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- PDB-5whh: Crystal Structure of Bcl-2-related protein A1 in complex with sta... -

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Basic information

Entry
Database: PDB / ID: 5whh
TitleCrystal Structure of Bcl-2-related protein A1 in complex with stapled peptide (AQ7)T(0EH)LRRFGD(MK8)INFRQ(NH2)
Components
  • (AQ7)T(0EH)LRRFGD(MK8)INFRQ(NH2)
  • Bcl-2-related protein A1
KeywordsAPOPTOSIS / stapled peptide
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
Bcl-2-related protein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2-related protein A1
B: (AQ7)T(0EH)LRRFGD(MK8)INFRQ(NH2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6903
Polymers20,6552
Non-polymers351
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-16 kcal/mol
Surface area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.710, 86.710, 40.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

21A-338-

HOH

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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 / 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: Protein/peptide (AQ7)T(0EH)LRRFGD(MK8)INFRQ(NH2)


Mass: 2058.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG3350 20%, 0.2M Sodium malonate

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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: 2.38→43.35 Å / Num. obs: 7168 / % possible obs: 99.3 % / Redundancy: 9.8 % / Net I/σ(I): 11.2
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.2 / % possible all: 92.1

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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: 2.38→43.36 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.293 360 5.03 %
Rwork0.211 --
obs0.214 7150 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.3 Å2
Refinement stepCycle: LAST / Resolution: 2.38→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 1 53 1326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051305
X-RAY DIFFRACTIONf_angle_d0.6041772
X-RAY DIFFRACTIONf_dihedral_angle_d8.81767
X-RAY DIFFRACTIONf_chiral_restr0.041196
X-RAY DIFFRACTIONf_plane_restr0.005229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3804-2.72480.36521090.28482194X-RAY DIFFRACTION98
2.7248-3.43270.35341340.23512250X-RAY DIFFRACTION100
3.4327-43.36220.23871170.1812346X-RAY DIFFRACTION100
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)
12.9151-2.3882-0.11372.5748-0.0093.91580.48170.69860.5251-0.2304-0.3183-0.48560.1189-0.0108-0.11660.4509-0.00160.03850.3217-0.0310.3414-1.476730.417435.8118
25.0353-4.54031.25268.0868-0.42890.4356-0.22970.8912-0.4543-0.7813-0.1158-1.43861.28520.53970.16850.87710.150.14870.4969-0.09080.5844-10.141526.333828.8315
33.025-0.82550.11123.20170.34850.6771-0.2001-0.2672-0.24480.28070.21070.5755-0.1117-0.2912-0.04960.59270.0233-0.03150.5435-0.00470.2598-13.973136.126742.8009
44.32340.98421.3316.5708-3.7898.82270.351-0.1080.11390.2730.14090.2231-0.15990.8796-0.50540.3576-0.01870.04110.3375-0.0050.3088-3.464645.502245.4758
52.249-0.45862.90482.0548-2.97218.7827-0.0567-0.34130.09120.29940.0520.1446-0.3045-0.6531-0.03780.32170.00890.02690.2449-0.03890.3102-7.698337.445945.533
60.2882-0.5807-0.23932.506-0.11523.07890.3795-0.31480.49750.2555-0.0544-0.47310.2804-0.098-0.23380.4937-0.0626-0.00680.4947-0.04830.3641-7.433346.28926.5998
72.97171.06951.68133.44650.55184.53570.05060.0578-0.3092-0.0709-0.199-0.1881.07290.3260.09030.46960.05150.02780.3344-0.06490.28590.728930.161743.8767
85.20370.183-0.38512.2009-0.69590.46510.15640.6330.23680.409-0.48030.5121.063-1.37710.64790.7271-0.23910.01520.9301-0.08860.3467-11.623332.233255.6425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 20 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 21 THROUGH 31 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 32 THROUGH 63 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 64 THROUGH 78 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 79 THROUGH 106 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 107 THROUGH 113 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 114 THROUGH 149 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 76 THROUGH 87 )

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