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- PDB-3mqp: Crystal Structure of human BFL-1 in complex with NOXA BH3 peptide... -

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Basic information

Entry
Database: PDB / ID: 3mqp
TitleCrystal Structure of human BFL-1 in complex with NOXA BH3 peptide, Northeast Structural Genomics Consortium Target HR2930
Components
  • Bcl-2-related protein A1
  • Phorbol-12-myristate-13-acetate-induced protein 1
KeywordsAPOPTOSIS / bcl-2 family / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


response to dsRNA / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of glucose metabolic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / Regulation of MITF-M-dependent genes involved in apoptosis / regulation of mitochondrial membrane permeability / Activation of NOXA and translocation to mitochondria / positive regulation of DNA damage response, signal transduction by p53 class mediator / mitochondrial fusion ...response to dsRNA / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of glucose metabolic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / Regulation of MITF-M-dependent genes involved in apoptosis / regulation of mitochondrial membrane permeability / Activation of NOXA and translocation to mitochondria / positive regulation of DNA damage response, signal transduction by p53 class mediator / mitochondrial fusion / Bcl-2 family protein complex / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / T cell homeostasis / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / proteasomal protein catabolic process / cellular response to glucose starvation / Nuclear events stimulated by ALK signaling in cancer / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway / reactive oxygen species metabolic process / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / channel activity / defense response to virus / cellular response to hypoxia / mitochondrial outer membrane / positive regulation of apoptotic process / apoptotic process / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
Phorbol-12-myristate-13-acetate-induced protein 1 / Phorbol-12-myristate-13-acetate-induced / 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-2 family ...Phorbol-12-myristate-13-acetate-induced protein 1 / Phorbol-12-myristate-13-acetate-induced / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phorbol-12-myristate-13-acetate-induced protein 1 / Bcl-2-related protein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsGuan, R. / Xiao, R. / Zhao, L. / Acton, T.B. / Gelinas, C. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of human BFL-1 in complex with NOXA BH3 peptide
Authors: Guan, R. / Xiao, R. / Zhao, L. / Acton, T.B. / Gelinas, C. / Montelione, G.T.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 1.3Sep 6, 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
B: Phorbol-12-myristate-13-acetate-induced protein 1


Theoretical massNumber of molelcules
Total (without water)21,6122
Polymers21,6122
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-18 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.138, 43.196, 46.387
Angle α, β, γ (deg.)90.00, 113.50, 90.00
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 / Protein BFL-1 / Hemopoietic-specific early response protein / Protein GRS


Mass: 18628.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2A1, BCL2L5, BFL1, GRS, HBPA1 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q16548
#2: Protein/peptide Phorbol-12-myristate-13-acetate-induced protein 1 / PMA-induced protein 1 / Immediate-early-response protein APR / Protein Noxa


Mass: 2983.468 Da / Num. of mol.: 1 / Fragment: NOXA BH3 peptide, residues 19-43 / Source method: obtained synthetically
Details: This sequence occurs naturally in humans. Peptide was synthesized from a commercial peptide synthesis service.
Source: (synth.) Homo sapiens (human) / References: UniProt: Q13794
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 1.95 Å3/Da / Density % sol: 36.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 1.5 M Sodium Malonate, 0.1 M sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.24→30.3 Å / Num. all: 7559 / Num. obs: 7385 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 45.125 Å2 / Rmerge(I) obs: 0.093
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.06 / Num. unique all: 643 / % possible all: 84.6

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXdev_377refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I1H

3i1h


Resolution: 2.24→30.3 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.23 715 10.14 %5% reflections
Rwork0.177 ---
obs0.182 7049 91.9 %-
Solvent computationShrinkage radii: 0.83 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.987 Å2
Refinement stepCycle: LAST / Resolution: 2.24→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 0 29 1453

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