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- PDB-7exe: Crystal structure of mouse 14-3-3zeta in complex with doubly phos... -

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Basic information

Entry
Database: PDB / ID: 7exe
TitleCrystal structure of mouse 14-3-3zeta in complex with doubly phosphorylated ADAM22 peptide
Components
  • 14-3-3 protein zeta/delta
  • Disintegrin and metalloproteinase domain-containing protein 22
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


NOTCH4 Activation and Transmission of Signal to the Nucleus / GP1b-IX-V activation signalling / KSRP (KHSRP) 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 / Schwann cell differentiation / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex ...NOTCH4 Activation and Transmission of Signal to the Nucleus / GP1b-IX-V activation signalling / KSRP (KHSRP) 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 / Schwann cell differentiation / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex / LGI-ADAM interactions / postsynaptic specialization / Rap1 signalling / synaptic target recognition / Golgi reassembly / regulation of programmed cell death / Interleukin-3, Interleukin-5 and GM-CSF signaling / establishment of Golgi localization / myelination in peripheral nervous system / histamine secretion by mast cell / respiratory system process / axon initial segment / regulation of synapse maturation / tube formation / gliogenesis / negative regulation of protein localization to nucleus / protein targeting to mitochondrion / neurotransmitter receptor localization to postsynaptic specialization membrane / cell leading edge / phosphoserine residue binding / protein targeting / regulation of ERK1 and ERK2 cascade / cellular response to glucose starvation / positive regulation of protein localization / negative regulation of TORC1 signaling / ERK1 and ERK2 cascade / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / lung development / postsynaptic density membrane / metalloendopeptidase activity / intracellular protein localization / melanosome / angiogenesis / DNA-binding transcription factor binding / transmembrane transporter binding / protein phosphorylation / protein domain specific binding / response to xenobiotic stimulus / axon / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / mitochondrion / proteolysis / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin ...ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / EGF-like domain, extracellular / EGF-like domain / 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 / Metallopeptidase, catalytic domain superfamily / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein zeta/delta / Disintegrin and metalloproteinase domain-containing protein 22
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsYan, L. / Okatsu, K. / Fukai, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03983 Japan
CitationJournal: Cell Rep / Year: 2021
Title: LGI1-ADAM22 levels regulate seizure thresholds through 14-3-3 in mice
Authors: Yokoi, N. / Fukata, Y. / Okatsu, K. / Yamagata, A. / Yan, L. / Sanbo, M. / Miyazaki, Y. / Goto, T. / Abe, M. / Natsume, R. / Aiba, A. / Sakimura, K. / Meijer, D. / Hirabayashi, M. / Fukai, S. / Fukata, M.
History
DepositionMay 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 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 zeta/delta
B: 14-3-3 protein zeta/delta
C: Disintegrin and metalloproteinase domain-containing protein 22


Theoretical massNumber of molelcules
Total (without water)61,0653
Polymers61,0653
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-18 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.197, 85.546, 111.869
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1 / SEZ-2


Mass: 28632.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ywhaz / Production host: Escherichia coli (E. coli) / References: UniProt: P63101
#2: Protein/peptide Disintegrin and metalloproteinase domain-containing protein 22 / ADAM 22


Mass: 3801.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9R1V6
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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→49.5 Å / Num. obs: 18575 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 71.81 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.351 / Rsym value: 0.337 / Net I/σ(I): 14.13
Reflection shellResolution: 2.75→2.92 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 2927 / CC1/2: 0.918 / Rrim(I) all: 2.311 / Rsym value: 2.222 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREPphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QJA

