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- PDB-3uzd: Crystal structure of 14-3-3 GAMMA -

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Basic information

Entry
Database: PDB / ID: 3uzd
TitleCrystal structure of 14-3-3 GAMMA
Components
  • 14-3-3 protein gamma
  • Histone deacetylase 4
KeywordsPROTEIN BINDING/HYDROLASE / Structural Genomics / SGC / Structural Genomics Consortium / Mainly Alpha / phosphoserine / phosphothreonine / PROTEIN BINDING-HYDROLASE complex
Function / homology
Function and homology information


RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / positive regulation of cell-cell adhesion / peptidyl-lysine deacetylation / phosphorylation-dependent protein binding / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / histone deacetylase activity, hydrolytic mechanism / positive regulation of T cell mediated immune response to tumor cell ...RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / positive regulation of cell-cell adhesion / peptidyl-lysine deacetylation / phosphorylation-dependent protein binding / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / histone deacetylase activity, hydrolytic mechanism / positive regulation of T cell mediated immune response to tumor cell / histone deacetylase / protein deacetylation / cardiac muscle hypertrophy in response to stress / negative regulation of glycolytic process / SUMO transferase activity / regulation of neuron differentiation / protein lysine deacetylase activity / histone deacetylase activity / DNA-binding transcription activator activity / type I interferon-mediated signaling pathway / Notch-HLH transcription pathway / protein kinase C inhibitor activity / negative regulation of gene expression, epigenetic / histone deacetylase complex / potassium ion binding / B cell activation / Regulation of localization of FOXO transcription factors / protein sumoylation / RUNX3 regulates p14-ARF / Activation of BAD and translocation to mitochondria / regulation of signal transduction / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / protein targeting / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / insulin-like growth factor receptor binding / negative regulation of TORC1 signaling / transcription repressor complex / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Transcriptional and post-translational regulation of MITF-M expression and activity / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein sequestering activity / response to interleukin-1 / epigenetic regulation of gene expression / B cell differentiation / protein kinase C binding / AURKA Activation by TPX2 / SUMOylation of chromatin organization proteins / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / SUMOylation of intracellular receptors / regulation of synaptic plasticity / receptor tyrosine kinase binding / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / cellular response to insulin stimulus / histone deacetylase binding / positive regulation of T cell activation / intracellular protein localization / Regulation of PLK1 Activity at G2/M Transition / nervous system development / regulation of protein localization / presynapse / DNA-binding transcription factor binding / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / mitochondrial matrix / inflammatory response / protein domain specific binding / focal adhesion / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / 14-3-3 domain / Delta-Endotoxin; domain 1 / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily ...Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / 14-3-3 domain / Delta-Endotoxin; domain 1 / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 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
NITRATE ION / Histone deacetylase 4 / 14-3-3 protein gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsXu, C. / Bian, C. / MacKenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Sci.Signal. / Year: 2012
Title: Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock.
Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / ...Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / Pawson, T. / Yang, X.J. / Min, J.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein gamma
B: Histone deacetylase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5106
Polymers30,3002
Non-polymers2104
Water2,486138
1
A: 14-3-3 protein gamma
B: Histone deacetylase 4
hetero molecules

A: 14-3-3 protein gamma
B: Histone deacetylase 4
hetero molecules

A: 14-3-3 protein gamma
B: Histone deacetylase 4
hetero molecules

A: 14-3-3 protein gamma
B: Histone deacetylase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,04024
Polymers121,1998
Non-polymers84116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area12720 Å2
ΔGint-95 kcal/mol
Surface area43740 Å2
MethodPISA
2
A: 14-3-3 protein gamma
B: Histone deacetylase 4
hetero molecules

A: 14-3-3 protein gamma
B: Histone deacetylase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,02012
Polymers60,6004
Non-polymers4218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area5410 Å2
ΔGint-39 kcal/mol
Surface area22820 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-14 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.511, 79.230, 122.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein 14-3-3 protein gamma / Protein kinase C inhibitor protein 1 / KCIP-1 / 14-3-3 protein gamma / N-terminally processed


Mass: 28423.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli (E. coli) / References: UniProt: P61981
#2: Protein/peptide Histone deacetylase 4 / HD4


