[English] 日本語
Yorodumi
- PDB-5zk1: Crystal Structure of the CRTC2(SeMet)-CREB-CRE complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zk1
TitleCrystal Structure of the CRTC2(SeMet)-CREB-CRE complex
Components
  • CREB-regulated transcription coactivator 2
  • Cyclic AMP-responsive element-binding protein 1
  • DNA (5'-D(*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)-3')
KeywordsTRANSCRIPTION/DNA / transcription factor / co-activator / CREB / CRE / CRTC / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


chemotaxis to arachidonate / positive regulation of membrane depolarization / response to erythropoietin / ATF4-CREB1 transcription factor complex / positive regulation of transforming growth factor beta3 production / lung saccule development / response to dehydroepiandrosterone / cAMP response element binding / response to hypobaric hypoxia / secretory granule organization ...chemotaxis to arachidonate / positive regulation of membrane depolarization / response to erythropoietin / ATF4-CREB1 transcription factor complex / positive regulation of transforming growth factor beta3 production / lung saccule development / response to dehydroepiandrosterone / cAMP response element binding / response to hypobaric hypoxia / secretory granule organization / positive regulation of CREB transcription factor activity / positive regulation of cardiac muscle tissue development / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / MECP2 regulates transcription of neuronal ligands / regulation of glial cell proliferation / cAMP response element binding protein binding / PKA-mediated phosphorylation of CREB / CREB phosphorylation / pituitary gland development / regulation of fibroblast proliferation / AKT phosphorylates targets in the nucleus / NOTCH2 intracellular domain regulates transcription / regulation of testosterone biosynthetic process / response to purine-containing compound / negative regulation of transcription by competitive promoter binding / hormone secretion / Gastrin-CREB signalling pathway via PKC and MAPK / NGF-stimulated transcription / positive regulation of hormone secretion / positive regulation of multicellular organism growth / arrestin family protein binding / positive regulation of osteoclast differentiation / cellular response to fatty acid / response to L-glutamate / MECP2 regulates transcription factors / response to glucagon / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CREB1 phosphorylation through the activation of Adenylate Cyclase / response to morphine / CaMK IV-mediated phosphorylation of CREB / cellular response to hepatocyte growth factor stimulus / cellular response to insulin-like growth factor stimulus / histone acetyltransferase binding / regulation of cell size / cellular response to zinc ion / Constitutive Signaling by AKT1 E17K in Cancer / type I pneumocyte differentiation / Regulation of MITF-M-dependent genes involved in pigmentation / cAMP/PKA signal transduction / Regulation of MECP2 expression and activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of fat cell differentiation / positive regulation of lipid biosynthetic process / MECP2 regulates neuronal receptors and channels / cellular response to platelet-derived growth factor stimulus / cellular response to retinoic acid / lactation / Hsp70 protein binding / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / cellular response to forskolin / transforming growth factor beta receptor signaling pathway / FCGR3A-mediated IL10 synthesis / axonogenesis / osteoclast differentiation / cellular response to leukemia inhibitory factor / positive regulation of long-term synaptic potentiation / response to activity / gluconeogenesis / response to nicotine / response to cocaine / mRNA transcription by RNA polymerase II / Heme signaling / euchromatin / Transcriptional activation of mitochondrial biogenesis / circadian rhythm / cellular response to nerve growth factor stimulus / visual learning / RNA polymerase II transcription regulator complex / transcription coactivator binding / memory / Transcriptional regulation of granulopoiesis / HCMV Early Events / sequence-specific double-stranded DNA binding / ADORA2B mediated anti-inflammatory cytokines production / : / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / protein homotetramerization / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein phosphorylation / protein stabilization / ciliary basal body / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mitochondrial matrix / response to xenobiotic stimulus
Similarity search - Function
cAMP response element binding (CREB) protein / Coactivator CBP, pKID / pKID domain / KID domain profile. / 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 ...cAMP response element binding (CREB) protein / Coactivator CBP, pKID / pKID domain / KID domain profile. / 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 / bZIP transcription factor / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Cyclic AMP-responsive element-binding protein 1 / CREB-regulated transcription coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 3.05 Å
AuthorsXiang, S. / Zhai, L. / Valencia-Swain, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570743 China
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural Insights into the CRTC2-CREB Complex Assembly on CRE.
Authors: Song, Y. / Zhai, L. / Valencia Swain, J. / Chen, Y. / Wang, P. / Chen, L. / Liu, Y. / Xiang, S.
History
DepositionMar 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: DNA (5'-D(*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)-3')
A: Cyclic AMP-responsive element-binding protein 1
C: CREB-regulated transcription coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3014
Polymers18,2363
Non-polymers651
Water00
1
B: DNA (5'-D(*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)-3')
A: Cyclic AMP-responsive element-binding protein 1
C: CREB-regulated transcription coactivator 2
hetero molecules

