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- PDB-5ktg: Crystal structure of mouse Bak BH3-in-groove homodimer (GFP) -

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Basic information

Entry
Database: PDB / ID: 5ktg
TitleCrystal structure of mouse Bak BH3-in-groove homodimer (GFP)
ComponentsGreen fluorescent protein, Bcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / BCL-2 family proteins / mitochondrial outer membrane permeabilization / apoptosis regulators / pore-forming proteins
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / leukocyte homeostasis / Pyroptosis / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration ...Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / leukocyte homeostasis / Pyroptosis / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of endoplasmic reticulum unfolded protein response / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / mitochondrial fusion / fibroblast apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / positive regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / vagina development / B cell homeostasis / homeostasis of number of cells / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / animal organ regeneration / negative regulation of peptidyl-serine phosphorylation / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / bioluminescence / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / generation of precursor metabolites and energy / establishment of localization in cell / mitochondrial membrane / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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 ...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 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Bcl-2 homologous antagonist/killer / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsMandal, T. / Choe, J.-Y. / Oh, K.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 R01 GM097508 United States
CitationJournal: Sci Rep / Year: 2016
Title: Assembly of Bak homodimers into higher order homooligomers in the mitochondrial apoptotic pore.
Authors: Mandal, T. / Shin, S. / Aluvila, S. / Chen, H.C. / Grieve, C. / Choe, J.Y. / Cheng, E.H. / Hustedt, E.J. / Oh, K.J.
History
DepositionJul 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein, Bcl-2 homologous antagonist/killer
B: Green fluorescent protein, Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)69,8052
Polymers69,8052
Non-polymers00
Water0
1
A: Green fluorescent protein, Bcl-2 homologous antagonist/killer
B: Green fluorescent protein, Bcl-2 homologous antagonist/killer

A: Green fluorescent protein, Bcl-2 homologous antagonist/killer
B: Green fluorescent protein, Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)139,6094
Polymers139,6094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area11510 Å2
ΔGint-83 kcal/mol
Surface area54920 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-33 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.641, 171.641, 98.194
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Green fluorescent protein, Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK


Mass: 34902.371 Da / Num. of mol.: 2 / Fragment: GFP, GS linker, BAK (UNP residues 66-144)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Mus musculus (house mouse)
Gene: GFP, Bak1, Bak / Production host: Escherichia coli (E. coli) / References: UniProt: P42212, UniProt: O08734

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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: 5.98 Å3/Da / Density % sol: 79.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 7-12% PEG3350, 20% MPD, 100 mM Tris, pH 7.0-8.5, 0.5% CHAPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 11, 2015
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 40122 / % possible obs: 97.4 % / Redundancy: 14.6 % / Rsym value: 0.151 / Net I/σ(I): 13.1
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4BDU

4bdu


Resolution: 2.802→49.548 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.74
RfactorNum. reflection% reflection
Rfree0.2746 1940 4.85 %
Rwork0.244 --
obs0.2455 39972 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.802→49.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4910 0 0 0 4910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195024
X-RAY DIFFRACTIONf_angle_d2.1556784
X-RAY DIFFRACTIONf_dihedral_angle_d19.1441834
X-RAY DIFFRACTIONf_chiral_restr0.091728
X-RAY DIFFRACTIONf_plane_restr0.011882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8019-2.87190.39411120.39272140X-RAY DIFFRACTION77
2.8719-2.94960.42831290.38722412X-RAY DIFFRACTION88
2.9496-3.03630.40991360.37712639X-RAY DIFFRACTION95
3.0363-3.13430.37711400.36342745X-RAY DIFFRACTION99
3.1343-3.24630.38521320.34962796X-RAY DIFFRACTION100
3.2463-3.37630.3471600.33292744X-RAY DIFFRACTION100
3.3763-3.52990.30881350.3072790X-RAY DIFFRACTION100
3.5299-3.71590.27651450.29632778X-RAY DIFFRACTION100
3.7159-3.94870.29891370.26692784X-RAY DIFFRACTION100
3.9487-4.25340.22841520.23652783X-RAY DIFFRACTION100
4.2534-4.68110.24161330.20482828X-RAY DIFFRACTION100
4.6811-5.35780.2521360.19392825X-RAY DIFFRACTION100
5.3578-6.74760.23571340.22242845X-RAY DIFFRACTION100
6.7476-49.55620.21861590.16412923X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 99.7068 Å / Origin y: -3.3914 Å / Origin z: -3.5146 Å
111213212223313233
T0.512 Å20.1026 Å2-0.1924 Å2-0.3686 Å2-0.047 Å2--0.3724 Å2
L-0.199 °2-0.1613 °2-0.3302 °2-0.393 °2-0.0127 °2---0.3109 °2
S-0.0444 Å °-0.0509 Å °-0.0583 Å °0.2861 Å °0.1302 Å °-0.3554 Å °0.1165 Å °-0.0988 Å °0.0251 Å °
Refinement TLS groupSelection details: all

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