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- PDB-4bpj: Mcl-1 bound to alpha beta Puma BH3 peptide 3 -

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Entry
Database: PDB / ID: 4bpj
TitleMcl-1 bound to alpha beta Puma BH3 peptide 3
Components
  • ALPHA BETA BH3-PEPTIDE
  • FUSION PROTEIN CONSISTING OF INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG
KeywordsAPOPTOSIS / CHIMERA / BIM
Function / homology
Function and homology information


positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / T cell apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / cellular homeostasis / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process ...positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / T cell apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / cellular homeostasis / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process / mitochondrial fusion / Activation of PUMA and translocation to mitochondria / Bcl-2 family protein complex / execution phase of apoptosis / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / apoptotic mitochondrial changes / BH3 domain binding / negative regulation of anoikis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / intrinsic apoptotic signaling pathway / negative regulation of autophagy / response to endoplasmic reticulum stress / release of cytochrome c from mitochondria / determination of adult lifespan / cellular response to ionizing radiation / apoptotic signaling pathway / 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 / cellular response to hypoxia / mitochondrial outer membrane / cell differentiation / positive regulation of apoptotic process / mitochondrial matrix / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / 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 ...Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / 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 homolog / Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-binding component 3, isoforms 1/2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsSmith, B.J. / Lee, E.F. / Checco, J.W. / Gellman, S.H. / Fairlie, W.D.
CitationJournal: Chembiochem / Year: 2013
Title: Structure-Guided Rational Design of Alpha/Beta-Peptide Foldamers with High Affinity for Bcl-2 Family Prosurvival Proteins.
Authors: Smith, B.J. / Lee, E.F. / Checco, J.W. / Evangelista, M. / Gellman, S.H. / Fairlie, W.D.
History
DepositionMay 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Source and taxonomy
Revision 2.0Apr 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.2May 15, 2024Group: Data collection / Category: chem_comp / Item: _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FUSION PROTEIN CONSISTING OF INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG
D: ALPHA BETA BH3-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,80111
Polymers20,3322
Non-polymers4699
Water2,180121
1
A: FUSION PROTEIN CONSISTING OF INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG
D: ALPHA BETA BH3-PEPTIDE
hetero molecules

A: FUSION PROTEIN CONSISTING OF INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG
D: ALPHA BETA BH3-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,60222
Polymers40,6644
Non-polymers93818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7840 Å2
ΔGint-379.4 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.458, 60.260, 44.804
Angle α, β, γ (deg.)90.00, 118.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1329-

CL

21A-2023-

HOH

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Components

#1: Protein FUSION PROTEIN CONSISTING OF INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG / BCL-2-RELATED PROTEIN EAT/MCL1 / BCL-2-LIKE PROTEIN 3 / BCL2- L-3 / BCL-2-RELATED PROTEIN EAT/MCL1 ...BCL-2-RELATED PROTEIN EAT/MCL1 / BCL-2-LIKE PROTEIN 3 / BCL2- L-3 / BCL-2-RELATED PROTEIN EAT/MCL1 / MCL1/EAT / MCL-1 BCL-2-LIKE PROTEIN 3 / BCL2-L-3 / BCL-2-RELATED PROTEIN EAT/MCL1 / MCL1/EAT


Mass: 18227.592 Da / Num. of mol.: 1
Fragment: FUSION PROTEIN OF MOUSE MCL-1, RESIDUES 152-189 AND HUMAN MCL-1 RESIDUES, 209-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse), (gene. exp.) HOMO SAPIENS (human)
Plasmid: PGEX6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P97287, UniProt: Q07820
#2: Protein/peptide ALPHA BETA BH3-PEPTIDE


Mass: 2104.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9BXH1*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHIMERA WITH MOUSE MCL-1

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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: 2.24 Å3/Da / Density % sol: 36.9 % / Description: NONE
Crystal growpH: 7 / Details: 0.2M IMADAZOLE, PH7.0 0.2M ZINC ACETATE

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.26511
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 11, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26511 Å / Relative weight: 1
ReflectionResolution: 1.6→19.69 Å / Num. obs: 24069 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.57 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.78
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.75 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.53 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NL9

2nl9


Resolution: 1.599→19.693 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 25.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 1204 5 %
Rwork0.1993 --
obs0.2008 24066 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.599→19.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 9 121 1441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061451
X-RAY DIFFRACTIONf_angle_d1.0891964
X-RAY DIFFRACTIONf_dihedral_angle_d14.115559
X-RAY DIFFRACTIONf_chiral_restr0.074213
X-RAY DIFFRACTIONf_plane_restr0.004258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5993-1.66330.30931290.26072443X-RAY DIFFRACTION97
1.6633-1.7390.27271330.23732537X-RAY DIFFRACTION100
1.739-1.83060.25981350.21952559X-RAY DIFFRACTION100
1.8306-1.94520.24571340.20712549X-RAY DIFFRACTION100
1.9452-2.09520.23591340.19822542X-RAY DIFFRACTION100
2.0952-2.30580.23541340.1842553X-RAY DIFFRACTION99
2.3058-2.63880.22661350.18942564X-RAY DIFFRACTION100
2.6388-3.3220.21711350.19992553X-RAY DIFFRACTION100
3.322-19.69470.21921350.19512562X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 13.0196 Å / Origin y: 18.1289 Å / Origin z: 8.5538 Å
111213212223313233
T0.114 Å2-0.0088 Å20.0102 Å2-0.1808 Å2-0.0037 Å2--0.1086 Å2
L2.4029 °2-0.9281 °20.1099 °2-3.0402 °2-0.5276 °2--3.3464 °2
S-0.1078 Å °-0.0913 Å °-0.1194 Å °0.1198 Å °0.0015 Å °-0.1602 Å °0.199 Å °0.2212 Å °0.0675 Å °
Refinement TLS groupSelection details: ALL

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