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- PDB-6wh0: Crystal structure of HyBcl-2-4 with HyBax BH3 -

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Basic information

Entry
Database: PDB / ID: 6wh0
TitleCrystal structure of HyBcl-2-4 with HyBax BH3
Components
  • Apoptosis regulator BAX
  • Maltodextrin-binding protein,Bcl-2-like 4
KeywordsAPOPTOSIS / Antiapoptotic / Bcl-2 / complex with BH3 motif
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / outer membrane-bounded periplasmic space / regulation of apoptotic process / membrane => GO:0016020 / apoptotic process
Similarity search - Function
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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltotriose / Bcl-2-like 4 / Maltodextrin-binding protein / Apoptosis regulator BAX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Hydra vulgaris (swiftwater hydra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsKvansakul, M. / Hinds, M.G. / Banjara, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190103591 Australia
CitationJournal: Biochem.J. / Year: 2020
Title: The structural basis of Bcl-2 mediated cell death regulation in hydra.
Authors: Banjara, S. / D Sa, J. / Hinds, M.G. / Kvansakul, M.
History
DepositionApr 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein,Bcl-2-like 4
B: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6493
Polymers62,1442
Non-polymers5041
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-2 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.401, 69.726, 72.523
Angle α, β, γ (deg.)90.000, 96.626, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Maltodextrin-binding protein,Bcl-2-like 4 / Bcl-2-like protein 1


Mass: 58992.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Hydra vulgaris (swiftwater hydra)
Gene: BCL2L1 / Production host: Escherichia coli (E. coli) / References: UniProt: C3SHQ8, UniProt: A7LM80
#2: Protein/peptide Apoptosis regulator BAX


Mass: 3151.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hydra vulgaris (swiftwater hydra) / References: UniProt: T2MDZ0
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.27 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1 Bis Tris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.99→71.8 Å / Num. obs: 34508 / % possible obs: 94.29 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.81 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.148 / Net I/σ(I): 3.7
Reflection shellResolution: 1.99→2 Å / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1855 / CC1/2: 0.45 / % possible all: 99.9

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Processing

Software
NameVersionClassification
xia21.17.1_3660data processing
PHASER1.17.1_3660phasing
DIALSdata reduction
Aimlessdata scaling
Cootmodel building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PQ1

1pq1


Resolution: 1.99→50.1 Å / SU ML: 0.2963 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.0329
RfactorNum. reflection% reflection
Rfree0.2681 1705 4.97 %
Rwork0.2305 --
obs0.2324 34337 93.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.67 Å2
Refinement stepCycle: LAST / Resolution: 1.99→50.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4336 0 0 192 4528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734437
X-RAY DIFFRACTIONf_angle_d0.99086017
X-RAY DIFFRACTIONf_chiral_restr0.0554660
X-RAY DIFFRACTIONf_plane_restr0.0071773
X-RAY DIFFRACTIONf_dihedral_angle_d17.47231602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.3461610.25541156X-RAY DIFFRACTION40.38
2.04-2.110.32921320.31852582X-RAY DIFFRACTION90.11
2.11-2.190.38541520.31472882X-RAY DIFFRACTION98.89
2.19-2.270.34761460.2982815X-RAY DIFFRACTION98.86
2.27-2.380.36791390.27742899X-RAY DIFFRACTION99.35
2.38-2.50.33191580.27132882X-RAY DIFFRACTION99.44
2.5-2.660.3041640.2592859X-RAY DIFFRACTION99.51
2.66-2.860.31271340.25032893X-RAY DIFFRACTION99.64
2.86-3.150.30841550.26152897X-RAY DIFFRACTION99.64
3.15-3.610.28641400.23212892X-RAY DIFFRACTION99.87
3.61-4.550.22181520.18422930X-RAY DIFFRACTION99.94
4.55-50.10.1881720.18362945X-RAY DIFFRACTION99.65
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)
10.975945321536-0.2492375419910.2112469889491.48645695437-0.2499511239740.9310283454930.00729361073633-0.0400579651472-0.0765015165216-0.06774113028610.00394449858192-0.1273053757130.2278301589540.03664780972830.0001461002993270.2521420105330.003252361726350.01553373486820.201980558478-0.001879896815850.17816542936410.5796881487-8.9058961092287.4855740154
20.786435802218-0.226819785210.06779477083930.6189784747150.2919025258570.4799565427280.08392928152690.006428456966140.21782329353-0.0726885294751-0.0670269358718-0.0371914339745-0.233059156043-0.08738891367381.39713075007E-50.309916338438-0.0007229331352490.02791012791990.231252674074-0.01249271579160.25194001306635.729647897824.579277374792.382878859
30.07674716010670.121119071041-0.08739993238540.5523425859740.02952799873790.109138875799-0.0821122705371-0.0948237715087-0.263697510340.3864680762250.0789173585263-0.535760883608-0.1252262789390.36549966565-0.02916003379830.4988569136740.01878293482810.001905177723870.45610418912-0.07837876505940.23469696319841.144092326526.6113504919105.91281777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -370 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 160 )
3X-RAY DIFFRACTION3chain 'B' and (resid 92 through 117 )

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