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- PDB-4e2e: Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-mono... -

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Basic information

Entry
Database: PDB / ID: 4e2e
TitleCrystal structure of a tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide (YWHAG) from Homo sapiens at 2.25 A resolution
Components14-3-3 protein gamma
KeywordsSIGNALING PROTEIN / 14-3-3 domain / signal transduction / cell signaling / protein binding / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / regulation of signal transduction / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting ...positive regulation of cell-cell adhesion / phosphorylation-dependent protein binding / positive regulation of T cell mediated immune response to tumor cell / regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / regulation of signal transduction / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / insulin-like growth factor receptor binding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Transcriptional and post-translational regulation of MITF-M expression and activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein sequestering activity / AURKA Activation by TPX2 / protein kinase C binding / negative regulation of protein kinase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / regulation of synaptic plasticity / receptor tyrosine kinase binding / positive regulation of T cell activation / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / presynapse / regulation of protein localization / mitochondrial matrix / protein domain specific binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / identical protein binding / nucleus / membrane / 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
14-3-3 protein gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activa tion protein, gamma polypeptide (YWHAG) from Homo sapiens at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionMar 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references / Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7842
Polymers28,7221
Non-polymers621
Water1,58588
1
A: 14-3-3 protein gamma
hetero molecules

A: 14-3-3 protein gamma
hetero molecules

A: 14-3-3 protein gamma
hetero molecules

A: 14-3-3 protein gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1368
Polymers114,8884
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_658-x+1,y,-z+31
crystal symmetry operation4_568x,-y+1,-z+31
Buried area6940 Å2
ΔGint-33 kcal/mol
Surface area44640 Å2
MethodPISA
2
A: 14-3-3 protein gamma
hetero molecules

A: 14-3-3 protein gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5684
Polymers57,4442
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_658-x+1,y,-z+31
Buried area2510 Å2
ΔGint-7 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.988, 78.515, 122.131
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A DIMER AND TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATES IN SOLUTION.

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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: 28721.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC020963, YWHAG / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: P61981
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 1-247) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 1-247) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.00M LiCl, 20.00% PEG-6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9786
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.25→27.685 Å / Num. obs: 14183 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.08 % / Biso Wilson estimate: 52.21 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.25-2.330.9041.580582613198
2.33-2.420.5722.378852534197.7
2.42-2.530.426391272689198.7
2.53-2.670.2914.293652780199.3
2.67-2.830.1896.285582564199.5
2.83-3.050.1199.184302696198.7
3.05-3.360.07114.989832682199.1
3.36-3.840.04721.788172647199
3.84-4.830.03725.881742652198.1
4.83-27.6850.0329.388822684198.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.25→27.685 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9299 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE REFINEMENT WAS RESTRAINED AGAINST THE SAD PHASES 4.1,2-ETHANE DIOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 712 5.02 %RANDOM
Rwork0.1892 ---
obs0.1912 14178 --
Displacement parametersBiso max: 157.11 Å2 / Biso mean: 61.2447 Å2 / Biso min: 23.84 Å2
Baniso -1Baniso -2Baniso -3
1--4.3057 Å20 Å20 Å2
2--5.8236 Å20 Å2
3----1.5179 Å2
Refinement stepCycle: LAST / Resolution: 2.25→27.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 4 88 1944
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d914SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes274HARMONIC5
X-RAY DIFFRACTIONt_it1896HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion253SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2256SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1896HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2568HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion2.93
LS refinement shellResolution: 2.25→2.43 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2487 159 5.58 %
Rwork0.2052 2693 -
all0.2076 2852 -
Refinement TLS params.Method: refined / Origin x: 21.6854 Å / Origin y: 59.4929 Å / Origin z: 165.915 Å
111213212223313233
T-0.0451 Å20.0475 Å2-0.1356 Å2--0.138 Å2-0.0214 Å2---0.1216 Å2
L1.3336 °2-0.044 °2-0.0611 °2-3.046 °20.8461 °2--1.2731 °2
S0.0761 Å °0.008 Å °-0.1472 Å °-0.7279 Å °-0.1408 Å °0.4419 Å °0.0143 Å °-0.1955 Å °0.0647 Å °

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