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- PDB-6twz: 14-3-3 sigma complexed with a phosphorylated 16E6 peptide -

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Basic information

Entry
Database: PDB / ID: 6twz
Title14-3-3 sigma complexed with a phosphorylated 16E6 peptide
Components
  • 14-3-3 protein sigma
  • phosphorylated 16E6 peptide
KeywordsPEPTIDE BINDING PROTEIN / phosphorylation / motif / 14-3-3 protein
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 protein sigma / 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
D(-)-TARTARIC ACID / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGogl, G. / Cousido-Siah, A. / Sluchanko, N.N. / Trave, G.
CitationJournal: Structure / Year: 2020
Title: Dual Specificity PDZ- and 14-3-3-Binding Motifs: A Structural and Interactomics Study.
Authors: Gogl, G. / Jane, P. / Caillet-Saguy, C. / Kostmann, C. / Bich, G. / Cousido-Siah, A. / Nyitray, L. / Vincentelli, R. / Wolff, N. / Nomine, Y. / Sluchanko, N.N. / Trave, G.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
E: phosphorylated 16E6 peptide
F: phosphorylated 16E6 peptide
G: phosphorylated 16E6 peptide
D000: phosphorylated 16E6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,17813
Polymers110,2968
Non-polymers8835
Water00
1
A: 14-3-3 protein sigma
B: 14-3-3 protein sigma
E: phosphorylated 16E6 peptide
D000: phosphorylated 16E6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4486
Polymers55,1484
Non-polymers3002
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-13 kcal/mol
Surface area22890 Å2
MethodPISA
2
C: 14-3-3 protein sigma
D: 14-3-3 protein sigma
F: phosphorylated 16E6 peptide
G: phosphorylated 16E6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7307
Polymers55,1484
Non-polymers5833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-13 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.580, 107.420, 79.600
Angle α, β, γ (deg.)90.000, 109.289, 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
Components on special symmetry positions
IDModelComponents
11D-302-

B3P

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Components

#1: Protein
14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin / CLU1


Mass: 26257.537 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide
phosphorylated 16E6 peptide


Mass: 1316.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 16
#3: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
Has ligand of interestY
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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.1M Bis-Tris-Propane (pH 6.5), 0.2M K/Na-tartarate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49 Å / Num. obs: 34835 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 70.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.23
Reflection shellResolution: 2.8→2.87 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2543 / CC1/2: 0.458

