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- PDB-4b4s: Crystal Structure of a pro-survival Bcl-2:Bim BH3 complex -

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Basic information

Entry
Database: PDB / ID: 4b4s
TitleCrystal Structure of a pro-survival Bcl-2:Bim BH3 complex
Components
  • BCL-2-LIKE PROTEIN 10
  • BCL-2-LIKE PROTEIN 11
KeywordsAPOPTOSIS
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / female gamete generation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / mitochondria-associated endoplasmic reticulum membrane contact site / developmental pigmentation ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / female gamete generation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / mitochondria-associated endoplasmic reticulum membrane contact site / developmental pigmentation / positive regulation of fibroblast apoptotic process / microtubule organizing center organization / caspase binding / apoptotic process involved in embryonic digit morphogenesis / ear development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / tube formation / mammary gland development / myeloid cell homeostasis / Bcl-2 family protein complex / cellular response to glucocorticoid stimulus / NRAGE signals death through JNK / thymocyte apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / B cell homeostasis / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / extrinsic apoptotic signaling pathway in absence of ligand / FLT3 Signaling / endomembrane system / response to endoplasmic reticulum stress / thymus development / release of cytochrome c from mitochondria / cell-matrix adhesion / post-embryonic development / positive regulation of protein-containing complex assembly / kidney development / spindle / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / channel activity / spermatogenesis / regulation of apoptotic process / nuclear membrane / microtubule binding / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / apoptotic process / calcium ion binding / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / membrane / cytosol
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 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. ...Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x / 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
Bcl-2-like protein 11 / Bcl-2-like protein 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsRautureau, G.J.P. / Hinds, M.G. / Kvansakul, M.
CitationJournal: Cell Death Dis. / Year: 2012
Title: The Restricted Binding Repertoire of Bcl-B Leaves Bim as the Universal Bh3-Only Prosurvival Bcl-2 Protein Antagonist.
Authors: Rautureau, G.J.P. / Yabal, M. / Yang, H. / Huang, D.C.S. / Kvansakul, M. / Hinds, M.G.
History
DepositionAug 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...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_special_symmetry / 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 / _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: BCL-2-LIKE PROTEIN 10
B: BCL-2-LIKE PROTEIN 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1123
Polymers22,9182
Non-polymers1941
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-14.8 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.843, 94.845, 96.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2024-

HOH

21A-2048-

HOH

31A-2066-

HOH

41A-2067-

HOH

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Components

#1: Protein BCL-2-LIKE PROTEIN 10 / BCL2-L-10 / ANTI-APOPTOTIC PROTEIN NRH / APOPTOSIS REGULATOR BCL-B


Mass: 19499.049 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-167 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET31B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9HD36
#2: Protein/peptide BCL-2-LIKE PROTEIN 11 / BCL2-L-11 / BCL2-INTERACTING MEDIATOR OF CELL DEATH


Mass: 3418.820 Da / Num. of mol.: 1 / Fragment: RESIDUES 51-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET31B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O43521
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.99 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M MGCL2, 20 % PEG 400, 20 % PEG 3350, 0.1 M TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.957
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.957 Å / Relative weight: 1
ReflectionResolution: 1.9→19.92 Å / Num. obs: 14793 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 26.72 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.7
Reflection shellHighest resolution: 1.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→19.614 Å / SU ML: 0.21 / σ(F): 1.38 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 747 5.1 %
Rwork0.1962 --
obs0.1974 14768 99.97 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 37.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.4229 Å20 Å20 Å2
2--8.5362 Å20 Å2
3----6.1133 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 13 88 1457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061404
X-RAY DIFFRACTIONf_angle_d0.8771903
X-RAY DIFFRACTIONf_dihedral_angle_d13.954517
X-RAY DIFFRACTIONf_chiral_restr0.048201
X-RAY DIFFRACTIONf_plane_restr0.005249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.04660.25511540.24172744X-RAY DIFFRACTION100
2.0466-2.25230.24311520.2012751X-RAY DIFFRACTION100
2.2523-2.57750.19311440.18272792X-RAY DIFFRACTION100
2.5775-3.24510.21891470.18222802X-RAY DIFFRACTION100
3.2451-19.61470.21641500.19862932X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.92450.3381-1.05434.3460.3264.3650.0217-0.2587-0.09180.4581-0.0848-0.24410.14440.31130.06680.1470.0114-0.03920.245-0.01250.1459-2.495716.731414.1287
25.0077-2.37951.494.0056-0.93035.56240.25550.5360.2342-0.3512-0.34260.02950.1358-0.05960.0810.09860.0108-0.00120.14630.00040.152-7.98516.01412.9681
31.9546-0.9091-0.50952.14610.82893.96780.11660.0879-0.09160.0838-0.35550.5203-0.0759-0.57290.12440.21080.01030.02840.3498-0.07430.2207-19.792921.902911.9078
42.97681.6292-0.66553.7720.27143.19020.14880.19590.3758-0.1633-0.14150.0048-0.4923-0.1295-0.0780.19150.02090.02140.2341-0.00450.1923-12.012323.62029.4458
52.56440.2154-0.99245.13940.63924.5943-0.0038-0.246-0.03030.7696-0.26830.2980.5409-0.13430.19130.2799-0.06020.05520.2660.01670.1742-12.984913.021419.4107
62.7455-0.3291-2.12674.06752.33447.0010.07960.2671-0.1648-0.2993-0.1193-0.01160.58730.06050.25110.33950.02290.01680.1257-0.02650.2424-8.88924.90682.379
75.0419-0.5203-2.29577.4021-1.45374.3821-0.5779-1.19570.89540.65910.22731.0693-0.7668-1.12880.11750.1890.263-0.11420.9442-0.09720.5671-28.664223.128712.2986
84.6903-1.7853-2.77026.57713.1736.4838-0.06020.2217-0.1032-0.1444-0.28820.7467-0.1694-1.03840.23990.15510.0299-0.02150.3322-0.09820.2524-21.928613.82913.0913
97.02944.3526-0.31635.00352.01873.43620.190.7141-0.6782-0.52060.45610.14950.7947-0.58990.40160.4796-0.0771-0.14250.3637-0.06080.3974-16.36795.468-3.3246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:32)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 33:48)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 49:82)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 83:121)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 122:150)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 151:164)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 53:61)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 62:71)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 72:76)

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