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- PDB-5x6h: Crystal Structure of SMAD5-MH1/GC-BRE DNA complex -

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Basic information

Entry
Database: PDB / ID: 5x6h
TitleCrystal Structure of SMAD5-MH1/GC-BRE DNA complex
Components
  • DNA (5'-D(P*GP*TP*AP*TP*GP*GP*CP*GP*CP*CP*AP*TP*AP*C)-3')
  • Mothers against decapentaplegic homolog 5
KeywordsMETAL BINDING PROTEIN/DNA / Smad MH1 domain / GC-rich DNA / METAL BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of Fas signaling pathway / Mullerian duct regression / Signaling by BMP / osteoblast fate commitment / heteromeric SMAD protein complex / DEAD/H-box RNA helicase binding / embryonic pattern specification / SMAD protein signal transduction / I-SMAD binding / cartilage development ...negative regulation of Fas signaling pathway / Mullerian duct regression / Signaling by BMP / osteoblast fate commitment / heteromeric SMAD protein complex / DEAD/H-box RNA helicase binding / embryonic pattern specification / SMAD protein signal transduction / I-SMAD binding / cartilage development / ureteric bud development / germ cell development / cellular response to organic cyclic compound / anatomical structure morphogenesis / BMP signaling pathway / positive regulation of osteoblast differentiation / cardiac muscle contraction / erythrocyte differentiation / transforming growth factor beta receptor signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / bone development / DNA-binding transcription repressor activity, RNA polymerase II-specific / angiogenesis / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Smad3; Chain A / SMAD 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 ...Smad3; Chain A / SMAD 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 / SMAD/FHA domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Mothers against decapentaplegic homolog 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChai, N. / Wang, J. / Wang, Z.X. / Wu, J.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31130062 China
China National Basic Research Program2013CB530600 China
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural basis for the Smad5 MH1 domain to recognize different DNA sequences.
Authors: Chai, N. / Li, W.X. / Wang, J. / Wang, Z.X. / Yang, S.M. / Wu, J.W.
History
DepositionFeb 22, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 15, 2017ID: 4ZL2
Revision 1.0Mar 15, 2017Provider: 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

Downloads & links

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Assembly

Deposited unit
B: Mothers against decapentaplegic homolog 5
E: DNA (5'-D(P*GP*TP*AP*TP*GP*GP*CP*GP*CP*CP*AP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6683
Polymers21,6032
Non-polymers651
Water00
1
B: Mothers against decapentaplegic homolog 5
E: DNA (5'-D(P*GP*TP*AP*TP*GP*GP*CP*GP*CP*CP*AP*TP*AP*C)-3')
hetero molecules

B: Mothers against decapentaplegic homolog 5
E: DNA (5'-D(P*GP*TP*AP*TP*GP*GP*CP*GP*CP*CP*AP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3376
Polymers43,2064
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+11
Buried area3630 Å2
ΔGint-20 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.867, 92.867, 83.709
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Mothers against decapentaplegic homolog 5 / Mothers against DPP homolog 5 / Dwarfin-C / Dwf-C / SMAD family member 5 / mSmad5


Mass: 17322.232 Da / Num. of mol.: 1 / Fragment: MH1 domain (UNP RESIDUES 1-143)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smad5, Madh5, Msmad5 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P97454
#2: DNA chain DNA (5'-D(P*GP*TP*AP*TP*GP*GP*CP*GP*CP*CP*AP*TP*AP*C)-3')


Mass: 4280.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


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

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Tris, pH 7.0, 12% PEG 3350, 0.2M KNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 4102 / % possible obs: 97.4 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Net I/σ(I): 25
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 4.28 / Num. unique obs: 402 / CC1/2: 0.968 / Rpim(I) all: 0.173 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMP

3kmp


Resolution: 3.1→46.434 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 181 4.44 %Random
Rwork0.2017 ---
obs0.2032 4079 97.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→46.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms849 287 1 0 1137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111193
X-RAY DIFFRACTIONf_angle_d1.2281680
X-RAY DIFFRACTIONf_dihedral_angle_d23.69444
X-RAY DIFFRACTIONf_chiral_restr0.06191
X-RAY DIFFRACTIONf_plane_restr0.007162
LS refinement shellResolution: 3.0996→46.4387 Å
RfactorNum. reflection% reflection
Rfree0.2311 181 -
Rwork0.2017 3898 -
obs--97 %
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)
11.3889-0.31950.5760.3206-1.06093.45070.25071.8433-0.562-2.47330.5858-0.9353-1.38660.4941-0.79952.0934-0.44870.07671.4472-0.11732.14689.4736-23.997424.7359
22.54761.48171.14772.142-1.22023.2437-0.20750.25180.12640.16590.0754-0.884-0.17710.9720.18890.586-0.18480.00190.95570.13380.68436.428-31.127528.0323
34.35751.93051.8981.19990.4247.45850.05031.02271.247-0.16561.10450.3399-0.45640.99530.55561.3562-0.53610.53121.47540.3090.74266.3798-31.188215.1507
45.8877-2.7613-4.38333.93913.81638.113-0.37370.65210.95450.3515-0.2789-0.8461-1.0018-1.53960.33512.10140.2249-0.27111.90870.26830.757-1.4918-29.651810.9268
51.18092.2462-1.7237.0825-6.27635.7409-0.19230.5506-0.6665-0.4314-0.2233-0.20830.3476-0.04050.3840.5320.0144-0.21910.8939-0.13090.7012-2.8516-43.038826.8949
64.39871.3321-2.41858.930.38738.52660.3293-1.03870.8623-1.17820.17810.1228-1.6768-0.5682-0.16280.72350.2052-0.09680.8276-0.10490.4901-5.8915-30.031329.419
75.4979-0.33271.05744.9299-2.38183.8142-0.09241.64550.1533-1.58240.44150.7906-0.4973-1.2214-0.09831.20340.1797-0.27621.4143-0.02850.5102-9.1391-34.569418.5846
82.86741.8335-0.99445.26190.5353.6914-0.4515-2.1473-0.6891-0.18290.0111-0.02570.56470.38810.11110.16220.0544-0.10161.47650.18460.68950.5167-42.253843.2898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 12 through 27 )
2X-RAY DIFFRACTION2chain 'B' and (resid 28 through 44 )
3X-RAY DIFFRACTION3chain 'B' and (resid 45 through 57 )
4X-RAY DIFFRACTION4chain 'B' and (resid 58 through 66 )
5X-RAY DIFFRACTION5chain 'B' and (resid 67 through 74 )
6X-RAY DIFFRACTION6chain 'B' and (resid 75 through 103 )
7X-RAY DIFFRACTION7chain 'B' and (resid 104 through 133 )
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 14 )

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