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- PDB-8eqh: The crystal structure of 14-3-3 Beta containing 3-nitrotyrosine a... -

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Basic information

Entry
Database: PDB / ID: 8eqh
TitleThe crystal structure of 14-3-3 Beta containing 3-nitrotyrosine at position Y213
Components14-3-3 protein beta/alpha
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


: / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / 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 / positive regulation of catalytic activity ...: / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / 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 / positive regulation of catalytic activity / Signaling by Hippo / vacuolar membrane / negative regulation of G protein-coupled receptor signaling pathway / Frs2-mediated activation / 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 / protein localization / melanosome / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / extracellular exosome / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
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
14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhu, P. / Cooley, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RM1GM144227 United States
CitationJournal: Protein Sci. / Year: 2023
Title: Genetic encoding of 3-nitro-tyrosine reveals the impacts of 14-3-3 nitration on client binding and dephosphorylation.
Authors: Zhu, P. / Nguyen, K.T. / Estelle, A.B. / Sluchanko, N.N. / Mehl, R.A. / Cooley, R.B.
History
DepositionOct 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 14-3-3 protein beta/alpha
A: 14-3-3 protein beta/alpha


Theoretical massNumber of molelcules
Total (without water)56,5632
Polymers56,5632
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-14 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.290, 115.030, 79.490
Angle α, β, γ (deg.)90.000, 119.537, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein 14-3-3 protein beta/alpha / Protein 1054 / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 28281.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAB / Production host: Escherichia coli (E. coli) / References: UniProt: P31946
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20%-27% PEG 3350, +/- 50 mM MgCl2, 100 mM Bis-Tris pH 5.5-6.5

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Data collection

DiffractionMean temperature: 96 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→44.22 Å / Num. obs: 52427 / % possible obs: 99.7 % / Redundancy: 26.3 % / Biso Wilson estimate: 48.49 Å2 / CC1/2: 1 / Net I/σ(I): 16.48
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 3903 / CC1/2: 0.197 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASER1.19.2_4158phasing
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BQ0

