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- PDB-5ulo: Crystal Structure of 14-3-3 zeta in Complex with a Serine 124-pho... -

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Basic information

Entry
Database: PDB / ID: 5ulo
TitleCrystal Structure of 14-3-3 zeta in Complex with a Serine 124-phosphorylated TBC1D7 peptide
Components
  • 14-3-3 protein zeta/delta
  • TBC1 domain family member 7
KeywordsSIGNALING PROTEIN/peptide / 14-3-3 / TBC1D7 / phosphorylation / protein-peptide interaction / Structural Genomics / Structural Genomics Consortium / SGC / SIGNALING PROTEIN-peptide complex
Function / homology
Function and homology information


TSC1-TSC2 complex / Golgi reassembly / synaptic target recognition / negative regulation of cilium assembly / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / establishment of Golgi localization / tube formation / response to growth factor ...TSC1-TSC2 complex / Golgi reassembly / synaptic target recognition / negative regulation of cilium assembly / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / establishment of Golgi localization / tube formation / response to growth factor / Rap1 signalling / activation of GTPase activity / negative regulation of protein localization to nucleus / negative regulation of TOR signaling / TBC/RABGAPs / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / protein sequestering activity / ERK1 and ERK2 cascade / negative regulation of innate immune response / cellular response to starvation / hippocampal mossy fiber to CA3 synapse / GTPase activator activity / regulation of ERK1 and ERK2 cascade / ciliary basal body / positive regulation of GTPase activity / positive regulation of protein ubiquitination / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / lung development / regulation of protein stability / small GTPase binding / melanosome / cytoplasmic vesicle / angiogenesis / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / blood microparticle / cadherin binding / protein domain specific binding / lysosomal membrane / protein phosphorylation / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / RNA binding / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / 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
L-PROLINAMIDE / 14-3-3 protein zeta/delta / TBC1 domain family member 7 / TBC1 domain family member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å
AuthorsDONG, A. / HU, J. / MADIGAN, J. / WALKER, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / TONG, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure of 14-3-3 zeta in Complex with a Serine 124-phosphorylated TBC1D7 peptide
Authors: HU, J. / DONG, A. / MADIGAN, J. / WALKER, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / TONG, Y. / Structural Genomics Consortium (SGC)
History
DepositionJan 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 4, 2023Group: 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

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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: TBC1 domain family member 7
D: TBC1 domain family member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,83616
Polymers58,4834
Non-polymers35212
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-24 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.709, 71.575, 129.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 27834.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R / References: UniProt: P63104
#2: Protein/peptide TBC1 domain family member 7


Mass: 1407.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5SZL8, UniProt: Q9P0N9*PLUS

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Non-polymers , 4 types, 71 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#5: Chemical ChemComp-LPD / L-PROLINAMIDE


Type: L-peptide linking / Mass: 114.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M HEPES pH7.5,5%~15% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 36479 / % possible obs: 99.5 % / Redundancy: 8 % / Biso Wilson estimate: 59.73 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.023 / Rrim(I) all: 0.063 / Χ2: 2.214 / Net I/σ(I): 14.4 / Num. measured all: 291490
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.14-2.188.20.97918300.8390.3631.037100
2.18-2.228.30.730.9120.2681.0771000.778
2.22-2.268.20.6110.9320.2251.2651000.652
2.26-2.318.30.4590.970.1691.1451000.49
2.31-2.368.30.3970.9670.1461.1951000.423
2.36-2.418.30.3310.9760.1221.211000.353
2.41-2.478.30.2750.9810.1011.2621000.293
2.47-2.548.30.2160.9910.081.321000.231
2.54-2.618.30.180.9930.0671.3691000.193
2.61-2.78.20.1610.9920.061.6081000.172
2.7-2.798.30.140.9920.0521.8381000.149
2.79-2.98.20.1210.9920.0452.2261000.129
2.9-3.048.10.1050.9950.042.6191000.113
3.04-3.28.10.0830.9970.0312.9741000.089
3.2-3.480.0670.9980.0253.16699.90.071
3.4-3.667.80.060.9980.0233.69799.90.065
3.66-4.037.40.0560.9980.0224.51199.80.06
4.03-4.617.20.050.9980.024.64399.60.054
4.61-5.817.40.0440.9980.0173.75799.70.047
5.81-506.80.0360.9990.0153.26192.70.04

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.54 Å31.29 Å
Translation7.54 Å31.29 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A38

1a38


Resolution: 2.14→29.89 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.199 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1101 3.03 %RANDOM
Rwork0.227 ---
obs0.228 36391 99.4 %-
Displacement parametersBiso max: 155.66 Å2 / Biso mean: 76.7 Å2 / Biso min: 28.92 Å2
Baniso -1Baniso -2Baniso -3
1--5.3721 Å20 Å20 Å2
2--9.4873 Å20 Å2
3----4.1152 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.14→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 32 60 3665
Biso mean--60.45 69.97 -
Num. residues----462
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1323SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes538HARMONIC5
X-RAY DIFFRACTIONt_it3701HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
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_contact4403SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3701HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5007HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion17.97
LS refinement shellResolution: 2.14→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.302 106 3.64 %
Rwork0.267 2804 -
all0.268 2910 -
obs--98.41 %
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)
11.9205-0.3280.29993.04591.16852.5885-0.039-0.31780.6399-0.30280.1034-0.0731-0.4762-0.0878-0.0643-0.12230.00590.035-0.199-0.1129-0.050449.45210.22420.012
24.053-1.0994-0.02522.5311-0.61022.8050.1361-0.093-1.0559-0.196-0.1283-0.00640.69740.3231-0.0077-0.1180.0617-0.0233-0.33190.0237-0.020362.086-23.5949.847
32.9051-0.65870.14480.79070.34661.48460.03110.05760.1646-0.16970.0407-0.0424-0.00180.1063-0.07180.0373-0.02990.0731-0.0675-0.0246-0.02554.583-5.45410.195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|229 }A1 - 229
2X-RAY DIFFRACTION2{ B|1 - B|229 }B1 - 229
3X-RAY DIFFRACTION3{ A|401 - A|430 C|301 - C|301 B|401 - B|427 D|301 - D|301 }A401 - 430
4X-RAY DIFFRACTION3{ A|401 - A|430 C|301 - C|301 B|401 - B|427 D|301 - D|301 }C301
5X-RAY DIFFRACTION3{ A|401 - A|430 C|301 - C|301 B|401 - B|427 D|301 - D|301 }B401 - 427
6X-RAY DIFFRACTION3{ A|401 - A|430 C|301 - C|301 B|401 - B|427 D|301 - D|301 }D301

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