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- PDB-2jcn: The crystal structure of BAK1 - a mitochondrial apoptosis regulator -

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Basic information

Entry
Database: PDB / ID: 2jcn
TitleThe crystal structure of BAK1 - a mitochondrial apoptosis regulator
ComponentsBCL-2 HOMOLOGOUS ANTAGONIST/KILLER
KeywordsAPOPTOSIS / MITOCHONDRIAL OUTER MEMBRANE PERMEABILIZATION / OLIGOMERIZATION / CYTOCHROME C RELEASE / MEMBRANE / TRANSMEMBRANE
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
T-superfamily conotoxin / chi-Conotoxin or t superfamily / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator proteins, Bcl-2 family / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.8 Å
AuthorsMoche, M. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. ...Moche, M. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Johansson, I. / Karlberg, T. / Kosinska, U. / Kotenyova, T. / Lundgren, S. / Nilsson, M.E. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Upsten, M. / Thorsell, A.G. / van den Berg, S. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Bak1 - an Apoptosis Trigger in the Mitochondrial Outer Membrane
Authors: Moche, M. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. ...Authors: Moche, M. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Johansson, I. / Karlberg, T. / Kosinska, U. / Kotenyova, T. / Lundgren, S. / Nilsson, M.E. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Upsten, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P.
History
DepositionDec 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 13, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4212
Polymers19,3251
Non-polymers961
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.770, 62.770, 138.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

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Components

#1: Protein BCL-2 HOMOLOGOUS ANTAGONIST/KILLER / APOPTOSIS REGULATOR BAK / BCL-2-LIKE 7 PROTEIN / BAK1


Mass: 19324.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUE 23-184 GAP AT 50-54 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16611
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCOMPARED TO OUR CLONED AND TEV CLEAVED CONSTRUCT WE MISS 4AA IN THE N-TERMINUS AND 6AA IN THE C- ...COMPARED TO OUR CLONED AND TEV CLEAVED CONSTRUCT WE MISS 4AA IN THE N-TERMINUS AND 6AA IN THE C-TERMINUS. IN ADDITION WE HAVE A GAP BETWEEN RESIDUE 50-54 IN THIS STRUCTURE.

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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: 39.2 %
Crystal growpH: 7.5
Details: 22% PEG3350, 20% GLYCEROL, 0.2M SODIUM SULPHATE, 2MM TCEP, 0.3M NACL, 20 MM HEPES PH7.5, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 313450 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 20.17 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 38
Reflection shellResolution: 1.8→2 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 8.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.8→19.69 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.156 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS A CYSTEINE S-S BRIDGE BETWEEN CYS166 AND CYS166 FROM A SYMMETRY MOLECULE
RfactorNum. reflection% reflectionSelection details
Rfree0.232 785 5 %RANDOM
Rwork0.187 ---
obs0.189 14832 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 5 89 1358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211318
X-RAY DIFFRACTIONr_bond_other_d0.0010.021164
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9241789
X-RAY DIFFRACTIONr_angle_other_deg0.91532687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.425159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47823.47272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56315209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1171511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
X-RAY DIFFRACTIONr_nbd_refined0.2360.2296
X-RAY DIFFRACTIONr_nbd_other0.1770.21154
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2671
X-RAY DIFFRACTIONr_nbtor_other0.0860.2717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.57921018
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85831257
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5544629
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4125531
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.236 73
Rwork0.183 1064
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)
12.5561.49650.202410.9955-1.31354.1806-0.10090.18390.0640.16730.2852-0.20580.13070.0489-0.1843-0.00560.01-0.00380.1187-0.01590.048435.52727.383-5.122
27.62067.1317-2.790510.7749-2.97632.9892-0.75590.99910.7434-1.15640.92580.85750.0115-0.4129-0.16990.0743-0.1027-0.03390.14970.13020.14437.35839.58-10.499
36.2799-7.2561-3.823621.22396.07188.36410.1930.2660.2127-0.3532-0.31070.5335-0.4685-0.93150.1177-0.01460.0203-0.04130.17860.00590.068527.70730.176-10.11
419.11120.32464.17165.152.333610.23830.38940.02870.9808-0.069-0.30360.5214-0.7939-0.9192-0.0858-0.00450.03650.12520.0284-0.03190.094930.95742.5037.286
54.0111.6568-1.09281.9382-0.73643.42580.2376-0.33690.24320.1065-0.09920.0836-0.15770.1368-0.1383-0.0217-0.01380.03020.0758-0.03070.067836.51433.8295.826
63.32330.06920.67982.1752-1.53388.1485-0.14620.1692-0.0508-0.07170.03380.04730.2264-0.18260.11240.0323-0.0439-0.00330.07710.00590.071527.7820.7470.703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 43
2X-RAY DIFFRACTION2A44 - 67
3X-RAY DIFFRACTION3A68 - 83
4X-RAY DIFFRACTION4A84 - 103
5X-RAY DIFFRACTION5A104 - 161
6X-RAY DIFFRACTION6A162 - 184

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