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- PDB-4bpi: Mcl-1 bound to alpha beta Puma BH3 peptide 2 -

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Basic information

Entry
Database: PDB / ID: 4bpi
TitleMcl-1 bound to alpha beta Puma BH3 peptide 2
Components
  • ALPHA BETA BH3PEPTIDE
  • 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 / protein transmembrane transporter activity / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of intrinsic apoptotic signaling pathway / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway / negative regulation of autophagy / response to endoplasmic reticulum stress / release of cytochrome c from mitochondria / cellular response to ionizing radiation / determination of adult lifespan / 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 / cytoplasm / cytosol
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: 1.982 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_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_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_rmsd_angle / 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUSION PROTEIN CONSISTING OF INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG
B: ALPHA BETA BH3PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0257
Polymers20,4632
Non-polymers5625
Water30617
1
A: FUSION PROTEIN CONSISTING OF INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG
B: ALPHA BETA BH3PEPTIDE
hetero molecules

A: FUSION PROTEIN CONSISTING OF INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG
B: ALPHA BETA BH3PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,05014
Polymers40,9264
Non-polymers1,12410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6050 Å2
ΔGint-94.4 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.780, 53.780, 93.965
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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 BH3PEPTIDE


Mass: 2235.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9BXH1*PLUS
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.89 Å3/Da / Density % sol: 51.3 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES, PH7.5 1M SODIUM ACETATE, 0.05M CADMIUM SULPHATE

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.265106
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: 1.265106 Å / Relative weight: 1
ReflectionResolution: 1.9→18.69 Å / Num. obs: 11279 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 10.09 % / Biso Wilson estimate: 37.16 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.88
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 15.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.95 / % possible all: 92.8

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Processing

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

2nl9


Resolution: 1.982→18.688 Å / SU ML: 0.17 / σ(F): 2.04 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 566 5 %
Rwork0.2169 --
obs0.2183 11279 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.982→18.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 5 17 1313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161338
X-RAY DIFFRACTIONf_angle_d1.2031770
X-RAY DIFFRACTIONf_dihedral_angle_d15.661503
X-RAY DIFFRACTIONf_chiral_restr0.08196
X-RAY DIFFRACTIONf_plane_restr0.004228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9824-2.18160.27341350.20642564X-RAY DIFFRACTION97
2.1816-2.49660.24091410.19612667X-RAY DIFFRACTION100
2.4966-3.1430.28111420.24512690X-RAY DIFFRACTION100
3.143-18.6890.22761480.21242792X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.1676 Å / Origin y: -13.5078 Å / Origin z: 8.2027 Å
111213212223313233
T0.4211 Å2-0.0178 Å20.0087 Å2-0.2091 Å2-0.0005 Å2--0.2587 Å2
L3.1489 °21.0133 °21.5528 °2-4.4709 °20.1178 °2--3.1175 °2
S0.0258 Å °0.1938 Å °-0.4084 Å °-0.2717 Å °0.1988 Å °0.0298 Å °0.5251 Å °-0.0781 Å °-0.1685 Å °
Refinement TLS groupSelection details: ALL

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