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- PDB-6mbe: Human Mcl-1 in complex with the designed peptide dM7 -

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Basic information

Entry
Database: PDB / ID: 6mbe
TitleHuman Mcl-1 in complex with the designed peptide dM7
Components
  • Induced myeloid leukemia cell differentiation protein Mcl-1
  • dM7
KeywordsAPOPTOSIS / anti-apoptotic Bcl-2 / inhibitor / design
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 / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / 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 / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / 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 / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
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-2 family ...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-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 / Orthogonal Bundle / Mainly Alpha
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsJenson, J.M. / Keating, A.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM110048 United States
CitationJournal: Structure / Year: 2019
Title: Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1.
Authors: Frappier, V. / Jenson, J.M. / Zhou, J. / Grigoryan, G. / Keating, A.E.
History
DepositionAug 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details

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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: dM7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2273
Polymers20,1922
Non-polymers351
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-22 kcal/mol
Surface area9090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.758, 80.758, 57.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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: 17580.984 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 dM7


Mass: 2611.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.7 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.4 M sodium citrate pH 6.5, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 10429 / % possible obs: 97.3 % / Redundancy: 17.6 % / Biso Wilson estimate: 39.34 Å2 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.031 / Rrim(I) all: 0.14 / Χ2: 1.03 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.2930.6043850.7080.3370.6990.48173.8
2.29-2.334.90.6944390.7550.3060.7650.51383.6
2.33-2.387.80.6124880.8540.210.650.54292.8
2.38-2.429.90.6895160.8940.2090.7230.5297.2
2.42-2.4812.50.5985080.9240.1650.6210.53699.8
2.48-2.5314.90.6475520.9180.1650.6680.54699.8
2.53-2.617.20.5075110.9570.1220.5220.589100
2.6-2.67190.4815260.9760.110.4930.666100
2.67-2.7520.50.4255240.9820.0950.4350.624100
2.75-2.8321.20.3595420.9790.0790.3680.638100
2.83-2.9421.30.3095350.9890.0680.3170.732100
2.94-3.0521.60.2555240.990.0550.2610.764100
3.05-3.1921.80.2095400.9950.0450.2140.869100
3.19-3.3621.70.1775370.9960.0390.1810.924100
3.36-3.5721.80.1465350.9960.0320.1491.148100
3.57-3.8521.60.1165340.9970.0250.1191.363100
3.85-4.2321.50.15420.9980.0220.1021.431100
4.23-4.8521.30.0955510.9980.0210.0971.663100
4.85-6.121.20.15520.9980.0220.1031.6100
6.1-5019.40.0735880.9990.0170.0752.29599

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PK1

3pk1


Resolution: 2.25→29.94 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.25
RfactorNum. reflection% reflection
Rfree0.2211 1051 10.09 %
Rwork0.1919 --
obs0.1951 10414 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.45 Å2 / Biso mean: 54.3414 Å2 / Biso min: 23.32 Å2
Refinement stepCycle: final / Resolution: 2.25→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 1 47 1464
Biso mean--33.58 42.21 -
Num. residues----176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2471-2.34940.25861110.2493957106882
2.3494-2.47320.2551280.23141136126497
2.4732-2.62810.22481350.219812101345100
2.6281-2.83080.2591300.219911771307100
2.8308-3.11540.26251340.218912041338100
3.1154-3.56560.22211370.208811961333100
3.5656-4.48990.2161300.166312171347100
4.4899-29.9430.18791460.165212661412100

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