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- PDB-7d8p: CRTC1 pSer151 peptide in complex with 14-3-3 zeta -

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Basic information

Entry
Database: PDB / ID: 7d8p
TitleCRTC1 pSer151 peptide in complex with 14-3-3 zeta
Components
  • 14-3-3 protein zeta/delta
  • CRTC1 pSer151 peptide
KeywordsPROTEIN BINDING / 14-3-3 / CRTC1 / protein complex
Function / homology
Function and homology information


positive regulation of CREB transcription factor activity / negative regulation of membrane hyperpolarization / cAMP response element binding protein binding / synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / regulation of synapse maturation / tube formation ...positive regulation of CREB transcription factor activity / negative regulation of membrane hyperpolarization / cAMP response element binding protein binding / synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / respiratory system process / regulation of synapse maturation / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / entrainment of circadian clock by photoperiod / 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 / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / regulation of ERK1 and ERK2 cascade / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / energy homeostasis / cellular response to cAMP / negative regulation of TORC1 signaling / protein sequestering activity / ERK1 and ERK2 cascade / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex / lung development / Negative regulation of NOTCH4 signaling / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of protein stability / memory / : / rhythmic process / protein localization / melanosome / angiogenesis / DNA-binding transcription factor binding / blood microparticle / protein homotetramerization / vesicle / transmembrane transporter binding / transcription coactivator activity / nuclear body / cadherin binding / protein phosphorylation / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Transducer of regulated CREB activity, N-terminal / Transducer of regulated CREB activity, middle domain / Transducer of regulated CREB activity, C-terminal / CREB-regulated transcription coactivator / Transducer of regulated CREB activity, N terminus / Transducer of regulated CREB activity middle domain / Transducer of regulated CREB activity, C terminus / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. ...Transducer of regulated CREB activity, N-terminal / Transducer of regulated CREB activity, middle domain / Transducer of regulated CREB activity, C-terminal / CREB-regulated transcription coactivator / Transducer of regulated CREB activity, N terminus / Transducer of regulated CREB activity middle domain / Transducer of regulated CREB activity, C terminus / 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
14-3-3 protein zeta/delta / CREB-regulated transcription coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, H. / Zhang, H. / Xiang, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071205 China
National Natural Science Foundation of China (NSFC)31870769 China
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural Insights into the Interaction Between CRTCs and 14-3-3.
Authors: Chen, H. / Zhang, H. / Chen, P. / Xiang, S.
History
DepositionOct 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 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: CRTC1 pSer151 peptide
D: CRTC1 pSer151 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8405
Polymers62,7484
Non-polymers921
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-26 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.466, 83.533, 112.077
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 14 or resid 16 through 41 or resid 43 through 230))
21(chain B and (resid 2 through 14 or resid 16...
12(chain C and resid 147 through 155)
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLUGLU(chain A and (resid 2 through 14 or resid 16 through 41 or resid 43 through 230))AA2 - 1422 - 34
121ALAALAARGARG(chain A and (resid 2 through 14 or resid 16 through 41 or resid 43 through 230))AA16 - 4136 - 61
131LEULEUSERSER(chain A and (resid 2 through 14 or resid 16 through 41 or resid 43 through 230))AA43 - 23063 - 250
211ASPASPGLUGLU(chain B and (resid 2 through 14 or resid 16...BB2 - 1422 - 34
221ALAALAARGARG(chain B and (resid 2 through 14 or resid 16...BB16 - 4136 - 61
231LEULEUGLUGLU(chain B and (resid 2 through 14 or resid 16...BB43 - 7063 - 90
241LYSLYSSERSER(chain B and (resid 2 through 14 or resid 16...BB74 - 20794 - 227
251SERSERSERSER(chain B and (resid 2 through 14 or resid 16...BB210 - 230230 - 250
112ARGARGLEULEU(chain C and resid 147 through 155)CC147 - 1552 - 10
212ARGARGLEULEUchain DDD147 - 1552 - 10

NCS ensembles :
ID
1
2

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Components

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


Mass: 29948.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Protein/peptide CRTC1 pSer151 peptide / CREB-regulated transcription coactivator 1 / Mucoepidermoid carcinoma translocated protein 1 / ...CREB-regulated transcription coactivator 1 / Mucoepidermoid carcinoma translocated protein 1 / Transducer of regulated cAMP response element-binding protein 1 / Transducer of CREB protein 1


Mass: 1425.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6UUV9
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200mM Ammonium acetate, 100mM Bis-Tris (pH6.5), 25% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 44934 / % possible obs: 97.1 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.015 / Rrim(I) all: 0.051 / Χ2: 1.099 / Net I/σ(I): 17.8 / Num. measured all: 459367
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.038.40.99319720.650.3481.0550.4987.1
2.03-2.078.80.84320090.7410.2870.8940.5988.8
2.07-2.1190.67820490.8340.2280.7170.63189.6
2.11-2.158.90.58620980.8540.1990.6210.7491.3
2.15-2.28.70.47920940.9270.1620.5070.57692.6
2.2-2.258.50.43521900.920.1490.4621.16995.6
2.25-2.318.10.34122380.9660.1210.3630.73997.8
2.31-2.378.80.23322770.9810.080.2470.55499.5
2.37-2.449.50.19622800.9880.0650.2080.60299.8
2.44-2.529.90.16722930.9910.0550.1760.596100
2.52-2.6110.20.12823170.9950.0420.1350.638100
2.61-2.7110.20.10722840.9960.0350.1120.714100
2.71-2.8410.60.08422990.9970.0270.0880.749100
2.84-2.99120.0723320.9980.0210.0730.926100
2.99-3.1712.40.05622900.9990.0170.0591.163100
3.17-3.4211.80.04623450.9990.0140.0481.522100
3.42-3.7612.20.04123310.9990.0120.0432.009100
3.76-4.3112.60.034234710.010.0352.07100
4.31-5.4311.80.03123850.9990.0090.0321.953100
5.43-5010.90.025250410.0080.0261.83399.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qjb

1qjb


Resolution: 2→24.43 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 2007 4.49 %
Rwork0.2009 42678 -
obs0.2022 44685 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.71 Å2 / Biso mean: 48.4658 Å2 / Biso min: 22.83 Å2
Refinement stepCycle: final / Resolution: 2→24.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 6 331 4135
Biso mean--40.53 50.33 -
Num. residues----473
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1318X-RAY DIFFRACTION3.618TORSIONAL
12B1318X-RAY DIFFRACTION3.618TORSIONAL
21C50X-RAY DIFFRACTION3.618TORSIONAL
22D50X-RAY DIFFRACTION3.618TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.36041210.31952694281588
2.05-2.110.34521210.27212774289589
2.11-2.170.2851360.26832832296892
2.17-2.240.28751470.25442908305594
2.24-2.320.34111310.26583032316398
2.32-2.410.27451550.22230933248100
2.41-2.520.25211630.225330973260100
2.52-2.650.2831660.220131173283100
2.65-2.820.27171260.223831443270100
2.82-3.040.23881230.229831573280100
3.04-3.340.22711550.212931623317100
3.34-3.820.22471350.183231643299100
3.82-4.810.18941600.158532003360100
4.81-24.430.18591680.17713304347299

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