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- PDB-5yqg: The structure of 14-3-3 and pNumb peptide -

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Basic information

Entry
Database: PDB / ID: 5yqg
TitleThe structure of 14-3-3 and pNumb peptide
Components
  • 14-3-3 protein eta
  • Peptide from Protein numb homolog
KeywordsPEPTIDE BINDING PROTEIN / Complex / Phosphorylation / non-canonical
Function / homology
Function and homology information


neuroblast division in subventricular zone / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / RHO GTPases activate PKNs / Activation of BAD and translocation to mitochondria / glucocorticoid catabolic process / regulation of postsynapse assembly / TP53 Regulates Metabolic Genes / Degradation of GLI1 by the proteasome / lateral ventricle development / negative regulation of dendrite morphogenesis ...neuroblast division in subventricular zone / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / RHO GTPases activate PKNs / Activation of BAD and translocation to mitochondria / glucocorticoid catabolic process / regulation of postsynapse assembly / TP53 Regulates Metabolic Genes / Degradation of GLI1 by the proteasome / lateral ventricle development / negative regulation of dendrite morphogenesis / Hedgehog 'on' state / membrane depolarization during action potential / intracellular glucocorticoid receptor signaling pathway / Recycling pathway of L1 / regulation of sodium ion transmembrane transporter activity / nuclear glucocorticoid receptor binding / alpha-catenin binding / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of protein localization to plasma membrane / adherens junction organization / positive regulation of dendrite morphogenesis / positive regulation of neurogenesis / clathrin-coated vesicle / regulation of neuron differentiation / regulation of mitotic nuclear division / neuroblast proliferation / sodium channel regulator activity / intercalated disc / regulation of sodium ion transport / forebrain development / clathrin-coated pit / cytoskeleton organization / axonogenesis / intracellular protein transport / beta-catenin binding / apical part of cell / nervous system development / actin binding / cytoplasmic vesicle / basolateral plasma membrane / transmembrane transporter binding / dendritic spine / postsynaptic density / early endosome / endosome membrane / positive regulation of cell migration / cadherin binding / protein heterodimerization activity / protein domain specific binding / synapse / glutamatergic synapse / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
NUMB domain / Numb/numb-like / NUMB domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. ...NUMB domain / Numb/numb-like / NUMB domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI 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 / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein eta / Protein numb homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, X. / Liu, Z. / Wen, W.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology of the People's Republic of China2014CB910201 China
the National Natural Science Foundation of China31422015, 31670730, 31270778 China
the Shanghai Municipal Education Commission14SG06 China
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural determinants controlling 14-3-3 recruitment to the endocytic adaptor Numb and dissociation of the Numb/alpha-adaptin complex.
Authors: Chen, X. / Liu, Z. / Shan, Z. / Yao, W. / Gu, A. / Wen, W.
History
DepositionNov 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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 eta
B: 14-3-3 protein eta
C: 14-3-3 protein eta
D: 14-3-3 protein eta
E: Peptide from Protein numb homolog
F: Peptide from Protein numb homolog


Theoretical massNumber of molelcules
Total (without water)122,7686
Polymers122,7686
Non-polymers00
Water8,719484
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-45 kcal/mol
Surface area45140 Å2
Unit cell
Length a, b, c (Å)59.260, 74.626, 134.136
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
14-3-3 protein eta


Mass: 28820.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ywhah / Production host: Escherichia coli (E. coli) / References: UniProt: P68510
#2: Protein/peptide Peptide from Protein numb homolog / / pNumb peptide


Mass: 3743.175 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Numb / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QZS3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: tri-Sodium Citrate dihydrate, isopropanol, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 66596 / % possible obs: 98.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 2.1
Reflection shellResolution: 2.1→2.14 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HKC

