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- PDB-5x6m: Crystal Structure of SMAD5-MH1 in complex with a composite DNA se... -

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Basic information

Entry
Database: PDB / ID: 5x6m
TitleCrystal Structure of SMAD5-MH1 in complex with a composite DNA sequence
Components
  • DNA (5'-D(P*AP*TP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*AP*TP*A)-3')
  • DNA (5'-D(P*TP*TP*AP*TP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*A)-3')
  • Mothers against decapentaplegic homolog 5
KeywordsMETAL BINDING PROTEIN/DNA / Smad5 MH1 domain / composite DNA / SBE DNA / GC-rich DNA / METAL BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of Fas signaling pathway / Signaling by BMP / Mullerian duct regression / osteoblast fate commitment / DEAD/H-box RNA helicase binding / SMAD protein signal transduction / embryonic pattern specification / cartilage development / ureteric bud development / germ cell development ...negative regulation of Fas signaling pathway / Signaling by BMP / Mullerian duct regression / osteoblast fate commitment / DEAD/H-box RNA helicase binding / SMAD protein signal transduction / embryonic pattern specification / cartilage development / ureteric bud development / germ cell development / positive regulation of osteoblast differentiation / BMP signaling pathway / cardiac muscle contraction / transforming growth factor beta receptor signaling pathway / erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / stem cell differentiation / bone development / DNA-binding transcription repressor activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / intracellular iron ion homeostasis / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / ubiquitin protein ligase binding / 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 / metal ion binding / nucleus / cytosol / cytoplasm
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: 3.2 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: 4ZL3
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
C: DNA (5'-D(P*AP*TP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*AP*TP*A)-3')
D: DNA (5'-D(P*TP*TP*AP*TP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*A)-3')
A: Mothers against decapentaplegic homolog 5
E: Mothers against decapentaplegic homolog 5
G: DNA (5'-D(P*AP*TP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*AP*TP*A)-3')
H: DNA (5'-D(P*TP*TP*AP*TP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*A)-3')
F: Mothers against decapentaplegic homolog 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,55812
Polymers96,2968
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-96 kcal/mol
Surface area38430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.464, 119.464, 93.067
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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


Mass: 6736.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*TP*AP*TP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*A)-3')


Mass: 6767.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-tris, pH 6.5, 0.2M LiNO3, 8% PEG 3350, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979065 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979065 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 24244 / % possible obs: 98.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.046 / Net I/σ(I): 22.11
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 4.55 / Num. unique obs: 2446 / CC1/2: 0.929 / Rpim(I) all: 0.257 / % 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: 3.2→29.937 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.47
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1234 5.11 %Random
Rwork0.2105 ---
obs0.2125 24146 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 125.1 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 1804 4 0 5383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115700
X-RAY DIFFRACTIONf_angle_d1.2318145
X-RAY DIFFRACTIONf_dihedral_angle_d23.1362130
X-RAY DIFFRACTIONf_chiral_restr0.069914
X-RAY DIFFRACTIONf_plane_restr0.009734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-3.32820.25551250.24352581X-RAY DIFFRACTION100
3.3282-3.47950.31351450.25782524X-RAY DIFFRACTION100
3.4795-3.66260.30921350.28462606X-RAY DIFFRACTION100
3.6626-3.89160.28341430.2682591X-RAY DIFFRACTION100
3.8916-4.19130.25791320.22742550X-RAY DIFFRACTION100
4.1913-4.61180.2671730.20252565X-RAY DIFFRACTION100
4.6118-5.27590.25951300.21492580X-RAY DIFFRACTION100
5.2759-6.63520.27931480.22182587X-RAY DIFFRACTION100
6.6352-29.93830.19871030.17022328X-RAY DIFFRACTION89
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)
13.78621.1975-0.26911.916-0.24843.954-0.3579-0.72961.26510.7241-0.10380.37-1.3279-0.25280.09721.46030.5-0.32840.804-0.36651.055493.7184-104.588611.843
23.5582-0.62422.841.0038-2.16446.42210.09110.10450.38950.48871.0133-0.2056-2.26041.12320.30811.40020.0204-1.25780.87180.58321.1988106.069-99.1171-6.6944
32.7294-0.48892.9712-0.3895-0.48455.1776-0.2798-0.1712-0.15980.50390.4798-0.4716-1.11480.26940.19551.2878-0.1652-0.73071.27820.29081.3492108.6544-99.4457-4.0803
41.73780.50880.61783.3450.74464.2433-0.37570.80960.1089-0.6217-0.0748-1.236-0.37021.15920.16930.5972-0.0850.15511.65130.48251.1362101.773-108.7483-36.1249
53.4777-0.08720.57944.4749-0.68435.3296-0.4688-0.3183-0.3240.6940.2935-0.61410.6285-0.53220.17161.0710.2550.13460.66510.05970.788992.0518-135.70710.4377
61.875-0.6915-1.26461.4010.37525.5383-0.072-0.3098-0.3771-0.20370.14380.26961.0008-0.33110.03541.42080.01250.38851.0193-0.11270.989476.2619-139.0362-6.1398
71.01320.3626-2.030.756-0.08554.94060.0546-0.3307-0.2610.22370.39720.52310.4867-0.2206-0.33631.0848-0.17960.38171.6217-0.21721.145174.1432-139.0925-3.3972
84.0141.4661-0.1824.6749-0.10494.06580.00670.93210.3216-0.0899-0.14570.88470.7856-0.41970.10220.5191-0.0517-0.01611.1208-0.15730.875.5105-126.025-34.8879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 13 through 134)
2X-RAY DIFFRACTION2(chain 'C' and resid 1 through 22)
3X-RAY DIFFRACTION3(chain 'D' and resid 1 through 22)
4X-RAY DIFFRACTION4(chain 'A' and resid 12 through 133)
5X-RAY DIFFRACTION5(chain 'E' and resid 13 through 133)
6X-RAY DIFFRACTION6(chain 'G' and resid 1 through 22)
7X-RAY DIFFRACTION7(chain 'H' and resid 1 through 22)
8X-RAY DIFFRACTION8(chain 'F' and resid 13 through 133)

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