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LU2

5lu2


Resolution: 2.8→48.56 Å / SU ML: 0.4231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4234
RfactorNum. reflection% reflection
Rfree0.2356 1761 5.06 %
Rwork0.2027 --
obs0.2043 34827 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 87.22 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7527 0 59 0 7586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00367684
X-RAY DIFFRACTIONf_angle_d0.554710358
X-RAY DIFFRACTIONf_chiral_restr0.03311153
X-RAY DIFFRACTIONf_plane_restr0.00231349
X-RAY DIFFRACTIONf_dihedral_angle_d19.16632903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.37111450.33672504X-RAY DIFFRACTION99.07
2.88-2.960.3621200.30452540X-RAY DIFFRACTION99.14
2.96-3.060.37031290.29232525X-RAY DIFFRACTION99.03
3.06-3.170.33061220.2872537X-RAY DIFFRACTION99.22
3.17-3.290.31291350.28022544X-RAY DIFFRACTION99.33
3.29-3.440.28421390.24622518X-RAY DIFFRACTION99.4
3.44-3.620.26861310.22172557X-RAY DIFFRACTION99.48
3.62-3.850.2531370.20552548X-RAY DIFFRACTION99.44
3.85-4.150.21641390.18122518X-RAY DIFFRACTION99.48
4.15-4.560.1761390.15832543X-RAY DIFFRACTION99.59
4.56-5.220.19721360.16392554X-RAY DIFFRACTION99.67
5.22-6.580.23181390.20532584X-RAY DIFFRACTION99.67
6.58-48.560.18791500.16352594X-RAY DIFFRACTION99.42
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)
16.72871327341.01049794874-2.016872119865.75852280204-0.648251614755.2970033410.7966430629981.004612205670.0622020136764-2.52489878911-0.4057041328130.735252835685-0.3839140043640.288417392746-0.3656471481472.056433820020.314464871115-0.1701623642020.637772122952-0.1019512149010.756963508726-79.82464562637.7827859999510.9190632239
23.64997600332-0.570190597281-1.189312166868.365591063521.468477327613.724314031720.1038642659840.0422318143405-0.265660259826-0.690086762819-0.2206039096921.285984832310.0875166900488-0.3880188395150.1104746801560.632157740374-0.0576982888902-0.1551044807910.451204117822-0.06284943134370.922421528937-86.17748540585.0478845971230.5490601613
35.98995114379-1.5102941003-0.9753145359226.751375732280.948747244895.87274657311-0.441967855957-0.1738637029880.1511807735641.258787210030.393915663144-0.1303651597930.8994069198220.3126209961660.03939065905120.9134895349120.0493233482667-0.1721840311910.353266541433-0.0304244058810.76847673216-74.6208998795-9.6670313692437.5912238692
41.60059896961-2.29146630746-3.33809866063.114082368424.573066199916.82239833143-0.33132745858-1.474008439241.428439874431.132933653080.3148982906140.5404768797310.330217742359-0.06925206379290.05440591849120.903223783807-0.05333556705220.1300068795840.51658968802-0.1793366861081.17159647295-91.135855058128.586948138142.1024314309
57.24960967028-0.463102311923-3.430353824215.542584554131.598535848829.07336335403-0.1782310423380.0642813571336-0.0282463051654-0.940874804294-0.05573059359980.6484317521440.13960535084-0.1831556245510.2576605499840.708653389661-0.0335772960995-0.1363112329930.336001652103-0.05225623161480.806634540065-81.9784377828.839000745228.3788103163
62.85400350121-1.36064558192-4.216275263517.541142106331.488864521176.31068875489-1.235529656970.487087284226-0.382126727021-0.616035134111-0.319226168997-1.312153563791.40382997541.225865475321.572860894231.283410709960.1572259983350.1169738984431.297969053730.06464564599850.964898024877-71.942675325415.78877215360.858076835017
74.608168043970.157714355851-1.659255739486.0312367924.877877304385.29621742668-0.08430500027630.5241470771740.565972305131-2.877928708430.07244778255430.957378391103-0.174721793945-0.410423498070.2273707113381.666996511050.00170153206809-0.489674956380.540761280370.001537320345060.857973413381-84.230665481927.724029168316.4545313144
86.487652952117.803996264873.144498300499.529867911163.80162900371.587911304350.300691897154-1.43492992421-0.106948712147-0.371143859999-0.4415727760171.15399584891-0.380836257286-1.177927831620.2262055966710.5959587631850.255793397481-0.02931355715320.8525956289390.008111400123391.46684969989-89.212826266846.349370784732.4531206337
93.848265620152.3462252591-1.182162090156.779478908823.087826534433.65807746826-0.3222928751670.2547726746920.299889976535-1.718797302110.3091597418760.655869380017-0.0665465221384-0.1370185399740.0127753744571.097749800820.00936834259473-0.1953525225360.3951493497710.03220355110770.804406490351-77.646257016443.990671380923.1844839507