2bq0


Resolution: 1.9→44.22 Å / SU ML: 0.3122 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2185 2616 5.02 %
Rwork0.1876 49535 -
obs0.1891 52151 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 0 144 3755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533695
X-RAY DIFFRACTIONf_angle_d0.72054997
X-RAY DIFFRACTIONf_chiral_restr0.0401565
X-RAY DIFFRACTIONf_plane_restr0.0061648
X-RAY DIFFRACTIONf_dihedral_angle_d14.26511389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.44081270.46122438X-RAY DIFFRACTION93.2
1.93-1.970.45931430.41562519X-RAY DIFFRACTION97.08
1.97-2.010.42641200.39132574X-RAY DIFFRACTION99.59
2.01-2.060.44861430.36592641X-RAY DIFFRACTION99.96
2.06-2.10.3231270.3132637X-RAY DIFFRACTION99.96
2.1-2.160.29821460.26992596X-RAY DIFFRACTION100
2.16-2.210.25391430.23712607X-RAY DIFFRACTION100
2.21-2.280.23911320.22092592X-RAY DIFFRACTION99.89
2.28-2.350.22071370.2072626X-RAY DIFFRACTION99.89
2.35-2.440.27411420.20592647X-RAY DIFFRACTION100
2.44-2.530.21981370.20482614X-RAY DIFFRACTION100
2.53-2.650.28521430.20652630X-RAY DIFFRACTION100
2.65-2.790.23971350.2032585X-RAY DIFFRACTION100
2.79-2.960.2461410.19552645X-RAY DIFFRACTION99.96
2.96-3.190.23481390.19832610X-RAY DIFFRACTION99.96
3.19-3.510.22531370.19012622X-RAY DIFFRACTION100
3.51-4.020.19331390.16152631X-RAY DIFFRACTION100
4.02-5.070.19031400.1442656X-RAY DIFFRACTION100
5.07-44.220.171450.16692665X-RAY DIFFRACTION99.79
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)
14.39073908211-0.05529332080610.2055034875829.3654228931-0.4526979706171.777138253250.139119017663-0.08436170750440.3874572003720.38162900292-0.335481181702-1.64901326619-0.3943775532750.2668591747570.08516900166490.4655369132980.0697958301174-0.0127927523470.4939815853120.04468325376060.58648316962325.955111751-13.742848036420.9552466167
25.07940027264-1.74876310297-1.372300811614.124365714921.72514354.33110861434-0.00672944065766-0.230732250139-0.4399720029070.142350515608-0.0734679237701-0.254203450760.0723906255177-0.05711338670350.06896216123930.3950943717420.085042579359-0.009441770186110.4213304126560.0535299874840.51110912344921.1865774419-34.777385340616.9333919963
36.638502314720.6512547347691.206791708430.609101777027-0.4805141374181.747265160680.1228686350561.30442839915-0.752206371567-0.319430109368-0.03382580861920.08207916024310.0899142427288-0.296659102645-0.1411084620310.520079241320.0756844420744-0.04179208085260.772783651631-0.1341585584140.66515563619215.2993245825-36.3088651813.23344113601
48.159954058843.49684264717-5.949274699844.56490237289-3.074696188097.76962757949-0.2830399647241.008716339960.608025455308-0.2042205770610.2149827532020.3764250231760.0347978882283-0.7716338465760.08690127228690.6333102722380.155226021591-0.1942412155161.106338525320.06839196721110.6836756799448.56758411976-30.79925845570.442776696169
58.387909293373.992373104221.087219449584.402246820444.677414426727.36731869776-0.169979167363-0.1980936657280.342347211041-1.05806480986-0.00568780410389-1.06978156881-0.7913834016680.5707346436280.1885732225650.6090532165980.0371595555239-0.004074220424260.523507741690.1378401921680.7816418537322.25988559643.207292581519.9289790335
63.51395843738-1.00639406607-1.580033842557.370708142240.05162871041014.15340437913-0.203674716621-0.6416958095210.3090946528620.5840663254850.156491683753-1.10169371271-0.1543785901830.6872848512830.1425150029720.5032118720070.0918272059888-0.1183336743050.575415049693-0.02050991794680.62032946785116.37605574184.6987875472724.679011051
78.242042152482.91785041179-1.234678415819.96347909199-0.5252363742561.21063049076-0.3534387812780.293903498779-0.203686298075-0.1484354011040.4517562643430.614263961015-0.0254687323065-0.14851821017-0.1307895380640.4799308131280.134524369783-0.01246552987780.4507454163550.004567633862680.3637270823972.99091001461-2.0866373995622.5093266825
80.0407166489768-0.00463279069165-0.0767191836881.022964692810.9488634698010.986079878522-0.1405595577050.6414211593681.745790879530.642273515288-0.64334535256-0.04523127587050.728360586325-0.8469156104150.2570118323840.8840637199440.127302831814-0.04800418165031.04904598412-0.0343661725731.63771493624-14.4291181852-22.861870714529.2858516349
95.545250696013.07839427805-0.966380678432.365149091670.4583875896822.988596391270.083138111089-1.0355478782-1.071174804421.25045840933-0.415294676332-0.6318184153430.23194209012-0.140200844260.230769599870.6771737345280.1945080680520.06331141060060.678913246650.09844807370220.555053492750.097548259079-6.1478498510833.1202525653
