421380.132926112749100
1.7378-1.84660.1881360.128125882724100
1.8466-1.9890.18691390.130726372776100
1.989-2.1890.16911370.12592616275399
2.189-2.50510.15851380.13082615275399
2.5051-3.1540.1741410.14392673281498
3.154-19.40640.19821460.15352771291796

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