[English] 日本語
Yorodumi
- PDB-7d8p: CRTC1 pSer151 peptide in complex with 14-3-3 zeta -

+
Open data


ID or keywords:

Loading...

-
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 / Golgi reassembly / synaptic target recognition / 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 / Golgi reassembly / synaptic target recognition / 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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / energy homeostasis / negative regulation of TORC1 signaling / protein sequestering activity / negative regulation of innate immune response / ERK1 and ERK2 cascade / hippocampal mossy fiber to CA3 synapse / regulation of ERK1 and ERK2 cascade / 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 / regulation of protein stability / Transcriptional activation of mitochondrial biogenesis / memory / protein localization / melanosome / Circadian Clock / rhythmic process / angiogenesis / DNA-binding transcription factor binding / protein homotetramerization / vesicle / blood microparticle / transmembrane transporter binding / nuclear body / cadherin binding / protein phosphorylation / protein domain specific binding / 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 / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / 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 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. ...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 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more