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- PDB-3qsv: Structural basis for DNA recognition by constitutive Smad4 MH1 dimers -

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Basic information

Entry
Database: PDB / ID: 3qsv
TitleStructural basis for DNA recognition by constitutive Smad4 MH1 dimers
Components
  • DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
  • Mothers against decapentaplegic homolog 4
KeywordsTRANSCRIPTION/DNA / MH1 / transcription factor / DNA binding / signaling / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Signaling by NODAL / FOXO-mediated transcription of cell cycle genes / : / : / Signaling by Activin / RUNX3 regulates CDKN1A transcription / : / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly ...Signaling by NODAL / FOXO-mediated transcription of cell cycle genes / : / : / Signaling by Activin / RUNX3 regulates CDKN1A transcription / : / positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / RUNX2 regulates bone development / : / regulation of binding / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / Signaling by BMP / TGF-beta receptor signaling activates SMADs / somite rostral/caudal axis specification / tissue morphogenesis / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / atrioventricular valve formation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / activin responsive factor complex / Downregulation of SMAD2/3:SMAD4 transcriptional activity / positive regulation of luteinizing hormone secretion / regulation of hair follicle development / filamin binding / sebaceous gland development / : / SMAD protein complex / formation of anatomical boundary / positive regulation of follicle-stimulating hormone secretion / regulation of transforming growth factor beta2 production / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / response to transforming growth factor beta / secondary palate development / cardiac septum development / negative regulation of cardiac muscle hypertrophy / brainstem development / left ventricular cardiac muscle tissue morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / atrioventricular canal development / chromatin => GO:0000785 / neuron fate commitment / sulfate binding / endoderm development / outflow tract septum morphogenesis / SMAD protein signal transduction / Ub-specific processing proteases / positive regulation of BMP signaling pathway / gastrulation with mouth forming second / I-SMAD binding / neural crest cell differentiation / endothelial cell activation / anterior/posterior pattern specification / embryonic digit morphogenesis / branching involved in ureteric bud morphogenesis / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / female gonad development / seminiferous tubule development / positive regulation of cardiac muscle cell apoptotic process / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / R-SMAD binding / uterus development / mesoderm development / positive regulation of SMAD protein signal transduction / developmental growth / single fertilization / BMP signaling pathway / positive regulation of epithelial to mesenchymal transition / ovarian follicle development / gastrulation / collagen binding / ERK1 and ERK2 cascade / transforming growth factor beta receptor signaling pathway / kidney development / cellular response to glucose stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / axon guidance / wound healing / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / negative regulation of cell growth / transcription coactivator binding / positive regulation of miRNA transcription / osteoblast differentiation / RNA polymerase II transcription regulator complex / male gonad development / regulation of cell population proliferation / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / intracellular iron ion homeostasis / in utero embryonic development / cell population proliferation / transcription regulator complex / transcription cis-regulatory region binding / response to hypoxia
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 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.708 Å
AuthorsBaburajendran, N. / Jauch, R. / Zhen, C.T.Y. / Kolatkar, P.R.
CitationJournal: To be Published
Title: Structural basis for DNA recognition by constitutive Smad4 MH1 dimers
Authors: Baburajendran, N. / Jauch, R. / Zhen, C.T.Y. / Kolatkar, P.R.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 4
B: Mothers against decapentaplegic homolog 4
C: Mothers against decapentaplegic homolog 4
D: Mothers against decapentaplegic homolog 4
E: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
F: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
G: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
H: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,94412
Polymers79,6828
Non-polymers2624
Water1629
1
A: Mothers against decapentaplegic homolog 4
D: Mothers against decapentaplegic homolog 4
E: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
F: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9726
Polymers39,8414
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-26 kcal/mol
Surface area17870 Å2
MethodPISA
2
B: Mothers against decapentaplegic homolog 4
C: Mothers against decapentaplegic homolog 4
G: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
H: DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9726
Polymers39,8414
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-27 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.357, 35.354, 139.544
Angle α, β, γ (deg.)90.00, 93.83, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23G
14F
24H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSERchain AAA10 - 1382 - 130
21PROPROSERSERchain BBB10 - 1382 - 130
12ASNASNVALVALchain CCC13 - 1365 - 128
22SERSERVALVALchain DDD12 - 1364 - 128
13DTDTDADAchain EEE1000 - 10151 - 16
23DTDTDADAchain GGG1000 - 10151 - 16
14DTDTDADAchain FFF2000 - 20151 - 16
24DTDTDADAchain HHH2000 - 20151 - 16

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Mothers against decapentaplegic homolog 4 / Smad4


Mass: 15022.306 Da / Num. of mol.: 4 / Fragment: smad4 MH1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smad4 / Production host: Escherichia coli (E. coli) / References: UniProt: P97471
#2: DNA chain
DNA (5'-D(P*TP*GP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*CP*A)-3')


