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- PDB-5zko: Crystal structure of the CRTC2-CREB-CRE complex -

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Basic information

Entry
Database: PDB / ID: 5zko
TitleCrystal structure of the CRTC2-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 / coactivator / CREB / CRE / CRTC / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


chemotaxis to arachidonate / response to erythropoietin / ATF4-CREB1 transcription factor complex / positive regulation of transforming growth factor beta3 production / response to dehydroepiandrosterone / response to hypobaric hypoxia / : / cAMP response element binding / regulation of glial cell proliferation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling ...chemotaxis to arachidonate / response to erythropoietin / ATF4-CREB1 transcription factor complex / positive regulation of transforming growth factor beta3 production / response to dehydroepiandrosterone / response to hypobaric hypoxia / : / cAMP response element binding / regulation of glial cell proliferation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / MECP2 regulates transcription of neuronal ligands / cAMP response element binding protein binding / PKA-mediated phosphorylation of CREB / CREB phosphorylation / regulation of fibroblast proliferation / AKT phosphorylates targets in the nucleus / NOTCH2 intracellular domain regulates transcription / regulation of testosterone biosynthetic process / positive regulation of membrane depolarization / : / Gastrin-CREB signalling pathway via PKC and MAPK / NGF-stimulated transcription / response to purine-containing compound / cellular response to fatty acid / arrestin family protein binding / MECP2 regulates transcription factors / response to glucagon / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / response to L-glutamate / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / cellular response to insulin-like growth factor stimulus / histone acetyltransferase binding / response to morphine / Constitutive Signaling by AKT1 E17K in Cancer / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Regulation of MECP2 expression and activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / cAMP/PKA signal transduction / positive regulation of fat cell differentiation / positive regulation of lipid biosynthetic process / MECP2 regulates neuronal receptors and channels / cellular response to retinoic acid / cellular response to platelet-derived growth factor stimulus / Transcriptional and post-translational regulation of MITF-M expression and activity / transforming growth factor beta receptor signaling pathway / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / NCAM signaling for neurite out-growth / FCGR3A-mediated IL10 synthesis / Hsp70 protein binding / cellular response to cAMP / cellular response to forskolin / response to activity / gluconeogenesis / positive regulation of long-term synaptic potentiation / response to nicotine / response to cocaine / Heme signaling / Transcriptional activation of mitochondrial biogenesis / euchromatin / circadian rhythm / cellular response to nerve growth factor stimulus / visual learning / mRNA transcription by RNA polymerase II / transcription coactivator binding / Transcriptional regulation of granulopoiesis / memory / 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 / protein homotetramerization / protein phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / response to ethanol / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / protein stabilization / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of apoptotic process / DNA-binding transcription factor activity / mitochondrial matrix / response to xenobiotic stimulus / negative regulation of gene expression / axon / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / chromatin / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
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 / molecular replacement / Resolution: 3.05 Å
AuthorsXiang, S. / Zhai, L. / Valecia-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 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,5706
Polymers43,5706
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, CREB and the CRE-containing dsDNA form a 2:1 complex (PDB 1dh3)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-87 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.300, 41.320, 122.580
Angle α, β, γ (deg.)90.000, 90.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyclic AMP-responsive element-binding protein 1 / cAMP-responsive element-binding protein 1


Mass: 7165.462 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P16220
#2: 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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein CREB-regulated transcription coactivator 2 / Transducer of regulated cAMP response element-binding protein 2 / Transducer of CREB protein 2


Mass: 8484.474 Da / Num. of mol.: 2 / 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(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q3U182

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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: 2.92 Å3/Da / Density % sol: 54.16 % / Description: plate
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% w/v polyethylene glycol 3350, 0.1 M hepes (pH 7.5), 0.2 M lithium sulfate, 0.3 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 9460 / % possible obs: 95.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 46.15 Å2 / Rpim(I) all: 0.071 / Rrim(I) all: 0.124 / Rsym value: 0.101 / Net I/av σ(I): 4.7 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3.05-3.212.90.4881.313770.3370.5960.48894.6
3.21-3.412.80.2071.713010.1560.2610.20795.5
3.41-3.652.90.2492.111800.1730.3040.24994.6
3.65-3.942.90.1653.811390.1140.2020.16595.7
3.94-4.312.80.0956.910800.0660.1160.09597.2
4.31-4.822.90.0827.39650.0550.0990.08297.9
4.82-5.572.90.06988700.0480.0850.06996.5
5.57-6.822.70.0748.27010.0520.0910.07493.5
6.82-9.6430.034145690.0230.0410.03496.4
9.64-46.7072.70.03115.42780.0220.0380.03178.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å46.71 Å
Translation2.8 Å46.71 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DH3