Mass: 1876.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polypeptide(L) / Source: (synth.) Homo sapiens (human) / References: UniProt: P56524, histone deacetylase
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.3M Mg (OAc)2, 20% PEG3350, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.86→66.48 Å / Num. obs: 24650 / % possible obs: 98.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.86-1.897.10.845196.1
1.89-1.937.10.78196.8
1.93-1.967.10.639196.6
1.96-27.10.497197
2-2.057.10.394197.3
2.05-2.097.10.319197.2
2.09-2.157.20.264197.4
2.15-2.217.10.218197.7
2.21-2.277.20.184198.2
2.27-2.347.20.147198.3
2.34-2.437.20.125198.5
2.43-2.527.20.109198.7
2.52-2.647.20.094198.5
2.64-2.787.20.073199.4
2.78-2.957.20.061199.1
2.95-3.187.20.046199.6
3.18-3.57.20.035199.8
3.5-4.017.20.027199.9
4.01-5.057.10.0231100
5.05-506.70.023199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B05

2b05


Resolution: 1.86→66.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0 / SU B: 6.113 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1252 5.1 %RANDOM
Rwork0.194 ---
obs0.196 24650 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.86→66.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 13 138 2013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221917
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9732592
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8885236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78924.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06715332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4261513
X-RAY DIFFRACTIONr_chiral_restr0.1580.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021442
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3311.51205
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10221909
X-RAY DIFFRACTIONr_scbond_it3.7973712
X-RAY DIFFRACTIONr_scangle_it5.7154.5683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 82 -
Rwork0.337 1681 -
obs--96.34 %
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)
12.08381.25321.44773.74234.30388.76480.00970.12770.12770.0295-0.06340.2658-0.043-0.46370.05370.05330.01610.02730.08980.06470.098-7.663328.879313.8176
23.4921-0.6385-4.16131.76531.23547.5197-0.0279-0.0031-0.17470.2427-0.0040.12040.2528-0.06520.03190.0479-0.0126-0.0060.04610.00910.0886-1.044823.715417.6449
31.2027-0.0684-2.8864.74951.392214.38370.03120.1354-0.1053-0.3414-0.0303-0.31540.21611.066-0.00080.09420.0498-0.01520.3086-0.01480.108616.061920.7127-0.6156
45.0441-16.8626-9.915856.373733.147719.49530.4141-0.16350.5302-1.27670.5818-1.7794-0.71030.2998-0.99580.4306-0.01620.15620.97840.03920.386723.414526.8232-12.1361
52.1083-1.0311-2.97110.97931.9929.44770.05570.11110.1651-0.06620.0519-0.1362-0.28620.3977-0.10760.0685-0.02810.00880.07340.02280.138110.649330.965610.3171
63.0814-1.7564-2.61972.6686-1.97149.6788-0.2713-0.5047-0.05350.56280.41740.1968-0.4380.0243-0.14610.302-0.03470.07280.1741-0.04550.20812.588426.776533.4488
73.3320.3766-2.21052.4556-0.55664.65130.03320.17110.13750.02420.0061-0.2011-0.1750.1975-0.03920.0406-0.0043-0.03920.04170.00050.068215.062124.914317.3737
84.36563.6379-8.01354.7598-7.56716.8570.0925-0.5235-0.08060.4196-0.2399-0.3254-0.15680.63220.14740.09110.0029-0.070.1203-0.01890.116214.044120.845229.8915
94.73141.459-0.88633.2981-1.30522.26870.0286-0.2156-0.15050.1115-0.0587-0.2380.09750.21740.03010.08080.021-0.040.0491-0.03160.070513.93339.753425.9527
1017.62390.2541-7.48683.0764-0.14256.9258-0.14080.1401-0.287-0.07650.0874-0.10350.14610.04690.05340.1152-0.0088-0.04010.0106-0.01420.05666.97624.526722.005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 35
2X-RAY DIFFRACTION2A36 - 55
3X-RAY DIFFRACTION3A56 - 70
4X-RAY DIFFRACTION4A71 - 81
5X-RAY DIFFRACTION5A82 - 109
6X-RAY DIFFRACTION6A110 - 120
7X-RAY DIFFRACTION7A121 - 147
8X-RAY DIFFRACTION8A148 - 165
9X-RAY DIFFRACTION9A166 - 211
10X-RAY DIFFRACTION10A212 - 234

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