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- PDB-8czf: Human BAK in complex with the dF2 peptide -

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Basic information

Entry
Database: PDB / ID: 8czf
TitleHuman BAK in complex with the dF2 peptide
Components
  • Bcl-2 homologous antagonist/killer
  • DF2 peptide
KeywordsAPOPTOSIS / BAK / activator / Bcl-2 family
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / 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 / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / 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 / Release of apoptotic factors from the mitochondria / 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 / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / 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 IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / vagina development / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / blood vessel remodeling / animal organ regeneration / Pyroptosis / negative regulation of peptidyl-serine phosphorylation / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / 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
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, 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
Similarity search - Domain/homology
Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsAguilar, F. / Keating, A.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM110048 United States
CitationJournal: Structure / Year: 2023
Title: Peptides from human BNIP5 and PXT1 and non-native binders of pro-apoptotic BAK can directly activate or inhibit BAK-mediated membrane permeabilization.
Authors: Aguilar, F. / Yu, S. / Grant, R.A. / Swanson, S. / Ghose, D. / Su, B.G. / Sarosiek, K.A. / Keating, A.E.
History
DepositionMay 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer
B: DF2 peptide


Theoretical massNumber of molelcules
Total (without water)21,6132
Polymers21,6132
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-19 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.130, 41.080, 56.390
Angle α, β, γ (deg.)90.000, 122.000, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-325-

HOH

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Components

#1: Protein Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 19037.320 Da / Num. of mol.: 1 / Mutation: C166S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16611
#2: Protein/peptide DF2 peptide


Mass: 2575.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.2 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.3→47.82 Å / Num. obs: 43728 / % possible obs: 96.6 % / Redundancy: 6.629 % / Biso Wilson estimate: 15.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.036 / Χ2: 1.066 / Net I/σ(I): 25.36 / Num. measured all: 289866
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.335.2770.5882.8112993335024620.8730.65373.5
1.33-1.375.9580.5093.6317726325029750.9110.55891.5
1.37-1.416.60.4374.620638314031270.9520.47599.6
1.41-1.456.7950.3276.6120623304630350.9730.35599.6
1.45-1.56.8250.2289.2620135296129500.9880.24799.6
1.5-1.556.7710.18711.1619427288928690.9910.20399.3
1.55-1.616.6220.15113.3618238278027540.9920.16499.1
1.61-1.686.4940.12115.7516327264325140.9950.13295.1
1.68-1.757.0860.09919.2918113256625560.9970.10799.6
1.75-1.847.0950.08222.3717488247724650.9970.08899.5
1.84-1.946.9310.06227.616100233123230.9980.06799.7
1.94-2.066.8550.04833.2715211223422190.9990.05299.3
2.06-2.26.5990.03839.4913508205720470.9990.04299.5
2.2-2.376.2490.03145.5811861194118980.9990.03497.8
2.37-2.67.1820.02755.2912877180517930.9990.02999.3
2.6-2.917.0540.02560.29113991622161610.02799.6
2.91-3.366.8130.02365.6196881438142210.02598.9
3.36-4.116.4410.0277.9178451231121810.02298.9
4.11-5.816.4520.01883.5608495994310.01998.3
5.81-47.826.6140.01888358555354210.01998

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vx0

5vx0


Resolution: 1.3→47.82 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1803 2006 4.59 %
Rwork0.1614 41700 -
obs0.1622 43706 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.47 Å2 / Biso mean: 25.812 Å2 / Biso min: 10.27 Å2
Refinement stepCycle: final / Resolution: 1.3→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 3 164 1624
Biso mean--29.23 35.73 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.330.36751100.33162257236773
1.33-1.370.34741370.2822773291091
1.37-1.410.27741380.245130443182100
1.41-1.450.21571500.20630363186100
1.45-1.510.23561520.201930403192100
1.51-1.570.26521380.217430653203100
1.57-1.640.20951480.18433001314998
1.64-1.720.20591450.17022976312198
1.72-1.830.1781500.166130703220100
1.83-1.970.19181420.160230693211100
1.97-2.170.17491510.143130613212100
2.17-2.490.15541520.13343055320799
2.49-3.130.17311410.155330913232100
3.13-47.820.14931520.14713162331499
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)
13.39272.5938-0.03396.9558-0.10562.38830.035-0.06820.06760.090.01450.27920.0696-0.0476-0.02310.12330.0150.0140.10410.00980.08116.559410.531516.7848
23.7646-0.0870.04124.9324-1.79875.33460.01190.13590.2626-0.41740.06970.0604-0.10890.0245-0.12630.22190.00740.02470.1101-0.02430.13126.964621.040420.2187
34.34452.3433-2.41692.6457-2.32564.57820.0415-0.36860.04130.36310.0028-0.07220.1490.2855-0.0460.19010.0293-0.00330.1438-0.02350.158513.79369.867621.8702
42.7352-0.0155-0.38774.1407-3.89399.2392-0.0904-0.24450.16190.04190.2015-0.437-0.2790.53910.05120.2302-0.0470.04990.2783-0.04990.254422.274120.00575.9774
51.1468-0.51960.37512.8978-0.45222.0682-0.00150.09570.1642-0.20110.0017-0.0972-0.15070.0765-0.0050.1337-0.01170.03180.09910.00390.114110.634916.01793.5443
60.8585-0.65050.48573.4148-1.22822.46720.0239-0.0234-0.0731-0.19320.07170.16920.2036-0.0124-0.10650.1490.00010.00860.10560.00360.11046.76744.060710.4353
72.799-1.58411.30146.0522-5.0688.9487-0.09940.1478-0.0269-0.3977-0.0675-0.23930.25870.25560.18670.1692-0.01520.06870.2006-0.04980.230221.40989.13183.7749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 46 )A20 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 69 )A47 - 69
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 82 )A70 - 82
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 100 )A83 - 100
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 150 )A101 - 150
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 184 )A151 - 184
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 22 )B1 - 22

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