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- PDB-6wgz: Crystal structure of HyBcl-2-4 with HyBak1 BH3 -

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Basic information

Entry
Database: PDB / ID: 6wgz
TitleCrystal structure of HyBcl-2-4 with HyBak1 BH3
Components
  • Bak
  • Bcl-2-like 4
  • Maltodextrin-binding protein
KeywordsAPOPTOSIS / Antiapoptotic / complex with BH3 motif
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / regulation of apoptotic process / membrane => GO:0016020 / periplasmic space / 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 / ACETATE ION / Maltodextrin-binding protein / Bak / Bcl-2-like 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Hydra vulgaris (swiftwater hydra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKvansakul, M. / Hinds, M.G. / Banjara, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190103591 Australia
CitationJournal: To Be Published
Title: Crystal structures of HyBcl-2-4 with HyBak1 BH3 and HyBax BH3
Authors: Banjara, S. / Sa, J.D. / Hinds, M.G. / Kvansakul, M.
History
DepositionApr 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 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

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Assembly

Deposited unit
A: Maltodextrin-binding protein
B: Bcl-2-like 4
C: Bak
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0536
Polymers62,4303
Non-polymers6233
Water2,306128
1
B: Bcl-2-like 4
C: Bak
hetero molecules

A: Maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0536
Polymers62,4303
Non-polymers6233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3890 Å2
ΔGint-24 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.245, 73.650, 140.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Maltodextrin-binding protein


Mass: 40759.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DAH37_23060 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Z0THX4
#2: Protein Bcl-2-like 4 / Bcl-2-like protein 1


Mass: 18756.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydra vulgaris (swiftwater hydra) / Gene: BCL2L1 / Production host: Escherichia coli (E. coli) / References: UniProt: A7LM80

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Protein/peptide / Sugars , 2 types, 2 molecules C

#3: Protein/peptide Bak


Mass: 2915.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hydra vulgaris (swiftwater hydra) / References: UniProt: A1E3K5
#4: 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

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Non-polymers , 2 types, 130 molecules

#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.4 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 0.2M Magnesium acetate tetra hydrate, 20% 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: 2.19→43.68 Å / Num. obs: 29115 / % possible obs: 98.49 % / Redundancy: 10.8 % / Biso Wilson estimate: 43.33 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.6
Reflection shellResolution: 2.19→2.27 Å / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2769 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
xia2data processing
PHASERphasing
DIALSdata reduction
Aimlessdata scaling
Cootmodel building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PQ1

1pq1


Resolution: 2.2→43.68 Å / SU ML: 0.2578 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9134
RfactorNum. reflection% reflection
Rfree0.2511 1439 4.96 %
Rwork0.2223 --
obs0.2238 29009 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 42 128 4368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00294355
X-RAY DIFFRACTIONf_angle_d0.62425911
X-RAY DIFFRACTIONf_chiral_restr0.038649
X-RAY DIFFRACTIONf_plane_restr0.0027762
X-RAY DIFFRACTIONf_dihedral_angle_d19.96461560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.36431300.36582509X-RAY DIFFRACTION90.84
2.28-2.370.35181430.30062732X-RAY DIFFRACTION98.43
2.37-2.470.28071410.27772727X-RAY DIFFRACTION98.86
2.47-2.610.29121470.26462727X-RAY DIFFRACTION99
2.61-2.770.28511490.27512699X-RAY DIFFRACTION98.27
2.77-2.980.30221460.2632778X-RAY DIFFRACTION99.49
2.98-3.280.27571650.25662758X-RAY DIFFRACTION99.15
3.28-3.760.2431280.21092801X-RAY DIFFRACTION99.25
3.76-4.730.19631370.17582856X-RAY DIFFRACTION99.57
4.73-43.680.22491530.19112983X-RAY DIFFRACTION99.52

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