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- PDB-2nl9: Crystal structure of the Mcl-1:Bim BH3 complex -

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Basic information

Entry
Database: PDB / ID: 2nl9
TitleCrystal structure of the Mcl-1:Bim BH3 complex
Components
  • Bcl-2-like protein 11
  • FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
KeywordsAPOPTOSIS / Bcl-2 / Mcl-1 / Bim
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / meiosis I / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / cellular homeostasis / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / cellular response to glucocorticoid stimulus / channel activity / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / BH domain binding / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / T cell homeostasis / odontogenesis of dentin-containing tooth / BH3 domain binding / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / negative regulation of autophagy / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / kidney development / response to cytokine / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / spermatogenesis / microtubule binding / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site ...: / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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
Bcl-2-like protein 11 / Induced myeloid leukemia cell differentiation protein Mcl-1 homolog / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsCzabotar, P.E. / Colman, P.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structural insights into the degradation of Mcl-1 induced by BH3 domains.
Authors: Czabotar, P.E. / Lee, E.F. / van Delft, M.F. / Day, C.L. / Smith, B.J. / Huang, D.C. / Fairlie, W.D. / Hinds, M.G. / Colman, P.M.
History
DepositionOct 19, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 14, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,67810
Polymers21,1852
Non-polymers4938
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-162 kcal/mol
Surface area8700 Å2
MethodPISA, PQS
2
A: FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
B: Bcl-2-like protein 11
hetero molecules

A: FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
B: Bcl-2-like protein 11
hetero molecules

A: FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
B: Bcl-2-like protein 11
hetero molecules

A: FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,71240
Polymers84,7388
Non-polymers1,97332
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area15130 Å2
ΔGint-1121 kcal/mol
Surface area30490 Å2
MethodPISA
3
A: FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
hetero molecules

A: FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
hetero molecules

A: FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
hetero molecules

A: FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
hetero molecules

B: Bcl-2-like protein 11
hetero molecules

B: Bcl-2-like protein 11
hetero molecules

B: Bcl-2-like protein 11
hetero molecules

B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,71240
Polymers84,7388
Non-polymers1,97332
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation5_545x+1/2,y-1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation8_555x+1/2,-y+1/2,-z+1/21
Buried area9840 Å2
ΔGint-1004 kcal/mol
Surface area35780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.380, 70.080, 117.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2001-

CL

21A-2040-

HOH

31A-2115-

HOH

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Components

#1: Protein FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog


Mass: 17909.926 Da / Num. of mol.: 1 / Fragment: residues 171-208 and residues 209-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Mcl1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P97287, UniProt: Q07820
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-interacting mediator of cell death


Mass: 3274.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43521
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 0.2M zinc acetate, 0.2M imidazole, 2mM TCEP, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791, 0.9792, 0.9715
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2005 / Details: monochrometer
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochrometer
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97921
30.97151
ReflectionResolution: 1.5→50 Å / Num. obs: 29809 / % possible obs: 85.1 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 160.5
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.503 / Num. unique all: 976 / % possible all: 28.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.55→34.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.279 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1469 5.1 %RANDOM
Rwork0.173 ---
obs0.174 28898 91.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.336 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.55→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1349 0 8 201 1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221422
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9391928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4075180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.73622.76376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50515260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3171517
X-RAY DIFFRACTIONr_chiral_restr0.0860.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021089
X-RAY DIFFRACTIONr_nbd_refined0.2130.2830
X-RAY DIFFRACTIONr_nbtor_refined0.320.21026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2167
X-RAY DIFFRACTIONr_metal_ion_refined0.0440.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.233
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0430.25
X-RAY DIFFRACTIONr_mcbond_it1.0611.5863
X-RAY DIFFRACTIONr_mcangle_it1.60421357
X-RAY DIFFRACTIONr_scbond_it2.4913635
X-RAY DIFFRACTIONr_scangle_it3.594.5562
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 52 -
Rwork0.286 1046 -
obs-1098 47.1 %
Refinement TLS params.Method: refined / Origin x: 21.1054 Å / Origin y: 14.634 Å / Origin z: 41.2183 Å
111213212223313233
T-0.019 Å20.0218 Å20.0046 Å2--0.0556 Å2-0.0139 Å2---0.0338 Å2
L1.5437 °20.1293 °20.3883 °2-1.1915 °2-0.2469 °2--1.4584 °2
S-0.0281 Å °-0.1429 Å °0.1107 Å °0.1842 Å °-0.0008 Å °0.0233 Å °-0.2472 Å °-0.0717 Å °0.029 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL

IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA172 - 3222 - 152
2BB53 - 753 - 25

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