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- PDB-7d8h: CRTC1 pSer64 peptide in complex with 14-3-3 zeta -

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Basic information

Entry
Database: PDB / ID: 7d8h
TitleCRTC1 pSer64 peptide in complex with 14-3-3 zeta
Components
  • 14-3-3 protein zeta/delta
  • CRTC1 pSer64 peptide
KeywordsPROTEIN BINDING / 14-3-3 / CRTC / 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 / 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 / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / regulation of ERK1 and ERK2 cascade / protein targeting / 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 / ERK1 and ERK2 cascade / Transcriptional and post-translational regulation of MITF-M expression and activity / lung development / protein sequestering activity / negative regulation of innate immune response / cellular response to cAMP / hippocampal mossy fiber to CA3 synapse / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / Heme signaling / Negative regulation of NOTCH4 signaling / Transcriptional activation of mitochondrial biogenesis / regulation of protein stability / memory / : / rhythmic process / intracellular protein localization / melanosome / angiogenesis / protein phosphatase binding / blood microparticle / protein homotetramerization / vesicle / DNA-binding transcription factor binding / transmembrane transporter binding / transcription coactivator activity / protein phosphorylation / nuclear body / cadherin binding / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / protein kinase binding / negative regulation of apoptotic process / 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 / cytoplasm / cytosol
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: 2.42 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 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

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: CRTC1 pSer64 peptide


Theoretical massNumber of molelcules
Total (without water)31,2402
Polymers31,2402
Non-polymers00
Water66737
1
A: 14-3-3 protein zeta/delta
B: CRTC1 pSer64 peptide

A: 14-3-3 protein zeta/delta
B: CRTC1 pSer64 peptide


Theoretical massNumber of molelcules
Total (without water)62,4794
Polymers62,4794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3790 Å2
ΔGint-21 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.690, 111.010, 71.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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.: 1
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 pSer64 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: 1291.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6UUV9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.78 Å3/Da / Density % sol: 55.83 %
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: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.42→71.5 Å / Num. obs: 13653 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Net I/σ(I): 6.4 / Num. measured all: 86987 / Scaling rejects: 126
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.42-2.486.60.41464879790.9480.1740.452.299.4
10.82-71.54.50.0688421890.9950.0340.0769.799.1

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Processing

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

1qjb


Resolution: 2.42→68.81 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 638 4.68 %
Rwork0.2109 12994 -
obs0.2125 13632 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.81 Å2 / Biso mean: 53.2707 Å2 / Biso min: 21.4 Å2
Refinement stepCycle: final / Resolution: 2.42→68.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 0 37 1920
Biso mean---55.73 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.42-2.610.35641180.271825542672
2.61-2.870.26821330.231325552688
2.87-3.280.25341300.218325682698
3.28-4.140.20711120.189626292741
4.14-68.810.23891450.204726882833

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