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- PDB-5zk1: Crystal Structure of the CRTC2(SeMet)-CREB-CRE complex -

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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


ATF4-CREB1 transcription factor complex / secretory granule organization / cAMP response element binding / positive regulation of cardiac muscle tissue development / lung saccule development / positive regulation of CREB transcription factor activity / 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 ...ATF4-CREB1 transcription factor complex / secretory granule organization / cAMP response element binding / positive regulation of cardiac muscle tissue development / lung saccule development / positive regulation of CREB transcription factor activity / 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 / pituitary gland development / AKT phosphorylates targets in the nucleus / regulation of testosterone biosynthetic process / NOTCH2 intracellular domain regulates transcription / response to purine-containing compound / hormone secretion / negative regulation of transcription by competitive promoter binding / positive regulation of hormone secretion / Gastrin-CREB signalling pathway via PKC and MAPK / NGF-stimulated transcription / positive regulation of multicellular organism growth / positive regulation of osteoclast differentiation / MECP2 regulates transcription factors / response to glucagon / cellular response to zinc ion / 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 hepatocyte growth factor stimulus / type I pneumocyte differentiation / regulation of cell size / Constitutive Signaling by AKT1 E17K in Cancer / Regulation of MITF-M-dependent genes involved in pigmentation / cAMP/PKA signal transduction / Regulation of MECP2 expression and activity / 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 retinoic acid / lactation / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to forskolin / NCAM signaling for neurite out-growth / osteoclast differentiation / FCGR3A-mediated IL10 synthesis / axonogenesis / cellular response to leukemia inhibitory factor / gluconeogenesis / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / euchromatin / memory / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / HCMV Early Events / circadian rhythm / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein stabilization / ciliary basal body / protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / centrosome / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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

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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

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Phasing

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

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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 )

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