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- PDB-5x6g: Crystal Structure of SMAD5-MH1/palindromic SBE DNA complex -

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Basic information

Entry
Database: PDB / ID: 5x6g
TitleCrystal Structure of SMAD5-MH1/palindromic SBE DNA complex
Components
  • DNA (5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)-3')
  • DNA (5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)-3')
  • Mothers against decapentaplegic homolog 5
KeywordsMETAL BINDING PROTEIN/DNA / Smad5 / MH1 domain / protein-DNA complex / SBE / 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: 3.05 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 21, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 15, 2017ID: 4ZKG
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
A: Mothers against decapentaplegic homolog 5
B: Mothers against decapentaplegic homolog 5
C: DNA (5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)-3')
D: DNA (5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5706
Polymers44,4394
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-21 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.535, 74.502, 83.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / 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*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)-3')


Mass: 4866.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)-3')


Mass: 4928.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 15% PEG 3350, 0.2M Magnesium Formate

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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: Jan 2, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 8122 / % possible obs: 89.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.1
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 4.66 / Num. unique obs: 458 / % 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: 3.05→34.035 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.99
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 361 4.59 %Random
Rwork0.2228 ---
obs0.2244 7870 87.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 90.2 Å2
Refinement stepCycle: LAST / Resolution: 3.05→34.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 617 2 0 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012697
X-RAY DIFFRACTIONf_angle_d1.213771
X-RAY DIFFRACTIONf_dihedral_angle_d22.3981063
X-RAY DIFFRACTIONf_chiral_restr0.059405
X-RAY DIFFRACTIONf_plane_restr0.008374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.4910.43131360.32612685X-RAY DIFFRACTION96
3.491-4.39680.2774970.25741966X-RAY DIFFRACTION70
4.3968-34.03750.19791280.18222858X-RAY DIFFRACTION97
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)
13.11210.61911.16784.8874-0.11883.3083-0.04640.0589-0.0393-0.2803-0.17290.4923-0.03930.08040.16830.64590.0258-0.01910.6742-0.02680.5315-6.75759.73065.0163
21.26610.15772.04292.20180.05174.4815-0.1079-0.1599-0.05110.0775-0.17580.30140.0633-0.16470.15380.4499-0.02820.05410.4894-0.05220.5358-16.2734-31.34116.8117
34.85060.74710.59994.8093-1.46291.7175-0.33590.4872-0.27880.9878-0.0539-0.02310.8164-0.33830.30480.9181-0.1032-0.03480.6253-0.06280.8233-14.3022-13.12877.5755
42.54012.62671.13254.8335-0.66834.7727-0.12210.50720.57720.20040.0340.17790.0788-0.5213-0.02630.748-0.02750.10240.81210.10811.0235-15.4887-8.4098.9828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 11 through 132)
2X-RAY DIFFRACTION2(chain 'B' and resid 11 through 133)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 15)
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 16)

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