4hkc


Resolution: 2.1→49.883 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 3327 5 %
Rwork0.1838 --
obs0.1858 66571 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7339 0 0 484 7823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077476
X-RAY DIFFRACTIONf_angle_d0.80310108
X-RAY DIFFRACTIONf_dihedral_angle_d16.2384571
X-RAY DIFFRACTIONf_chiral_restr0.041154
X-RAY DIFFRACTIONf_plane_restr0.0041299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0998-2.12980.29661140.23041991X-RAY DIFFRACTION73
2.1298-2.16160.27741420.2292299X-RAY DIFFRACTION86
2.1616-2.19540.28481220.22262483X-RAY DIFFRACTION92
2.1954-2.23140.29391160.20992531X-RAY DIFFRACTION94
2.2314-2.26990.29311160.20292622X-RAY DIFFRACTION96
2.2699-2.31110.24931330.20152640X-RAY DIFFRACTION99
2.3111-2.35560.25151570.19382670X-RAY DIFFRACTION100
2.3556-2.40370.23791440.18642698X-RAY DIFFRACTION100
2.4037-2.45590.24921440.18472714X-RAY DIFFRACTION100
2.4559-2.51310.2411280.19282671X-RAY DIFFRACTION100
2.5131-2.57590.25911610.19062738X-RAY DIFFRACTION100
2.5759-2.64550.21211380.18722667X-RAY DIFFRACTION100
2.6455-2.72340.23391170.18322727X-RAY DIFFRACTION100
2.7234-2.81130.2691330.18672705X-RAY DIFFRACTION100
2.8113-2.91180.22791260.19972710X-RAY DIFFRACTION100
2.9118-3.02830.21681350.19662713X-RAY DIFFRACTION100
3.0283-3.16610.23661420.20052710X-RAY DIFFRACTION100
3.1661-3.3330.22231490.18632699X-RAY DIFFRACTION100
3.333-3.54180.24441500.1782704X-RAY DIFFRACTION100
3.5418-3.81520.19041640.16332686X-RAY DIFFRACTION99
3.8152-4.19890.2071290.15252738X-RAY DIFFRACTION100
4.1989-4.80610.17631620.1492673X-RAY DIFFRACTION99
4.8061-6.05350.25151350.18952761X-RAY DIFFRACTION100
6.0535-49.8970.17171700.18782694X-RAY DIFFRACTION96
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)
14.3894-0.8080.37965.53224.19727.7665-0.0780.00330.00080.2505-0.06810.1289-0.0823-0.3060.13380.1275-0.01730.00590.13470.03140.1334-23.6606-6.0385-32.0201
26.0654-1.9075-3.66022.48871.8427.0631-0.0797-0.0201-0.53780.2007-0.06650.07050.23340.31420.19730.13710.0044-0.04470.15710.00190.1698-10.9133-11.8511-32.6907
34.04870.8239-2.95471.1957-1.65683.2995-0.1493-0.03640.1407-0.16910.1602-0.363-0.39961.1108-0.12260.2087-0.11270.00490.4673-0.05030.26090.4866-5.8412-40.0923
41.2342-0.7376-0.09463.8651-0.04743.1242-0.0949-0.2016-0.16570.54330.1461-0.08070.30960.3244-0.02740.28110.0632-0.07060.31180.00490.2221-3.5569-19.6516-20.3396
57.12320.1508-3.93491.8646-1.01725.4637-0.05640.23480.3206-0.1424-0.0025-0.5023-0.38961.36330.12210.263-0.11760.04670.573-0.04940.3161-0.5169-7.1868-58.2791
62.8829-0.7717-0.53212.2587-1.0238.7271-0.00410.01050.0974-0.06160.0635-0.3091-0.78920.6545-0.0690.2007-0.09450.02780.1894-0.06090.2251-8.4242-5.15-59.4649
78.22751.5962-6.64022.2048-0.70977.7683-0.10930.0973-0.114-0.0515-0.09890.12930.2575-0.30230.21140.127-0.0151-0.04320.1175-0.03450.1626-23.062-12.0486-52.2104
83.18940.0075-3.5261.310.046.63530.1357-0.06190.2134-0.12780.00620.1427-0.219-0.2594-0.18240.17770.033-0.04120.1333-0.02270.1877-28.6609-4.012-48.8271
97.20450.06090.07394.12781.63298.0617-0.18221.217-0.0337-0.8161-0.0457-0.3718-0.49290.85850.18070.52490.03370.13150.34340.02980.3178-14.0534-4.3137-76.3749
106.31210.8301-3.8452.8341-0.34886.8802-0.21150.2931-0.1638-0.3238-0.0558-0.16930.1012-0.14770.23560.18670.013-0.00760.0985-0.02110.171-23.3566-10.428-65.8941
117.5714-4.6135-6.45277.86445.53386.84720.28240.8518-0.0607-0.8241-0.52760.3895-0.5874-0.84580.21210.27770.0587-0.08620.2475-0.04280.209-30.1285-10.6628-70.7894
123.1553-1.3962-0.84984.69891.01284.0960.03640.2104-0.497-0.2461-0.1769-0.03920.0639-0.34220.13620.2096-0.0216-0.00480.176-0.1080.2279-26.7875-20.3816-68.4883
132.0018-1.3537-1.48922.63440.79024.0479-0.3280.7704-0.7277-0.4232-0.22920.15720.2416-0.15810.60050.3824-0.05850.02630.2521-0.10890.404-25.0136-29.7934-73.5136
145.2367-4.7894-4.34236.47482.82457.7887-0.2976-0.1552-1.02390.6930.1074-0.07590.47450.18140.23760.4311-0.0585-0.0420.1542-0.03230.3728-22.6225-30.4822-64.9807
157.0734-0.72893.71891.4595-1.31332.9217-0.0406-0.3617-0.13070.47640.0381-0.7550.20161.26160.11940.33870.1263-0.08910.6223-0.07560.34590.059611.9037-8.4185
