- PDB-9qnl: BAD pS118 phosphopeptide binding to 14-3-3sigma -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 9qnl
Title
BAD pS118 phosphopeptide binding to 14-3-3sigma
Components
14-3-3 protein sigma
Bcl2-associated agonist of cell death
Keywords
PEPTIDE BINDING PROTEIN / 14-3-3 protein-protein interactions
Function / homology
Function and homology information
ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / BAD-BCL-2 complex / glucose catabolic process / pore complex assembly / cysteine-type endopeptidase activator activity / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / type B pancreatic cell proliferation / regulation of mitochondrial membrane permeability ...ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / BAD-BCL-2 complex / glucose catabolic process / pore complex assembly / cysteine-type endopeptidase activator activity / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / type B pancreatic cell proliferation / regulation of mitochondrial membrane permeability / cellular response to lipid / AKT phosphorylates targets in the cytosol / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of mitochondrial membrane potential / positive regulation of B cell differentiation / positive regulation of T cell differentiation / NRAGE signals death through JNK / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of release of cytochrome c from mitochondria / regulation of cell-cell adhesion / positive regulation of proteolysis / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / extrinsic apoptotic signaling pathway via death domain receptors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / ATP metabolic process / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of autophagy / positive regulation of cell adhesion / intrinsic apoptotic signaling pathway / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / positive regulation of epithelial cell proliferation / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to mechanical stimulus / positive regulation of insulin secretion / phospholipid binding / cellular response to nicotine / cytokine-mediated signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / glucose homeostasis / regulation of protein localization / positive regulation of cell growth / protein phosphatase binding / cellular response to hypoxia / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process / cadherin binding / apoptotic process / lipid binding / protein kinase binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function
Bcl2-associated agonist of cell death / Pro-apoptotic Bcl-2 protein, BAD / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein Similarity search - Domain/homology
Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 14, 2024
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.873128 Å / Relative weight: 1
Reflection
Resolution: 1.3→45.76 Å / Num. obs: 63729 / % possible obs: 89.1 % / Redundancy: 13 % / CC1/2: 1 / Net I/σ(I): 19.4
Reflection shell
Resolution: 1.3→1.33 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3427 / CC1/2: 0.589
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Processing
Software
Name
Classification
PDB-REDO
refinement
autoPROC
datareduction
Aimless
datascaling
MOLREP
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→45.76 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.896 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19484
3239
5.1 %
RANDOM
Rwork
0.16284
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obs
0.16453
60467
89.08 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 25.216 Å2
Baniso -1
Baniso -2
Baniso -3
1-
4.64 Å2
0 Å2
-0 Å2
2-
-
-2.03 Å2
0 Å2
3-
-
-
-2.62 Å2
Refinement step
Cycle: LAST / Resolution: 1.3→45.76 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1942
0
6
238
2186
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.016
2046
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.016
1961
X-RAY DIFFRACTION
r_angle_refined_deg
0.932
1.823
2768
X-RAY DIFFRACTION
r_angle_other_deg
0.411
1.568
4538
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.778
5.281
285
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.892
10
402
X-RAY DIFFRACTION
r_chiral_restr
0.045
0.2
304
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
2424
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
448
X-RAY DIFFRACTION
r_mcbond_it
14.258
2.088
1006
X-RAY DIFFRACTION
r_mcbond_other
14.253
2.091
1007
X-RAY DIFFRACTION
r_mcangle_it
17.062
3.77
1261
X-RAY DIFFRACTION
r_mcangle_other
17.07
3.773
1262
X-RAY DIFFRACTION
r_scbond_it
36.943
2.695
1040
X-RAY DIFFRACTION
r_scbond_other
36.934
2.698
1041
X-RAY DIFFRACTION
r_scangle_other
44.597
4.657
1495
X-RAY DIFFRACTION
r_long_range_B_refined
40.446
29.09
2460
X-RAY DIFFRACTION
r_long_range_B_other
40.552
26.79
2395
X-RAY DIFFRACTION
r_rigid_bond_restr
12.319
3
4007
LS refinement shell
Resolution: 1.303→1.337 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.345
279
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Rwork
0.344
4875
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obs
-
-
98.43 %
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