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- PDB-7d9v: CRTC1 pSer245 peptide in complex with 14-3-3 zeta -

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Basic information

Entry
Database: PDB / ID: 7d9v
TitleCRTC1 pSer245 peptide in complex with 14-3-3 zeta
Components
  • 14-3-3 protein zeta/delta
  • CRTC1 pSer245 peptide
KeywordsPROTEIN BINDING / 14-3-3 / CRTC
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 / tube formation / regulation of synapse maturation ...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 / tube formation / regulation of synapse maturation / 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 / regulation of ERK1 and ERK2 cascade / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / energy homeostasis / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / cellular response to cAMP / ERK1 and ERK2 cascade / Transcriptional and post-translational regulation of MITF-M expression and activity / protein sequestering activity / 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 / Heme signaling / Negative regulation of NOTCH4 signaling / Transcriptional activation of mitochondrial biogenesis / regulation of protein stability / memory / rhythmic process / : / melanosome / intracellular protein localization / angiogenesis / protein phosphatase binding / protein homotetramerization / blood microparticle / vesicle / DNA-binding transcription factor binding / transmembrane transporter binding / transcription coactivator activity / nuclear body / protein phosphorylation / cadherin binding / 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: 2.21 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 14, 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 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: CRTC1 pSer245 peptide
D: CRTC1 pSer245 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5587
Polymers62,2814
Non-polymers2763
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-31 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.975, 83.158, 110.831
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
11chain A
21chain B
12chain C
22(chain D and resid 244 through 249)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSERchain AAA1 - 23021 - 250
21METMETSERSERchain BBB1 - 23021 - 250
12GLYGLYLEULEUchain CCC244 - 2495 - 10
22GLYGLYLEULEU(chain D and resid 244 through 249)DD244 - 2495 - 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 pSer245 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: 1192.151 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
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: 1.2782 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 36010 / % possible obs: 98.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.053 / Rrim(I) all: 0.129 / Χ2: 0.686 / Net I/σ(I): 4 / Num. measured all: 207559
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.244.80.79516010.8960.3680.8790.50488.4
2.24-2.285.10.70416570.9110.3180.7750.51591.5
2.28-2.325.10.61916810.9310.280.6820.51894.7
2.32-2.375.10.60317530.9280.2790.6670.49496.9
2.37-2.425.30.60217740.9240.2810.6670.51198.9
2.42-2.485.20.48217960.9550.230.5350.51299.4
2.48-2.545.60.47818180.9610.220.5280.52799.5
2.54-2.616.20.45417710.9680.20.4970.50499.9
2.61-2.696.20.38217920.9780.1690.4190.514100
2.69-2.776.10.32818250.9810.1460.360.56699.9
2.77-2.8760.27318210.9860.1230.30.568100
2.87-2.995.70.24718090.9890.1140.2730.57799.9
2.99-3.126.20.18918290.9910.0840.2070.64799.9
3.12-3.296.30.16318300.9930.0720.1780.696100
3.29-3.496.10.12118200.9950.0550.1330.83299.9
3.49-3.765.70.09518400.9950.0450.1050.97199.9
3.76-4.146.40.07718450.9970.0340.0841.08199.9
4.14-4.746.20.06418710.9980.0290.071.10499.9
4.74-5.976.10.05618840.9990.0250.0620.88100
5.97-505.70.04119930.9980.0190.0450.87999.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
AUTOMARdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4O

1a4o


Resolution: 2.21→46.11 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 1955 6.16 %
Rwork0.2058 29803 -
obs0.208 31758 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.15 Å2 / Biso mean: 47.7096 Å2 / Biso min: 28.08 Å2
Refinement stepCycle: final / Resolution: 2.21→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3781 0 18 218 4017
Biso mean--45.56 50.84 -
Num. residues----473
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1396X-RAY DIFFRACTION3.213TORSIONAL
12B1396X-RAY DIFFRACTION3.213TORSIONAL
21C28X-RAY DIFFRACTION3.213TORSIONAL
22D28X-RAY DIFFRACTION3.213TORSIONAL
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 (%)
2.21-2.260.26951280.23591918204687
2.26-2.320.30171330.23092128226195
2.32-2.390.25781450.22052147229297
2.39-2.470.25151320.212168230097
2.47-2.560.26631310.21612147227896
2.56-2.660.26551390.2182161230097
2.66-2.780.2551430.2112191233497
2.78-2.930.28761560.21442141229797
2.93-3.110.23241350.21772167230296
3.11-3.350.25831480.22432136228495
3.35-3.690.25841530.2092101225494
3.69-4.220.21321260.19162072219890
4.22-5.320.21871400.19112057219790
5.32-46.110.21091460.19492269241594

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