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- PDB-7co1: Crystal structure of SMAD2 in complex with wild-type CBP -

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Basic information

Entry
Database: PDB / ID: 7co1
TitleCrystal structure of SMAD2 in complex with wild-type CBP
Components
  • CREB-binding protein
  • Mothers against decapentaplegic homolog 2
KeywordsSIGNALING PROTEIN / TGF-beta / Complex / Transcription factor
Function / homology
Function and homology information


zygotic specification of dorsal/ventral axis / regulation of binding / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / endoderm formation ...zygotic specification of dorsal/ventral axis / regulation of binding / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / endoderm formation / co-SMAD binding / heteromeric SMAD protein complex / determination of left/right asymmetry in lateral mesoderm / odontoblast differentiation / secondary palate development / pericardium development / FOXO-mediated transcription of cell cycle genes / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / Transcriptional regulation of pluripotent stem cells / regulation of transforming growth factor beta receptor signaling pathway / embryonic foregut morphogenesis / peptide lactyltransferase activity / transforming growth factor beta receptor binding / primary miRNA processing / Germ layer formation at gastrulation / pulmonary valve morphogenesis / type I transforming growth factor beta receptor binding / Formation of definitive endoderm / activin receptor signaling pathway / signal transduction involved in regulation of gene expression / Signaling by Activin / SMAD protein signal transduction / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Formation of axial mesoderm / positive regulation of BMP signaling pathway / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / Signaling by NODAL / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / response to cholesterol / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / MRF binding / I-SMAD binding / aortic valve morphogenesis / pancreas development / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / insulin secretion / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / anterior/posterior pattern specification / ureteric bud development / endocardial cushion morphogenesis / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / organ growth / embryonic digit morphogenesis / adrenal gland development / homeostatic process / protein acetylation / Notch-HLH transcription pathway / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / TGF-beta receptor signaling activates SMADs / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / acetyltransferase activity / R-SMAD binding / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / cellular response to nutrient levels / mesoderm formation / positive regulation of double-strand break repair via homologous recombination / histone acetyltransferase complex / anatomical structure morphogenesis / phosphatase binding / Attenuation phase / cell fate commitment / cis-regulatory region sequence-specific DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of epithelial to mesenchymal transition / regulation of cellular response to heat
Similarity search - Function
MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain ...MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / SMAD-like domain superfamily / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Coactivator CBP, KIX domain superfamily / Histone acetylation protein / Histone acetylation protein / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / SMAD/FHA domain superfamily / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Mothers against decapentaplegic homolog 2 / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMiyazono, K. / Wada, H. / Ito, T. / Tanokura, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K14708 Japan
Japan Society for the Promotion of Science (JSPS)17K19581 Japan
Japan Society for the Promotion of Science (JSPS)23228003 Japan
Japan Society for the Promotion of Science (JSPS)20H02910 Japan
CitationJournal: Sci.Signal. / Year: 2020
Title: Structural basis for transcriptional coactivator recognition by SMAD2 in TGF-beta signaling.
Authors: Miyazono, K.I. / Ito, T. / Fukatsu, Y. / Wada, H. / Kurisaki, A. / Tanokura, M.
History
DepositionAug 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 2
B: CREB-binding protein
C: Mothers against decapentaplegic homolog 2
D: CREB-binding protein
E: Mothers against decapentaplegic homolog 2
F: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)79,8576
Polymers79,8576
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-41 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.922, 70.395, 163.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mothers against decapentaplegic homolog 2 / / Mothers against DPP homolog 2 / JV18-1 / Mad-related protein 2 / hMAD-2 / SMAD family member 2 / hSMAD2


Mass: 23481.596 Da / Num. of mol.: 3 / Mutation: S465E, S467E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD2, MADH2, MADR2 / Plasmid: pET48 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15796
#2: Protein/peptide CREB-binding protein / / Histone lysine acetyltransferase CREBBP / Protein-lysine acetyltransferase CREBBP


Mass: 3137.308 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Plasmid: pET48 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92793, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 1 M sodium phosphate monobasic monohydrate-potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→47.17 Å / Num. obs: 11297 / % possible obs: 90.4 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.052 / Rrim(I) all: 0.117 / Net I/σ(I): 10.8 / Num. measured all: 50331
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.3-3.563.60.976716920070.780.5361.1221.879.9
8.73-47.175.10.03337877440.9990.0160.03736.798.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZOJ

5zoj


Resolution: 3.3→43.169 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 32.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 953 4.96 %
Rwork0.2553 --
obs0.2566 11244 82.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→43.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5054 0 0 0 5054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025179
X-RAY DIFFRACTIONf_angle_d0.537035
X-RAY DIFFRACTIONf_dihedral_angle_d12.2833071
X-RAY DIFFRACTIONf_chiral_restr0.041754
X-RAY DIFFRACTIONf_plane_restr0.005923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.4740.4291490.37471998X-RAY DIFFRACTION65
3.474-3.69160.37241050.32482218X-RAY DIFFRACTION70
3.6916-3.97640.31431440.30342467X-RAY DIFFRACTION79
3.9764-4.37620.27561080.27472653X-RAY DIFFRACTION83
4.3762-5.00870.26531520.23892706X-RAY DIFFRACTION87
5.0087-6.30730.24771520.2593072X-RAY DIFFRACTION97
6.3073-43.1690.25731430.20873129X-RAY DIFFRACTION99
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)
10.09160.1813-0.37390.3968-1.0344.00990.12210.2349-0.2130.8078-0.4549-0.5379-0.98660.8144-0.52140.9890.3547-0.13511.51070.1141.851714.36-17.7089-24.2725
22.2451-1.05050.90680.88290.42252.09910.08710.05990.1949-0.008-0.16510.06030.19260.00390.06880.7134-0.06030.02240.7565-0.02070.9347-28.36446.1123-10.9622
31.3525-0.54610.45680.86060.60851.1461-0.11260.2189-1.22190.0803-0.075-0.6139-0.36910.2909-0.05790.557-0.05680.11010.95280.01711.1009-13.793423.5369-1.0345
40.9994-0.23790.65722.22880.65011.99670.17430.181-0.2867-0.1808-0.0667-0.08390.3606-0.0101-0.0510.86590.0448-0.01360.8274-0.02660.9666-22.9156-17.6637-30.3251
51.5517-0.43090.16351.59440.79051.43760.22560.98410.11350.1116-0.23960.5501-0.32870.18040.12440.9536-0.0246-0.13080.962-0.02741.2502-34.5634-2.719-46.579
62.0726-0.0827-0.16751.44151.41263.2248-0.0721-0.1103-0.3495-0.03630.1588-0.09020.73490.5061-0.23820.91240.1397-0.11740.8377-0.02841.1749-2.5526-11.0336-7.6772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'F' and resid 1953 through 1970)
2X-RAY DIFFRACTION2(chain 'A' and resid 265 through 458)
3X-RAY DIFFRACTION3(chain 'B' and resid 1951 through 1970)
4X-RAY DIFFRACTION4(chain 'C' and resid 266 through 458)
5X-RAY DIFFRACTION5(chain 'D' and resid 1951 through 1970)
6X-RAY DIFFRACTION6(chain 'E' and resid 266 through 457)

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