1dh3


Resolution: 3.05→46.707 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / Phase error: 31.45
RfactorNum. reflection% reflection
Rfree0.2848 465 4.98 %
Rwork0.2422 --
obs0.2443 9336 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.51 Å2 / Biso mean: 89.6873 Å2 / Biso min: 28.63 Å2
Refinement stepCycle: final / Resolution: 3.05→46.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 814 0 0 2404
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022508
X-RAY DIFFRACTIONf_angle_d0.3743516
X-RAY DIFFRACTIONf_chiral_restr0.016391
X-RAY DIFFRACTIONf_plane_restr0.001313
X-RAY DIFFRACTIONf_dihedral_angle_d20.7071062
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.05-3.49120.26681410.29262863300491
3.4912-4.39810.28991650.24632974313996
4.3981-46.71230.28891590.22323034319394
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)
10.23580.1380.38130.3788-0.17221.7765-0.1284-0.0364-0.0279-0.32060.0184-0.0011-0.05240.0584-0.13890.38340.1927-0.00550.20640.1023-0.007126.0815-41.5461151.6808
20.7003-0.5860.36480.5622-0.22860.5562-0.1643-0.0019-0.178-0.0474-0.2046-0.1043-0.028-0.0463-0.65920.5821.20950.01260.6920.14140.843120.3275-45.2079170.9434
30.3593-0.0382-0.28710.3026-0.01251.1209-0.1888-0.1380.0231-0.23520.0353-0.09310.0317-0.0985-0.08090.32760.15090.28120.1553-0.13950.072117.3633-46.9409150.7965
40.6587-0.5303-0.19771.61230.13340.4646-0.15090.01960.020.0508-0.0908-0.1834-0.0271-0.1077-0.47220.61241.09920.03820.77910.02850.721320.0465-44.4818170.9533
50.43870.3881-0.16860.42940.42613.8365-0.2390.1307-0.1399-0.29980.1225-0.02250.080.03970.07730.78130.31860.26510.65120.23470.429732.6472-46.1538146.773
60.59880.2939-2.0030.1856-1.137.2221-0.31450.98290.1859-0.86790.22110.1408-0.28310.45790.0881.8136-0.22380.12541.17550.19010.572729.4657-36.8868116.5376
74.0534-0.76651.66126.0921-0.25794.4910.11050.23320.3441-0.728-0.1832-0.33-0.67050.1760.06911.26840.3731-0.14521.2264-0.11421.009510.7188-33.9912155.2999
80.14480.1509-0.01120.15780.06012.0844-0.10970.07040.0114-0.24910.09060.0025-0.3385-0.26640.03250.58660.2181-0.05160.5691-0.20290.181811.6537-43.9217142.7603
90.16880.17171.14470.19371.16387.7487-0.25831.1856-0.3264-0.8806-0.0632-0.13690.1091-1.28920.30091.4955-0.09290.03391.137-0.17290.535619.1521-50.4899115.0353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 285 through 337 )A285 - 337
2X-RAY DIFFRACTION2chain 'B' and (resid -10 through 10 )B-10 - 10
3X-RAY DIFFRACTION3chain 'C' and (resid 285 through 337 )C285 - 337
4X-RAY DIFFRACTION4chain 'D' and (resid -10 through 10 )D-10 - 10
5X-RAY DIFFRACTION5chain 'G' and (resid 16 through 43 )G16 - 43
6X-RAY DIFFRACTION6chain 'G' and (resid 44 through 58 )G44 - 58
7X-RAY DIFFRACTION7chain 'H' and (resid 15 through 21 )H15 - 21
8X-RAY DIFFRACTION8chain 'H' and (resid 22 through 43 )H22 - 43
9X-RAY DIFFRACTION9chain 'H' and (resid 44 through 58 )H44 - 58

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