109.09433440815-1.06923330847-1.099307549928.54320342428-1.157980673938.162949322010.306603031430.92100909690.220217738292-1.368242171370.137022336944-0.3589951638250.8393134139180.129081529639-0.4574727581450.5849459145840.01921537022640.03379705111420.371192785484-0.0172999011470.505113703465-68.792318856542.657978764922.8303419082
116.111231689191.802885541043.573638325314.989684229175.390198345787.388324335620.2352154150650.1827195813821.52656895005-1.740858214690.108398901567-0.798391737231-1.898073290791.42347501725-0.1312012919110.745878214038-0.08063146890550.2489074814330.56013520407-0.001668457968010.992404718234-60.67933953548.1314994926.1376069771
125.04208944417-0.05703140226711.558901161199.201428628295.569242225874.03831869025-0.155416100894-0.66355611683-0.161453955927-0.1091098776310.252684653152-0.09967777102260.0584597557571.400478889430.02251647878610.635467372897-0.05258897113480.06947132610750.6669050958930.01541301486290.872942428289-61.216817876241.714305326135.6477704931
135.97715992231-1.87763757537-3.182449916297.30766793205-2.799820984953.899118286680.1291430546780.204244388791-0.547274596948-0.154082105147-0.4445328934430.845921330490.954687996075-0.5306428087810.1798487226520.713499777053-0.1842498524410.05365156916550.480769367508-0.08501215502330.615210263515-34.59647286330.8227480057747.58565634366
143.35989565315-3.34131136728-0.1840721250984.610018204342.173382139053.024217866990.000928851859420.248808881528-0.4860534093390.0181939938992-0.2315107071810.9274142796120.410701877491-0.7374223737750.06988654390110.5916224978-0.09450034436630.04631455640760.509065696333-0.0672358634740.574854186351-39.15066954283.927514441213.524948568
153.071240405111.15670527393-0.9909754760432.4264251543-3.359487467564.916586141950.005327988075990.2117947889480.3747847916432.085908312580.134604656102-0.201015895522-1.02385859953-0.064182608602-0.09452652038920.5664816984210.08517051604580.0213728671250.4419971406020.004247263185950.569382964823-31.981106149719.950457755916.4651570941
167.42729501136-3.02106218583-2.378580664133.50310325575-0.6165500262732.296608066660.177135765184-0.4109189460951.04468576396-0.3817857545581.20718675138-1.7316115681-0.632250278388-0.324578866812-1.159046226891.58443842999-0.01872952723790.4629351189950.5124541076760.2271884030541.56587207731-33.031678829146.185134408412.3095395772
172.503767614-1.30328279393-2.521931780437.99666267943-0.9083156671033.69870543147-0.004881206355361.09120856080.6672122541730.1773021994641.009958574790.535391310525-0.790721775851-1.39559662721-1.037316434990.4992475134120.1592946921520.05387974191890.6266549836440.1316356685360.601237110804-41.126348188323.714771841214.0303602675
186.869036544751.103767499610.004105192095566.17590529188-1.877187196377.644725063740.0434121866192-0.3429736638020.037765365670.9874116183280.09756341331990.50420422804-0.636533619705-0.836305213845-0.1124624291320.579485640380.06087861320670.1332592260560.512650854659-0.0627367142780.412660848456-40.271679401214.500500660329.4407121445
197.148191250671.113913104232.382737936244.08601612581-1.460798027096.351123661860.045217564457-0.5948660171920.2388896015540.693144812646-0.186561604641-0.20571715356-0.923816946256-0.190839896170.1460857639540.724290653758-0.0884450275450.05579392999710.464684900268-0.07515758762060.506617537597-27.663371498416.657160802936.8446320294
204.584620439-4.244498433931.739047186324.20410530669-2.133306830445.421575739460.2500440633880.0213241892507-0.3149399868851.18756336142-0.409379828093-0.678250732467-0.3834270037690.4898301943280.172952280880.573763795521-0.179015712903-0.02471606548680.5871875405040.08837822536790.713918865979-18.22622929111.208419045833.3431646656
215.60287552994-1.41859072251-1.653206546428.89961726293-2.213671945456.604861557-0.3145834320680.9618666789591.001047725460.382269506415-0.0113458099996-0.732098760945-1.4635545618-0.6742601093150.2822210901620.9335184252710.2144413253150.08644581439580.6489929073250.2815366709780.84234268667-33.074319076336.8974193569-1.67254551688