104.36449561121-1.461081614010.8299439121646.37097808226-0.2009407656652.56448218432-0.255688594059-0.2213596541870.3468346119010.4433828498510.0626263699742-0.0399064279184-0.1486789879410.2341198441560.1993997311050.6066223011550.142157798044-0.05056802645190.545550629822-0.06470179898220.4604074769062.5083714594511.639358120926.2515308341
115.286925016820.962195979832-1.352413279816.85021226512-2.552703058765.12971572001-0.35926718286-0.4676732064970.2972115865030.9132434232860.2267834630280.465259802967-0.419891553806-0.3889940709440.08630192286550.6252949640160.189551475380.0350622922920.502280645924-0.1134465710280.551660914401-6.6266262608314.626807845627.4858943363
125.28875496014-2.082683715493.910082168658.136824954592.825133321835.48901986452-0.2337884669050.3317669102281.0831966512-0.390946325475-0.389935082313-0.40878026501-1.403758564890.7183649887810.3795866585520.676115317117-0.0155531207599-0.02074044164040.5882922342250.09864431265680.7142526515350.37255009216521.348541318610.9890054713
132.514423809860.542335561756-0.1876428376671.69074107389-0.721862847612.79005745232-0.123562445756-0.183357533722-0.02979698044210.2500095379630.1451815071690.4427385048630.151948575089-0.0865270947941-0.002779653075980.4978100785760.1049424849770.06324620641490.4321242533760.02652307811020.576225664468-8.711313993159.6234121651118.6914467827
145.919743799793.75561067408-4.28964818567.54918404651-4.798336672647.546506459540.04756419396010.661513426342-0.06696308964270.5422276961750.00884067956398-0.0730636621815-0.468979347105-0.41377909777-0.1755378687370.4656028915260.086495797755-0.007697747561630.507448131631-0.004709424704460.661360705704-11.87288013515.458570653110.4875957991
153.311300930442.25319474052-4.443064826881.64624015167-3.2256435736.63116350590.207724217375-0.1728934616350.832086486036-0.220989598204-0.5595580062890.624730783657-1.53255009287-0.6768157731880.1219628863940.9516056790120.03306637033510.02863461336371.01984373380.09263007745140.717581234531-5.3767596483321.1459809799-3.17034162617
162.51849370112-2.51521102832-2.771509498963.523646575312.572098665255.15696408331-0.386495619768-0.588504522593-1.14424561740.1720372623780.04932313181090.3210962800880.398388532477-0.4322252996810.2578673176840.58641328123-0.129370754717-0.007204801043290.5229574701370.03176014455660.530666345784.011116098338.26566521884-6.7365237305
175.15538810342-1.681236572020.7828349935419.37859111546-0.1694993046311.31946554947-0.0712236770294-0.53923057894-0.175725288940.8817365491590.2315043336391.002391724450.102948124551-0.323588997579-0.1864514298250.5499332772870.0652690589760.09503129363160.5577269975940.07292138336380.6020857120644.58421850313-25.697060050228.8141486099
185.946803996452.41069510663-2.988647662273.81159301185-1.095298900643.15609617043-0.07356645302210.862154714064-0.188448351605-0.3926710871950.394346732985-0.294886642442-0.280446208489-0.600724274569-0.2664645604950.5281075810530.1150700736340.03168202913910.503908535190.06166340546860.55555659784415.7222991741-18.795673165616.4389089389
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 71 through 105 )B0Z0B71 - 10569 - 103
22chain 'A' and (resid 106 through 161 )B0Z0B106 - 161104 - 159
33chain 'A' and (resid 162 through 209 )B0Z0B162 - 209160 - 205
44chain 'A' and (resid 210 through 233 )B0Z0B210 - 233206 - 229
55chain 'B' and (resid 3 through 17 )BA3 - 171 - 15
66chain 'B' and (resid 18 through 39 )BA18 - 3916 - 37
77chain 'B' and (resid 40 through 69 )BA40 - 6938 - 67
88chain 'B' and (resid 70 through 74 )BA70 - 7468 - 72
99chain 'B' and (resid 75 through 105 )BA75 - 10573 - 103
1010chain 'B' and (resid 106 through 136 )BA106 - 136104 - 134
1111chain 'B' and (resid 137 through 161 )BA137 - 161135 - 159
1212chain 'B' and (resid 162 through 166 )BA162 - 166160 - 164
1313chain 'B' and (resid 167 through 186 )BA167 - 186165 - 184
1414chain 'B' and (resid 187 through 204 )BA187 - 204185 - 202
1515chain 'B' and (resid 205 through 209 )BA205 - 209203 - 207
1616chain 'B' and (resid 210 through 232 )BA210 - 232208 - 230
1717chain 'A' and (resid 3 through 39 )B0Z0B3 - 391 - 37
1818chain 'A' and (resid 40 through 70 )B0Z0B40 - 7038 - 68

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