[English] 日本語
Yorodumi
- PDB-7d9v: CRTC1 pSer245 peptide in complex with 14-3-3 zeta -

+
Open data


ID or keywords:

Loading...

-
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


negative regulation of membrane hyperpolarization / positive regulation of CREB transcription factor activity / cAMP response element binding protein binding / Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA ...negative regulation of membrane hyperpolarization / positive regulation of CREB transcription factor activity / cAMP response element binding protein binding / Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / 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 / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / energy homeostasis / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / negative regulation of innate immune response / protein sequestering activity / regulation of ERK1 and ERK2 cascade / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / Heme signaling / Transcriptional activation of mitochondrial biogenesis / memory / rhythmic process / melanosome / Circadian Clock / protein homotetramerization / blood microparticle / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / nuclear body / cadherin binding / protein phosphorylation / 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 / 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 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: 2.21 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

-
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 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

-
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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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