224.084036187861.82249523801-2.405791805234.477202010173.524085806229.48416195561-0.1464089424660.6574016022461.202682041210.378417997842-0.08688552167180.258663808499-0.563516192867-0.2911025483390.4576568980580.4772788355580.1520442543780.04060768750020.5259526380190.25788920270.88762483247-31.368284095329.7366474127-4.78262842967
233.5757211149-0.124747962095-0.7544966713127.91700680085-2.170121139846.15308274174-0.02547225205160.393984979421-0.2251845423150.108106089544-0.0880503506544-0.1954627655260.727343331479-0.3606613720920.05398863393980.359908567045-0.03538060471580.06431475236630.487431400385-0.03973933140490.386074681777-27.06911905610.5980756398-4.98641561743
248.43843881689-0.1008350928291.118192073545.21725373105-1.896412876682.56506707927-0.2303731333631.190903759120.627744401159-0.6682798999810.2575161816780.0280625622693-0.0924730404891-0.319046057697-0.03629761881220.601850642826-0.002968035245980.09121380252750.8203516107850.1260715353830.411453645786-20.649429887820.2441057179-18.6251075054
257.811101015050.7549645951183.164751893858.476233180382.030871539656.35802178562-0.3504719987540.7516815804740.937959340417-0.04074226583530.15649970445-0.758014985166-0.341823557510.316440674660.1443594746480.365829572637-0.007065613023580.1024335607260.56316153870.1848810556120.708664457485-4.6785821602921.58020345-11.2624660331
263.564178255660.691701512531-2.851337452543.12691697428-2.962453675774.45714677621.01529222342-2.50657098465-2.01571116532-0.5984942045350.354282463025-0.2660742044841.244828702420.0804448471197-1.126700669280.655488700994-0.0135038363833-0.09905542615490.766747158270.01693979143680.879085853687-67.298603128832.822468766926.1589488187
274.92454897286-5.45862211169-2.982322593926.206134151613.650757681692.64354968390.2475212655562.00516329674-0.820875753817-0.1059306324680.10987128403-2.532383469070.4871598500061.34360265448-0.1649529656850.814132352679-0.0348184830504-0.2709044890190.824906832282-0.09001370565640.947273722294-24.658938598520.220980297724.8230056551
283.47206851874-3.71874915322-0.608698616044.249569735471.544972542172.59658672114-1.19479285484-2.132241109180.2825006673411.637050632110.7860416014140.1743195057570.349077242374-1.836782684330.4881155337810.5511782743210.0516343157839-0.003684902392990.703248987885-0.1603924168330.909895998547-12.409419432915.6281359096-3.75385496721
295.3726275638-5.22247291141-4.451982580745.094199951794.338697192753.686044359780.3431171326770.4109892467312.35674392194-0.3112389470851.18239993608-2.86029964384-1.914699658561.83579379077-1.573415549240.795518680122-0.0349057000814-0.1228801830970.923313689788-0.0922034091631.23894907752-74.45560154272.1656251470238.8901021653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 231 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 15 )
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 69 )
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 79 )
7X-RAY DIFFRACTION7chain 'B' and (resid 80 through 105 )
8X-RAY DIFFRACTION8chain 'B' and (resid 106 through 113 )
9X-RAY DIFFRACTION9chain 'B' and (resid 114 through 166 )
10X-RAY DIFFRACTION10chain 'B' and (resid 167 through 186 )
11X-RAY DIFFRACTION11chain 'B' and (resid 187 through 203 )
12X-RAY DIFFRACTION12chain 'B' and (resid 204 through 231 )
13X-RAY DIFFRACTION13chain 'C' and (resid -1 through 18 )
14X-RAY DIFFRACTION14chain 'C' and (resid 19 through 37 )
15X-RAY DIFFRACTION15chain 'C' and (resid 38 through 69 )
16X-RAY DIFFRACTION16chain 'C' and (resid 70 through 79 )
17X-RAY DIFFRACTION17chain 'C' and (resid 80 through 105 )
18X-RAY DIFFRACTION18chain 'C' and (resid 106 through 161 )
19X-RAY DIFFRACTION19chain 'C' and (resid 162 through 203 )
20X-RAY DIFFRACTION20chain 'C' and (resid 204 through 231 )
21X-RAY DIFFRACTION21chain 'D' and (resid -2 through 15 )
22X-RAY DIFFRACTION22chain 'D' and (resid 16 through 37 )
23X-RAY DIFFRACTION23chain 'D' and (resid 38 through 105 )
24X-RAY DIFFRACTION24chain 'D' and (resid 106 through 161 )
25X-RAY DIFFRACTION25chain 'D' and (resid 162 through 231 )
26X-RAY DIFFRACTION26chain 'E' and (resid 151 through 158 )
27X-RAY DIFFRACTION27chain 'F' and (resid 151 through 158 )
28X-RAY DIFFRACTION28chain 'G' and (resid 151 through 158 )
29X-RAY DIFFRACTION29chain 'I' and (resid 151 through 158 )

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