B: DNA (5'-D(*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)-3')
A: Cyclic AMP-responsive element-binding protein 1
C: CREB-regulated transcription coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6028
Polymers36,4716
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11240 Å2
ΔGint-88 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.271, 242.878, 40.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1000-

ZN

-
Components

#1: DNA chain DNA (5'-D(*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)-3')


Mass: 6134.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Cyclic AMP-responsive element-binding protein 1 / CREB / cAMP-responsive element-binding protein 1


Mass: 7133.333 Da / Num. of mol.: 1 / Fragment: bZIP domain / Mutation: C300S, C377S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREB1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Rosetta / References: UniProt: P16220
#3: Protein/peptide CREB-regulated transcription coactivator 2 / Transducer of regulated cAMP response element-binding protein 2 / Transducer of CREB protein 2


Mass: 4967.357 Da / Num. of mol.: 1 / Fragment: binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crtc2, Torc2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Rosetta / References: UniProt: Q3U182
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.79 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% w/v polyethylene glycol 3,350, 0.1 M hepes (pH 7.5), 0.2 M lithium sulfate, 0.3 M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 5064 / % possible obs: 96.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.056 / Rrim(I) all: 0.149 / Χ2: 2.619 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.05-3.151.5132290.6350.6571.660.49389.1
3.1-3.165.11.0312460.70.4431.1280.69591.4
3.16-3.224.90.3472300.9610.1590.3832.66795
3.22-3.295.40.1562300.9960.0710.1721.61293.1
3.29-3.365.70.3952400.9390.1720.4332.35593.4
3.36-3.436.60.2392470.9790.0990.261.07493.2
3.43-3.526.60.572380.8790.2320.6181.85898.8
3.52-3.627.20.4392620.9120.170.4721.11696.7
3.62-3.727.20.4742360.9320.1950.5161.47792.9
3.72-3.847.40.3942490.9630.1550.4251.68698.8
3.84-3.9870.3172460.920.1260.3431.90696.9
3.98-4.146.90.2372550.980.0950.2571.85397
4.14-4.336.60.2362540.960.0990.2572.21399.6
4.33-4.568.40.1772720.9840.0630.1882.427100
4.56-4.848.60.1512470.9920.0550.1622.811100
4.84-5.218.50.1062720.9960.0380.1132.725100
5.21-5.748.40.1382720.9980.0510.1483.01100
5.74-6.577.90.1312670.9920.050.143.31100
6.57-8.276.70.072710.9980.030.0774.76195.8
8.27-506.10.0643010.9980.0290.079.82999.3

-
Phasing

Phasing
Method
SAD
molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.01 Å49.23 Å
Translation3.01 Å49.23 Å

-
Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DH3

1dh3


Resolution: 3.05→34.932 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.75
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2686 464 9.4 %
Rwork0.2284 --
obs0.232 4828 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 220.95 Å2 / Biso mean: 110.5848 Å2 / Biso min: 47.96 Å2
Refinement stepCycle: final / Resolution: 3.05→34.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 407 1 0 1170
Biso mean--135.88 --
Num. residues----112
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0501-3.2410.45391200.40581117123781
3.241-3.49110.42851310.31791181131286
3.4911-3.8420.30481210.26621322144394
3.842-4.3970.2521510.2221319147097
4.397-5.53620.2451530.220313731526100
5.5362-34.93440.21711230.18311390151398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5310.24830.90470.8401-0.18743.4866-0.1644-0.1797-0.0333-0.18630.16370.097-0.3636-0.43410.17211.3140.1599-1.00530.8638-0.11011.57850.187748.481110.4315
22.98792.9809-0.46833.79630.31322.2269-0.57580.19410.5855-0.35850.2739-0.25330.340.19540.1420.6815-0.057-0.34810.46160.09270.77094.654329.07827.5136
33.10342.79281.27743.88642.95313.4646-0.2826-0.35290.0336-0.09460.2447-0.79930.5619-0.07360.03440.80860.0468-0.13320.4687-0.08330.68249.35513.90069.0498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid -10 through 10 )
2X-RAY DIFFRACTION2chain 'A' and ((resid 285 through 337) or (resid 1000 through 1000 ))
3X-RAY DIFFRACTION3chain 'C' and (resid 18 through 56 )

+
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