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- PDB-4cim: Complex of a Bcl-w BH3 mutant with a BH3 domain -

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Basic information

Entry
Database: PDB / ID: 4cim
TitleComplex of a Bcl-w BH3 mutant with a BH3 domain
Components(BCL-2-LIKE PROTEIN 2) x 2
KeywordsAPOPTOSIS / CELL DEATH
Function / homology
Function and homology information


negative regulation of mitochondrial membrane permeability / Sertoli cell proliferation / BH domain binding / Bcl-2 family protein complex / negative regulation of release of cytochrome c from mitochondria / cellular response to glycine / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to estradiol stimulus / response to ischemia ...negative regulation of mitochondrial membrane permeability / Sertoli cell proliferation / BH domain binding / Bcl-2 family protein complex / negative regulation of release of cytochrome c from mitochondria / cellular response to glycine / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to estradiol stimulus / response to ischemia / cellular response to amyloid-beta / intrinsic apoptotic signaling pathway in response to DNA damage / disordered domain specific binding / spermatogenesis / regulation of apoptotic process / mitochondrial outer membrane / protein heterodimerization activity / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Apoptosis regulator, Bcl-W / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / 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-W / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / 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
Similarity search - Domain/homology
Bcl-2-like protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsColman, P.M. / Lee, E.F. / Fairlie, W.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Functional Differences of Pro-Survival and Pro-Apoptotic B Cell Lymphoma 2 (Bcl-2) Proteins Depend on Structural Differences in Their Bcl-2 Homology 3 (Bh3) Domains
Authors: Lee, E.F. / Dewson, G. / Evangelista, M. / Pettikiriarachchi, A. / Zhu, H. / Colman, P.M. / Fairlie, W.D.
History
DepositionDec 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 2
B: BCL-2-LIKE PROTEIN 2
P: BCL-2-LIKE PROTEIN 2
Q: BCL-2-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,27020
Polymers40,2774
Non-polymers99316
Water4,990277
1
B: BCL-2-LIKE PROTEIN 2
Q: BCL-2-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5739
Polymers20,1382
Non-polymers4347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-2 kcal/mol
Surface area8310 Å2
MethodPISA
2
A: BCL-2-LIKE PROTEIN 2
P: BCL-2-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,69711
Polymers20,1382
Non-polymers5599
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-2.2 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.922, 60.726, 67.098
Angle α, β, γ (deg.)90.00, 105.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BCL-2-LIKE PROTEIN 2 / BCL2-L-2 / APOPTOSIS REGULATOR BCL-W


Mass: 17801.867 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92843
#2: Protein/peptide BCL-2-LIKE PROTEIN 2 / BCL2-L-2 / APOPTOSIS REGULATOR BCL-W


Mass: 2336.583 Da / Num. of mol.: 2 / Fragment: RESIDUES 38-58 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PEPTIDE FROM PROTEOLYTIC CLEAVAGE BCL-W DURING PURIFICATION
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92843
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS IN SEQUENCE AS FOLLOWS C29S H43G M46L A49I A128E C-TERMINAL TRUNCATION OF 29 RESIDUES

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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: 2.04 Å3/Da / Density % sol: 39.7 % / Description: NONE
Crystal growpH: 8 / Details: 1 M TRISODIUM CITRATE 0.1 M IMIDAZOLE, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 51625 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.78 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.93
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.57 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y6W

2y6w


Resolution: 1.5→44.229 Å
RfactorNum. reflection% reflection
Rfree0.2096 2581 5 %
Rwork0.1862 --
obs0.1874 51587 99.38 %
Refinement stepCycle: LAST / Resolution: 1.5→44.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 64 277 2910
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)
10.54880.42390.65631.13860.45990.84990.0069-0.0121-0.0018-0.04020.024-0.0116-0.0088-0.00360.05010.09670.00830.01360.1012-0.02610.1052-11.28236.4536-32.8691
20.6366-0.1020.74081.0182-0.67051.3514-0.0281-0.03020.0150.01490.0708-0.02130.0221-0.065300.11760.02150.0050.1195-0.0240.1068-1.89096.4460.5801
30.04150.04410.04870.0912-0.0090.10480.1129-0.2094-0.11740.06180.0093-0.03750.1415-0.09640.00010.1556-0.0205-0.01380.151-0.02970.1358-7.25175.6388-19.9967
40.0232-0.03770.02710.0568-0.02960.0522-0.01580.0440.0452-0.09570.03650.03810.17-0.039100.1695-0.0101-0.01070.1644-0.01550.1202-5.99315.6431-12.0353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN P
4X-RAY DIFFRACTION4CHAIN Q

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