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- PDB-2bq0: 14-3-3 Protein Beta (Human) -

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Basic information

Entry
Database: PDB / ID: 2bq0
Title14-3-3 Protein Beta (Human)
Components14-3-3 BETA/ALPHA
KeywordsCELL REGULATOR PROTEIN / 14-3-3 / YWHAB / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / ALTERNATIVE INITIATION / MULTIGENE FAMILY / PHOSPHORYLATION
Function / homology
Function and homology information


negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling ...negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / Frs2-mediated activation / positive regulation of catalytic activity / protein kinase inhibitor activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / histone deacetylase binding / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / melanosome / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 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 ...14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYang, X. / Elkins, J.M. / Fedorov, O. / Longman, E.J. / Sobott, L. / Ball, L.J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Doyle, D.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural Basis for Protein-Protein Interactions in the 14-3-3 Protein Family.
Authors: Yang, X. / Lee, W.H. / Sobott, F. / Papagrigoriou, E. / Robinson, C.V. / Grossmann, J.G. / Sundstrom, M. / Doyle, D.A. / Elkins, J.M.
History
DepositionApr 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2005Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 BETA/ALPHA
B: 14-3-3 BETA/ALPHA


Theoretical massNumber of molelcules
Total (without water)56,4732
Polymers56,4732
Non-polymers00
Water1,15364
1
A: 14-3-3 BETA/ALPHA

B: 14-3-3 BETA/ALPHA


Theoretical massNumber of molelcules
Total (without water)56,4732
Polymers56,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
MethodPQS
2
B: 14-3-3 BETA/ALPHA

A: 14-3-3 BETA/ALPHA


Theoretical massNumber of molelcules
Total (without water)56,4732
Polymers56,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
MethodPQS
Unit cell
Length a, b, c (Å)51.605, 123.790, 54.755
Angle α, β, γ (deg.)90.00, 114.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 68
2115B1 - 68
1215A80 - 135
2215B80 - 135
1315A140 - 163
2315B140 - 163
1125A164 - 245
2125B164 - 245

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.58479, -0.16656, 0.7939), (0.16258, -0.9829, -0.08646), (0.79473, 0.07852, 0.60187)
Vector: -16.90796, -85.31619, -21.58131)

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Components

#1: Protein 14-3-3 BETA/ALPHA / PROTEIN KINASE C INHIBITOR PROTEIN-1 / KCIP-1 / PROTEIN 1054


Mass: 28236.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: THE MAMMALIAN GENE COLLECTION, I.M.A.G.E. CONSORTIUM CLONEID 3051079
Plasmid: PTVHR21-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31946
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 240-245 ARE CLONING ARTEFACT FOR CHAINS A AND B. THE UNIPROT CROSS-REFERENCE GIVEN IN THE ...RESIDUES 240-245 ARE CLONING ARTEFACT FOR CHAINS A AND B. THE UNIPROT CROSS-REFERENCE GIVEN IN THE DBREF RECORDS BELOW CORRESPONDS TO GENBANK ENTRY BC001359.2 (HOMO SAPIENS TYROSINE 3-MONOOXYGENASE ACTIVATION PROTEIN BETA POLYPEPTIDE TRANSCRIPT VARIANT 2)

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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: 2.7 Å3/Da / Density % sol: 54.6 %
Crystal growpH: 8
Details: 0.05M MGCL2,0.1M HEPES PH7.5, 30% PEG MME 550, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 8, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→38.72 Å / Num. obs: 21068 / % possible obs: 97.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJA

1qja


Resolution: 2.5→61.9 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.864 / SU B: 9.583 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1074 5.1 %RANDOM
Rwork0.214 ---
obs0.217 19984 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-1.1 Å2
2---1.31 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.5→61.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 0 64 3721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223711
X-RAY DIFFRACTIONr_bond_other_d0.0010.023323
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9675007
X-RAY DIFFRACTIONr_angle_other_deg0.77637770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5625.604182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71615693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0651519
X-RAY DIFFRACTIONr_chiral_restr0.0680.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02701
X-RAY DIFFRACTIONr_nbd_refined0.2260.2926
X-RAY DIFFRACTIONr_nbd_other0.1650.23227
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21841
X-RAY DIFFRACTIONr_nbtor_other0.0860.22195
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2129
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0970.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5791.52503
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89623688
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.33831551
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1274.51319
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1857medium positional0.420.5
2410medium positional0.660.5
11352loose positional0.655
2645loose positional1.075
1857medium thermal1.212
2410medium thermal1.042
11352loose thermal1.9410
2645loose thermal1.5810
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 70
Rwork0.244 1462

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