1qja


Resolution: 2.75→49.48 Å / SU ML: 0.4585 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.0421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2666 938 5.09 %
Rwork0.2422 17498 -
obs0.2436 18436 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.26 Å2
Refinement stepCycle: LAST / Resolution: 2.75→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 0 0 3704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263755
X-RAY DIFFRACTIONf_angle_d0.41235046
X-RAY DIFFRACTIONf_chiral_restr0.033553
X-RAY DIFFRACTIONf_plane_restr0.0029649
X-RAY DIFFRACTIONf_dihedral_angle_d14.09041452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.90.36381170.38552438X-RAY DIFFRACTION98.23
2.9-3.080.35531280.33622453X-RAY DIFFRACTION99.15
3.08-3.320.34951210.2962470X-RAY DIFFRACTION98.89
3.32-3.650.31961410.27162456X-RAY DIFFRACTION98.93
3.65-4.180.26581360.22262514X-RAY DIFFRACTION99.77
4.18-5.260.24341600.20562509X-RAY DIFFRACTION99.93
5.26-49.480.21231350.21822658X-RAY DIFFRACTION99.54
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)
15.427744398690.300517626295-0.4101123599364.492152023781.540317140594.16969221710.265120840823-0.811465175349-0.6289314722410.5110640622630.1643334426681.397747366710.2532171170740.481593244139-0.1940560606680.624451162664-0.04529275854960.07103508572460.6109726630050.1240711230310.791805195975-37.8169149424-6.528969886218.4286360097
24.39988851101-0.966682189616-0.4036824128254.378489246831.908869019536.87306462483-0.3058114078920.0634773597224-0.6513244825990.0384521286901-0.4815339548330.960248830304-0.256886378253-1.18537835888-0.09511429357690.523283612176-0.106230009241-0.1047440369810.8130859037180.1671128266151.21742862131-47.4010110596-3.296523563787.28855686773
34.34337216926-1.60604876558-2.144482089883.231276325770.8064523445519.14215226160.09997507498620.799514182947-1.23147105571-0.512036326086-0.1316392532240.9380206295061.2504160849-1.69865886527-0.3361699187120.747115199948-0.169734246544-0.2509783038420.815860694597-0.03433780282171.58909987365-49.8884388333-11.7409484932-4.13543650297
44.36854757218-4.03358172891-0.2961523310076.46772010433.62358002884.20145160024-0.0355020876294-0.438192425661-0.7177830680370.9288728648490.3549811733150.45767205113-0.564521289324-0.572491152146-0.529495222171.1976009302-0.1007703101110.2270712790591.236655431970.6242787953731.14565733187-56.0191111496-8.3594895790625.4833675161
53.343278841920.4430326019581.928571125074.94309448087-1.484145592984.5329392080.29972747116-0.7233563680960.04439241242650.4138508442790.06866030230111.911206929920.529994715426-1.18274509975-0.5399442579690.620973471374-0.063356449720.1454125710771.034770200350.4459277661691.76085080489-57.4053880789-3.7715185516512.3148388826
61.909749833091.430029168651.172138025574.546407181980.7363686483222.1389374374-0.189568630203-0.646017811632-0.4096091720580.3795704842550.2622192037191.97222883933-0.173329200336-0.721188302771-0.08739605821580.6913772522370.05686421508090.1325058666231.338595855370.3094133543242.25183275314-63.32504459346.2796322716512.8567415307
78.3327342285-1.991510326820.5918533785598.70714452738-2.49155240946.24171020217-0.2631913782140.6023221865660.2559382062940.02601131657810.02088259872081.37462376039-0.8180689656020.4581547128520.3046770458570.5381127217730.005681658681410.06278727044690.70225234296-0.04523878363871.46796533049-55.808548456415.55059289468.77935014425
83.68422813199-1.03083744766-2.481982619961.760328371280.1522286765413.529255269020.372783762830.86929062865-0.20168619683-0.878042526942-0.3845688682160.533887691597-0.111193120244-0.419757225106-0.09549770464550.897207982588-0.0100919103731-0.4261039849390.781238416305-0.08922867643170.779182068548-32.4691895347-10.195950972-13.676630869
92.61073232232-0.874715875967-1.564835791542.197204612910.6715272311695.535292159970.126117945091-0.123573834525-0.3176595498880.1179091220360.143858046080.3005578335950.06550582812530.669352279488-0.2593156233150.560473457201-0.0126696513525-0.100533221510.555717194377-0.007373880577830.422163035812-23.5439944146-5.711915637446.95174569186
103.993815637560.112627340348-1.231400026214.60030083968-1.551967573890.825119370212-0.01236428702070.706340900379-0.103446846239-0.4477452110780.0009114656848830.1234455620940.548834372450.164756269867-0.2654927773490.618287285165-0.0139667678354-0.06148572921730.565902953313-0.1361270560850.373723673025-15.6086233223-6.37877276037-11.4666405183
111.33133339338-0.895952397897-1.308552970242.334339251080.8550198137881.288336446380.121187298724-0.650480049937-0.2934074475780.7724892377370.107403292477-0.5321479597881.177391491360.880766622699-0.8219444754010.7827294073180.254775461357-0.7012265947311.6942343181-0.312573593408-0.168772940648-11.5379733972-7.302936267448.96316253274
123.987794740990.98079242096-0.8781296724084.85576802969-3.47485726377.62604356432-0.0611343725778-0.10401896232-0.314122860289-0.356243143602-0.357261244191-0.9275250292720.8363491803082.05812573324-0.08497567892450.5928854061460.118053223965-0.09337932109890.979371207416-0.2324143410040.561253560902-6.46603370157-2.38884628981-8.36542788208
134.622406992110.01589501323030.2597113519414.3028032164-1.834933340234.49589790972-0.213929871035-0.2634833303570.2533095147650.327248562222-0.427653372359-0.1252252548820.202474582747-0.265570057056-0.2797642176470.472810072899-0.0574755610732-0.02965805364680.603730210687-0.2414461545950.545103153611-11.46268591786.14555340895-7.76150513039
149.112432743590.5450630011662.550716767735.92816675256-0.348435896348.30155065954-0.04124129781221.344642161131.31030762572-0.330874386338-0.459178134070.1402198700270.05990543325231.38250410724-0.2165577646020.543798144036-0.1000823662290.01692068689150.851830283129-0.2403273534310.709776379913-9.2450895101314.7558305885-11.9261852356
157.220860949920.1673576248140.2182158591566.29086928282-0.6788997713366.484934317610.284948228643-0.962309102610.604407495257-0.05735369286770.06134633450260.223095489744-1.03751664977-0.654064545168-0.2968543739670.652036996678-0.09297755798620.1975588013850.505947722246-0.1371438932860.59899744817-18.037155482214.7908040518-8.54612345981
164.150553478320.434944251885-2.213980694970.0765928006327-0.1641592334681.626048231840.6583803201081.137936291351.654640733870.3462657823890.09103335246060.592124866887-0.188171643537-0.191071112984-0.2510324339990.822413571869-0.01205539165990.1293456588460.5597096739670.196233964550.996105291656-35.80775899077.590734633830.967773836495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 111 )
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 136 )
6X-RAY DIFFRACTION6chain 'A' and (resid 137 through 210 )
7X-RAY DIFFRACTION7chain 'A' and (resid 211 through 230 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 39 )
9X-RAY DIFFRACTION9chain 'B' and (resid 40 through 103 )
10X-RAY DIFFRACTION10chain 'B' and (resid 104 through 130 )
11X-RAY DIFFRACTION11chain 'B' and (resid 131 through 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 159 )
13X-RAY DIFFRACTION13chain 'B' and (resid 160 through 184 )
14X-RAY DIFFRACTION14chain 'B' and (resid 185 through 209 )
15X-RAY DIFFRACTION15chain 'B' and (resid 210 through 229 )
16X-RAY DIFFRACTION16chain 'C' and (resid 828 through 856 )

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