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- PDB-1dh3: CRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FO... -

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Basic information

Entry
Database: PDB / ID: 1dh3
TitleCRYSTAL STRUCTURE OF A CREB BZIP-CRE COMPLEX REVEALS THE BASIS FOR CREB FAIMLY SELECTIVE DIMERIZATION AND DNA BINDING
Components
  • DNA (5'-D(*CP*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)-3')
  • TRANSCRIPTION FACTOR CREB
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


AKT phosphorylates targets in the nucleus / NGF-stimulated transcription / ATF4-CREB1 transcription factor complex / CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / NCAM signaling for neurite out-growth / secretory granule organization / cAMP response element binding ...AKT phosphorylates targets in the nucleus / NGF-stimulated transcription / ATF4-CREB1 transcription factor complex / CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / NCAM signaling for neurite out-growth / secretory granule organization / cAMP response element binding / positive regulation of cardiac muscle tissue development / lung saccule development / lung epithelium development / inhibition of non-skeletal tissue mineralization / pituitary gland development / regulation of testosterone biosynthetic process / response to purine-containing compound / hormone secretion / negative regulation of transcription by competitive promoter binding / positive regulation of hormone secretion / mammary gland development / positive regulation of multicellular organism growth / positive regulation of osteoclast differentiation / response to glucagon / cellular response to zinc ion / cellular response to hepatocyte growth factor stimulus / type I pneumocyte differentiation / regulation of cell size / cAMP/PKA signal transduction / positive regulation of fat cell differentiation / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / lactation / cellular response to forskolin / osteoclast differentiation / axonogenesis / cellular response to leukemia inhibitory factor / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mRNA transcription by RNA polymerase II / euchromatin / cellular response to growth factor stimulus / memory / RNA polymerase II transcription regulator complex / circadian rhythm / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / protein stabilization / response to xenobiotic stimulus / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
cAMP response element binding (CREB) protein / Coactivator CBP, pKID / pKID domain / KID domain profile. / 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 ...cAMP response element binding (CREB) protein / Coactivator CBP, pKID / pKID domain / KID domain profile. / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsSchumacher, M.A. / Goodman, R.H. / Brennan, R.G.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The structure of a CREB bZIP.somatostatin CRE complex reveals the basis for selective dimerization and divalent cation-enhanced DNA binding
Authors: Schumacher, M.A. / Goodman, R.H. / Brennan, R.G.
History
DepositionNov 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)-3')
D: DNA (5'-D(*CP*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)-3')
A: TRANSCRIPTION FACTOR CREB
C: TRANSCRIPTION FACTOR CREB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2465
Polymers26,2224
Non-polymers241
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.610, 49.320, 79.250
Angle α, β, γ (deg.)90.00, 122.18, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 6424.148 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein TRANSCRIPTION FACTOR CREB


Mass: 6686.831 Da / Num. of mol.: 2 / Fragment: RESIDUES 201-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q01147
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 3.42 Å3/Da / Density % sol: 64.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 8000, MGCL2, (NH4)2SO4, MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2(NH4)2SO411
3MES11
4PEG 800011
5PEG 800012
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 mMZIP dimer1drop
21 mMCRE duplex1drop
312 %PEG80001reservoir
410 mM1reservoirMgCl2
5100 mMammonium sulfate1reservoir
650 mMMES1reservoirpH5.6

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→10 Å / Num. all: 7436 / Num. obs: 7316 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17
Reflection shellResolution: 3→3.2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.258 / % possible all: 95
Reflection
*PLUS
% possible obs: 95 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 87.4 % / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
EPMRphasing
TNTrefinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 3→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1
Details: THE FIRST AND LAST TWO RESIDUES ARE DISORDERED AND NOT MODELED. THE DENSITY IS WEAK FOR RESIDUES 334-339 IN BOTH PROTEIN CHAINS. PROCHECK REVEALED NO BAD CONTACTS AND NO RAMACHANDRAN OUTLIERS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 694 10 %RANDOM
Rwork0.223 ---
all0.218 7436 --
obs0.218 7316 98 %-
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 852 7 11 1804
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg1.906
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS

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