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- PDB-5wfu: Structural basis for the interaction of 14-3-3beta with Tricarbox... -

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Basic information

Entry
Database: PDB / ID: 5wfu
TitleStructural basis for the interaction of 14-3-3beta with Tricarboxylic Acid Cycle intermediate Malate
Components14-3-3 protein beta/alpha
KeywordsPROTEIN BINDING / 14-3-3 beta / Malate / Malic acid
Function / homology
Function and homology information


Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Regulation of localization of FOXO transcription factors / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / RHO GTPases activate PKNs / Activation of BAD and translocation to mitochondria / Frs2-mediated activation / MTOR signalling / Signaling by Hippo / Negative regulation of MAPK pathway ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Regulation of localization of FOXO transcription factors / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / RHO GTPases activate PKNs / Activation of BAD and translocation to mitochondria / Frs2-mediated activation / MTOR signalling / Signaling by Hippo / Negative regulation of MAPK pathway / negative regulation of protein dephosphorylation / TP53 Regulates Metabolic Genes / RAF activation / mTORC1-mediated signalling / MAP2K and MAPK activation / cytoplasmic sequestering of protein / Rap1 signalling / negative regulation of G protein-coupled receptor signaling pathway / protein kinase inhibitor activity / phosphoserine residue binding / protein targeting / transcription repressor complex / phosphoprotein binding / intracellular protein transport / histone deacetylase binding / melanosome / protein domain specific binding / negative regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / enzyme binding / signal transduction / protein-containing complex / identical protein binding / cytosol / cytoplasm
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
D-MALATE / 14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.97 Å
AuthorsHou, Z.Q. / Liu, X.Y.
CitationJournal: To Be Published
Title: Structural basis for the interaction of 14-3-3beta with Tricarboxylic Acid Cycle intermediate Malate
Authors: Hou, Z.Q. / Su, L.J. / Liu, X.Y.
History
DepositionJul 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein beta/alpha
B: 14-3-3 protein beta/alpha
C: 14-3-3 protein beta/alpha
D: 14-3-3 protein beta/alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0108
Polymers112,4744
Non-polymers5364
Water6,774376
1
A: 14-3-3 protein beta/alpha
B: 14-3-3 protein beta/alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5054
Polymers56,2372
Non-polymers2682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-9 kcal/mol
Surface area23200 Å2
MethodPISA
2
C: 14-3-3 protein beta/alpha
hetero molecules

C: 14-3-3 protein beta/alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5054
Polymers56,2372
Non-polymers2682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2850 Å2
ΔGint-10 kcal/mol
Surface area23300 Å2
MethodPISA
3
D: 14-3-3 protein beta/alpha
hetero molecules

D: 14-3-3 protein beta/alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5054
Polymers56,2372
Non-polymers2682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area2770 Å2
ΔGint-9 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.392, 85.604, 56.066
Angle α, β, γ (deg.)90.00, 101.73, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA1 - 2321 - 232
21SERSERBB1 - 2321 - 232
12SERSERAA1 - 2321 - 232
22SERSERCC1 - 2321 - 232
13ASNASNAA1 - 2341 - 234
23ASNASNDD1 - 2341 - 234
14GLUGLUBB1 - 2331 - 233
24GLUGLUCC1 - 2331 - 233
15SERSERBB1 - 2321 - 232
25SERSERDD1 - 2321 - 232
16SERSERCC1 - 2321 - 232
26SERSERDD1 - 2321 - 232

NCS ensembles :
ID
6
1
2
3
4
5

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Components

#1: Protein
14-3-3 protein beta/alpha / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 28118.404 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ywhab / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQV8
#2: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7 / Details: 2.1M DL-Malic Acid pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 83288 / % possible obs: 99.2 % / Redundancy: 5.9 % / Net I/σ(I): 21.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementResolution: 1.97→46.96 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.222 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.143 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22435 4132 5 %RANDOM
Rwork0.18983 ---
obs0.19157 78469 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.002 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.04 Å2
2--0.48 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.97→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7453 0 36 376 7865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197585
X-RAY DIFFRACTIONr_bond_other_d0.010.027197
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.97210209
X-RAY DIFFRACTIONr_angle_other_deg1.647316605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1295930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07825.753372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.596151458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4561537
X-RAY DIFFRACTIONr_chiral_restr0.1190.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028593
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021644
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8762.5233732
X-RAY DIFFRACTIONr_mcbond_other2.8752.5223731
X-RAY DIFFRACTIONr_mcangle_it4.0123.7664658
X-RAY DIFFRACTIONr_mcangle_other4.0123.7684659
X-RAY DIFFRACTIONr_scbond_it4.8093.1573853
X-RAY DIFFRACTIONr_scbond_other4.8093.1593854
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.34.4955552
X-RAY DIFFRACTIONr_long_range_B_refined9.12321.1079272
X-RAY DIFFRACTIONr_long_range_B_other9.12820.9979165
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A121200.14
12B121200.14
21A124830.14
22C124830.14
31A126550.13
32D126550.13
41B125810.12
42C125810.12
51B122910.13
52D122910.13
61C123920.14
62D123920.14
LS refinement shellResolution: 1.972→2.023 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 274 -
Rwork0.227 5203 -
obs--89.36 %

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