Mass: 4898.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA synthetically manufactured
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 200mM MgCl2, 100mM Tris, 30% PEG 4000, 10mM spermine, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24301 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 68.38 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.708→24.89 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / σ(F): 0.14 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 1156 5.11 %random
Rwork0.2123 ---
obs0.2153 22643 92.74 %-
all-24301 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.959 Å2 / ksol: 0.253 e/Å3
Displacement parametersBiso max: 383.88 Å2 / Biso mean: 91.1948 Å2 / Biso min: 22.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.6453 Å20 Å21.4397 Å2
2---3.5316 Å20 Å2
3---1.8863 Å2
Refinement stepCycle: LAST / Resolution: 2.708→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 1312 4 9 5401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045634
X-RAY DIFFRACTIONf_angle_d0.9267874
X-RAY DIFFRACTIONf_chiral_restr0.074875
X-RAY DIFFRACTIONf_plane_restr0.003771
X-RAY DIFFRACTIONf_dihedral_angle_d20.6942170
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1034X-RAY DIFFRACTIONPOSITIONAL0.029
12B1034X-RAY DIFFRACTIONPOSITIONAL0.029
21C1001X-RAY DIFFRACTIONPOSITIONAL0.015
22D1001X-RAY DIFFRACTIONPOSITIONAL0.015
31E328X-RAY DIFFRACTIONPOSITIONAL0.034
32G328X-RAY DIFFRACTIONPOSITIONAL0.034
41F328X-RAY DIFFRACTIONPOSITIONAL0.034
42H328X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7077-2.83080.39811220.31682306X-RAY DIFFRACTION82
2.8308-2.97980.35431500.28042644X-RAY DIFFRACTION92
2.9798-3.16610.29531370.22632680X-RAY DIFFRACTION94
3.1661-3.410.28671420.22722631X-RAY DIFFRACTION92
3.41-3.75210.29041530.21362784X-RAY DIFFRACTION96
3.7521-4.29270.25561380.19362738X-RAY DIFFRACTION94
4.2927-5.39920.23081590.1862704X-RAY DIFFRACTION93
5.3992-24.89150.24731550.18533000X-RAY DIFFRACTION98
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)
12.88750.6222-0.34771.11591.14495.87860.2374-0.1284-0.16770.0543-0.12380.22780.7240.1487-0.10080.442-0.05520.00520.0135-0.03380.183930.31566.5868-56.7196
22.8036-0.06270.15780.6941-0.75275.32940.0657-0.0428-0.1813-0.00570.0862-0.0944-0.6849-0.1651-0.16150.5971-0.03360.07660.1210.03480.2266-21.83422.5045-57.8606
33.30460.834-0.41372.3974-1.35770.7789-0.0386-1.3624-0.11960.47830.32530.3828-0.12-0.5291-0.29960.297-0.0870.04371.33050.31730.2384-14.668413.1366-15.3281
44.4084-1.08170.74432.78960.29280.5-0.0429-1.62470.19640.62990.3127-0.03950.1732-0.21-0.230.401-0.12570.0331.2342-0.24760.189720.868518.6758-15.4351
59.68998.1462-0.34279.67222.44295.71970.0416-2.16770.6519-0.5112-0.67450.55720.20170.24630.34960.1263-0.135-0.0030.4732-0.07290.43725.689411.9928-34.4068
69.86062.0982-1.30763.56881.27451.5692-0.6991-1.1317-1.0127-0.57720.3252-0.5559-0.11660.27620.24910.4646-0.25190.1060.3932-0.08580.441425.806311.0192-36.9435
78.43227.77580.85239.36780.70082.28360.2557-2.6934-0.884-0.6573-0.6551-0.4782-0.1068-0.2920.14740.3595-0.23340.01210.56910.19220.5705-18.59217.9284-34.8264
89.90514.73171.91136.34040.5611.1093-0.8454-1.5743-0.1554-0.93180.52790.2510.0942-0.12620.07330.4076-0.2248-0.00970.40040.07810.2818-18.601518.7881-37.4529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 10:138)A10 - 138
2X-RAY DIFFRACTION2(chain B and resid 10:138)B10 - 138
3X-RAY DIFFRACTION3(chain C and resid 13:136)C13 - 136
4X-RAY DIFFRACTION4(chain D and resid 12:136)D12 - 136
5X-RAY DIFFRACTION5(chain E and resid 1000:1015)E1000 - 1015
6X-RAY DIFFRACTION6(chain F and resid 2000:2015)F2000 - 2015
7X-RAY DIFFRACTION7(chain G and resid 1000:1015)G1000 - 1015
8X-RAY DIFFRACTION8(chain H and resid 2000:2015)H2000 - 2015

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