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- PDB-5whi: Crystal Structure of Bcl-2-related protein A1 -

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Basic information

Entry
Database: PDB / ID: 5whi
TitleCrystal Structure of Bcl-2-related protein A1
ComponentsBcl-2-related protein A1
KeywordsAPOPTOSIS
Function / homology
Function and homology information


channel activity / mitochondrial fusion / Nuclear events stimulated by ALK signaling in cancer / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of apoptotic process ...channel activity / mitochondrial fusion / Nuclear events stimulated by ALK signaling in cancer / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of apoptotic process / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
Bcl-2-related protein A1 / Blc2-like / Apoptosis Regulator Bcl-x / 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 ...Bcl-2-related protein A1 / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLIC ACID / Bcl-2-related protein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
CitationJournal: Structure / Year: 2018
Title: Crystal Structures of Anti-apoptotic BFL-1 and Its Complex with a Covalent Stapled Peptide Inhibitor.
Authors: Harvey, E.P. / Seo, H.S. / Guerra, R.M. / Bird, G.H. / Dhe-Paganon, S. / Walensky, L.D.
History
DepositionJul 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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: Bcl-2-related protein A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7342
Polymers18,5961
Non-polymers1381
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint3 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.510, 43.090, 43.440
Angle α, β, γ (deg.)90.000, 104.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bcl-2-related protein A1 / Bcl-2-like protein 5 / Bcl2-L-5 / Hemopoietic-specific early response protein / Protein BFL-1 / Protein GRS


Mass: 18596.062 Da / Num. of mol.: 1 / Fragment: BFL1 / Mutation: C4S, C19S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2A1, BCL2L5, BFL1, GRS, HBPA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16548
#2: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE / Cacodylic acid


Mass: 137.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7AsO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.69→30.12 Å / Num. obs: 15715 / % possible obs: 98.1 % / Redundancy: 3.3 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.05 / Net I/σ(I): 13.6 / Num. measured all: 51640
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.1 / Num. measured all: 2693 / Num. unique all: 812 / Rpim(I) all: 0.708 / Rrim(I) all: 1.297 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3i1h

3i1h


Resolution: 1.69→30.12 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.27
RfactorNum. reflection% reflection
Rfree0.2334 780 4.97 %
Rwork0.1954 --
obs0.1973 15699 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.29 Å2 / Biso mean: 47.7643 Å2 / Biso min: 21.28 Å2
Refinement stepCycle: final / Resolution: 1.69→30.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 5 54 1240
Biso mean--157.52 50.37 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081214
X-RAY DIFFRACTIONf_angle_d0.8631642
X-RAY DIFFRACTIONf_chiral_restr0.057181
X-RAY DIFFRACTIONf_plane_restr0.006211
X-RAY DIFFRACTIONf_dihedral_angle_d2.6351007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6901-1.79590.3981250.3362467259297
1.7959-1.93460.34141140.27612479259399
1.9346-2.12920.27321210.22792512263399
2.1292-2.43720.22421440.20742479262398
2.4372-3.07010.24571380.20652491262998
3.0701-30.12590.20721380.1692491262997
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)
13.7799-2.2417-0.08944.0362-0.3468.33070.0677-0.05240.18890.44750.0622-0.2579-0.80370.4564-0.18470.3343-0.0581-0.03770.1696-0.04080.29385.616212.8995-11.5698
24.2761-2.74972.68324.0312-3.57573.7087-0.02120.6256-0.6587-0.7580.32760.12230.4985-0.04-0.22940.4527-0.09590.01960.3154-0.02590.3349-0.27383.9388-19.8815
35.76240.7784-1.43997.0395-1.30832.0683-0.03970.6397-0.7633-0.60240.74950.464-0.4816-2.1246-0.64380.57730.0843-0.04060.92940.20840.5407-14.125316.3136-25.3008
45.39420.02552.2542.9035-3.39886.70520.1416-0.8861-0.03531.05250.57731.3337-0.2872-1.4938-0.61680.4730.15550.13270.78420.10140.4584-13.727814.3918-13.3949
53.3387-1.4814-0.35193.0944-0.69074.9082-0.05650.21230.180.19630.25020.6695-0.324-0.7961-0.12230.20270.0324-0.01140.3098-0.0150.2218-7.158111.5091-16.2485
63.04971.3861-0.95748.1055-2.80857.09850.24680.07550.39161.257-0.2899-0.2187-1.2527-0.3408-0.07930.46530.02070.09070.31760.02070.2775-4.32412.7572-6.1974
78.2166-1.4536-3.48832.82332.21254.0726-0.01990.2563-0.38040.62620.1128-0.20261.0435-0.1091-0.00260.5977-0.0290.00550.2520.00470.29233.8077-3.2387-7.4101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 31 )A4 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 51 )A32 - 51
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 63 )A52 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 78 )A64 - 78
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 111 )A79 - 111
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 136 )A112 - 136
7X-RAY DIFFRACTION7chain 'A' and (resid 137 through 151 )A137 - 151

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