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- PDB-8vjp: Histidine-covalent stapled alpha-helical peptide (155H1) targetin... -

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Basic information

Entry
Database: PDB / ID: 8vjp
TitleHistidine-covalent stapled alpha-helical peptide (155H1) targeting hMcl-1
Components
  • Histidine-covalent stapled alpha-helical peptide
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOPTOSIS / Histidine-covalent stapled alpha-helical peptides
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / mitochondrial fusion / channel activity / Bcl-2 family protein complex / 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 / cellular homeostasis / cell fate determination / mitochondrial fusion / channel activity / Bcl-2 family protein complex / 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 / Signaling by ALK fusions and activated point mutants / 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 / 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 ...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 (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
Similarity search - Domain/homology
: / : / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsMuzzarelli, K.M. / Assar, Z. / Alboreggia, G. / Pellecchia, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Histidine-Covalent Stapled Alpha-Helical Peptides Targeting hMcl-1.
Authors: Alboreggia, G. / Udompholkul, P. / Baggio, C. / Muzzarelli, K. / Assar, Z. / Pellecchia, M.
History
DepositionJan 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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: Histidine-covalent stapled alpha-helical peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6094
Polymers19,2662
Non-polymers3432
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.039, 62.811, 81.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+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: 17850.330 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 Histidine-covalent stapled alpha-helical peptide


Mass: 1415.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-A1AJE / (S~1~R)-3-carbamoyl-4-methoxybenzene-1-sulfinic acid


Mass: 215.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1AJD / (4Z)-oct-4-en-1-ol


Mass: 128.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Imidazole, pH 8.0 and 10% (w/v) PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 8, 2023
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.13→31.41 Å / Num. obs: 55764 / % possible obs: 91.13 % / Redundancy: 9 % / Biso Wilson estimate: 15.34 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.11
Reflection shellResolution: 1.13→1.17 Å / Num. unique obs: 3405 / CC1/2: 0.375 / % possible all: 49.8

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→31.41 Å / SU ML: 0.1202 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.793
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2205 1986 3.61 %
Rwork0.1913 53017 -
obs0.1924 55003 91.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.88 Å2
Refinement stepCycle: LAST / Resolution: 1.13→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 122 225 1572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921369
X-RAY DIFFRACTIONf_angle_d1.29931843
X-RAY DIFFRACTIONf_chiral_restr0.101202
X-RAY DIFFRACTIONf_plane_restr0.024237
X-RAY DIFFRACTIONf_dihedral_angle_d7.6139241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.160.3105850.30181874X-RAY DIFFRACTION46.18
1.16-1.190.3327920.28172559X-RAY DIFFRACTION62.11
1.19-1.220.29311180.26083127X-RAY DIFFRACTION76.68
1.22-1.260.2991570.24583822X-RAY DIFFRACTION93.73
1.26-1.310.26441510.22074036X-RAY DIFFRACTION98.03
1.31-1.360.22611380.21194096X-RAY DIFFRACTION99.02
1.36-1.420.22181410.1934102X-RAY DIFFRACTION99.3
1.42-1.50.20731520.18284119X-RAY DIFFRACTION99.6
1.5-1.590.20041600.17724108X-RAY DIFFRACTION99.74
1.59-1.720.22881510.18014167X-RAY DIFFRACTION99.91
1.72-1.890.21651560.18064148X-RAY DIFFRACTION99.93
1.89-2.160.21311580.18064195X-RAY DIFFRACTION100
2.16-2.720.23961470.18154250X-RAY DIFFRACTION100
2.72-31.410.20251800.19344414X-RAY DIFFRACTION99.98

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