163.8143-0.73972.43121.89340.19874.89220.01220.04240.02330.1682-0.0251-0.10640.07360.14880.02050.1540.00980.02280.0912-0.02490.1466-17.207414.2802-12.0173
173.13610.20013.45591.12880.15797.11190.1224-0.0099-0.21130.1090.02080.11670.1898-0.445-0.15960.1698-0.03570.04470.1439-0.0370.2118-28.68428.8642-18.248
186.4421-0.66973.42423.4132-0.02676.0929-0.0231-0.58520.18720.543-0.1423-0.30090.0867-0.20020.14040.2329-0.040.00340.1412-0.01580.2045-20.581713.46232.1051
194.37282.42044.09496.65624.05896.60720.1296-0.71950.25410.6104-0.38980.24080.2576-0.6730.25610.2691-0.0260.06310.1961-0.05110.1893-28.024317.67924.5533
203.28921.32850.93985.75441.53014.0725-0.0557-0.07870.5046-0.0669-0.0981-0.149-0.3354-0.0620.160.28080.04230.01370.164-0.0860.3053-25.371831.64261.0713
212.90920.7966-0.80285.79185.27758.1182-0.03450.04010.1559-0.3521-0.07770.1695-0.1298-0.24710.08070.12210.0289-0.00630.13210.02890.1427-23.491211.0191-35.0917
226.25292.47373.21283.25261.50445.53970.05560.11260.3063-0.1309-0.0353-0.0763-0.14290.65930.01580.13590.01350.06780.2302-0.02980.1622-9.123516.9016-32.9764
234.2087-0.1993.35851.1447-1.15954.62290.0570.0182-0.3510.14090.2359-0.3770.51011.1511-0.33740.20260.1218-0.00820.4238-0.06260.2632-0.38439.8879-27.8473
241.94660.81160.05183.8699-0.31242.8483-0.05690.24630.2147-0.52180.1099-0.1075-0.12680.4058-0.04870.2482-0.0230.07760.3316-0.01410.2032-3.688619.8637-46.9484
253.7302-0.52620.37826.42310.35826.0568-0.34030.32670.4358-0.59240.0279-0.092-0.96970.29320.15020.4741-0.11950.07830.2579-0.01250.3262-3.702836.5009-45.5447
263.7745-4.43344.41145.2315-5.13985.21770.06520.07090.05590.2173-0.4532-1.11410.2170.8460.04530.30540.0153-0.13290.32560.03480.5987-15.0114-23.8241-54.5018
277.40884.53111.69824.39843.26524.27420.08491.1998-0.6246-1.26990.07490.42591.14130.1097-0.2530.54760.1422-0.14130.4062-0.04550.3556-7.0817-25.0207-34.4306
288.02196.3591-6.95096.368-3.67358.56430.56380.29271.0825-0.393-0.6382-0.9209-0.94610.95020.06570.3176-0.04180.10170.28880.00360.6192-20.902526.5107-8.4508
292.6842-0.27581.02289.3477-8.7528.4124-0.9187-2.5351-1.61932.2932-0.5021-0.1940.25280.91611.37761.16850.06030.10.77580.17530.7089-7.574332.4573-21.2092
306.0302-3.7565-1.81123.5225-0.54827.90770.3556-1.37190.45011.4034-0.13251.1871-1.13170.0807-0.24590.4655-0.1440.15990.3859-0.06140.5006-6.097628.6559-34.9831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 106 )
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 234 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 16 )
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 38 )
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 72 )
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 106 )
9X-RAY DIFFRACTION9chain 'B' and (resid 107 through 116 )
10X-RAY DIFFRACTION10chain 'B' and (resid 117 through 139 )
11X-RAY DIFFRACTION11chain 'B' and (resid 140 through 164 )
12X-RAY DIFFRACTION12chain 'B' and (resid 165 through 189 )
13X-RAY DIFFRACTION13chain 'B' and (resid 190 through 212 )
14X-RAY DIFFRACTION14chain 'B' and (resid 213 through 236 )
15X-RAY DIFFRACTION15chain 'C' and (resid 0 through 16 )
16X-RAY DIFFRACTION16chain 'C' and (resid 17 through 72 )
17X-RAY DIFFRACTION17chain 'C' and (resid 73 through 106 )
18X-RAY DIFFRACTION18chain 'C' and (resid 107 through 139 )
19X-RAY DIFFRACTION19chain 'C' and (resid 140 through 169 )
20X-RAY DIFFRACTION20chain 'C' and (resid 170 through 236 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 33 )
22X-RAY DIFFRACTION22chain 'D' and (resid 34 through 70 )
23X-RAY DIFFRACTION23chain 'D' and (resid 71 through 106 )
24X-RAY DIFFRACTION24chain 'D' and (resid 107 through 189 )
25X-RAY DIFFRACTION25chain 'D' and (resid 190 through 234 )
26X-RAY DIFFRACTION26chain 'E' and (resid 262 through 277 )
27X-RAY DIFFRACTION27chain 'E' and (resid 278 through 287 )
28X-RAY DIFFRACTION28chain 'F' and (resid 263 through 273 )
29X-RAY DIFFRACTION29chain 'F' and (resid 274 through 279 )
30X-RAY DIFFRACTION30chain 'F' and (resid 280 through 286 )

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