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- PDB-3kmp: Crystal Structure of SMAD1-MH1/DNA complex -

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Basic information

Entry
Database: PDB / ID: 3kmp
TitleCrystal Structure of SMAD1-MH1/DNA complex
Components
  • 5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)-3'
  • 5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)-3'
  • SMAD1-MH1
KeywordsTRANSCRIPTION REGULATOR/DNA / protein-DNA complex / Smad1 / SBE DNA / MH1 domain / beta hairpin / Nucleus / Transcription / Transcription regulation / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


: / : / RUNX2 regulates bone development / mesodermal cell fate commitment / Signaling by BMP / osteoblast fate commitment / co-SMAD binding / positive regulation of cartilage development / primary miRNA binding / DEAD/H-box RNA helicase binding ...: / : / RUNX2 regulates bone development / mesodermal cell fate commitment / Signaling by BMP / osteoblast fate commitment / co-SMAD binding / positive regulation of cartilage development / primary miRNA binding / DEAD/H-box RNA helicase binding / response to xenobiotic stimulus => GO:0009410 / gamete generation / hindbrain development / cellular response to BMP stimulus / embryonic pattern specification / Ub-specific processing proteases / SMAD protein signal transduction / I-SMAD binding / cartilage development / nuclear inner membrane / cardiac muscle cell proliferation / ureteric bud development / midbrain development / homeostatic process / positive regulation of sprouting angiogenesis / cellular response to organic cyclic compound / BMP signaling pathway / positive regulation of osteoblast differentiation / transforming growth factor beta receptor signaling pathway / positive regulation of cell differentiation / bone development / positive regulation of miRNA transcription / MAPK cascade / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / protein phosphorylation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / identical protein binding / metal ion binding / nucleus / 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 1 / MH1 domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBaburajendran, N. / Palasingam, P. / Narasimhan, K. / Jauch, R. / Kolatkar, P.R.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-beta effectors.
Authors: BabuRajendran, N. / Palasingam, P. / Narasimhan, K. / Sun, W. / Prabhakar, S. / Jauch, R. / Kolatkar, P.R.
History
DepositionNov 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Mar 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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: SMAD1-MH1
B: SMAD1-MH1
C: 5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)-3'
D: 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)38,2538
Polymers37,9384
Non-polymers3154
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-23 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.938, 77.490, 83.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

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
11SERSERALAALAchain A resid 11:30AA11 - 303 - 22
21SERSERALAALAchain B and resid 11:30BB11 - 303 - 22
12LYSLYSCYSCYSchain A resid 32:109AA32 - 10924 - 101
22LYSLYSCYSCYSchain B and resid 32:109BB32 - 10924 - 101
13PHEPHEGLUGLUchain A resid 111:131AA111 - 131103 - 123
23PHEPHEGLUGLUchain B and resid 111:131BB111 - 131103 - 123

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SMAD1-MH1


Mass: 14368.723 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 9-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smad1 / Plasmid: pETG60A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8CC31, UniProt: P70340*PLUS

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain 5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)-3'


Mass: 4577.011 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)-3'


Mass: 4624.021 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 13 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / 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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium tartrate dibasic, 20% PEG 3350, 10% glycerol, 3% 2-propanol (additive), vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 13667 / Num. obs: 13623 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 56.33 Å2

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→23.413 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.48 / σ(F): 1.35 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 683 5.01 %RANDOM
Rwork0.206 12940 --
all0.208 13667 --
obs0.208 13623 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.245 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 285.28 Å2 / Biso mean: 64.761 Å2 / Biso min: 20.74 Å2
Baniso -1Baniso -2Baniso -3
1-7.724 Å2-0 Å2-0 Å2
2---4.539 Å2-0 Å2
3----3.185 Å2
Refinement stepCycle: LAST / Resolution: 2.7→23.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 617 14 9 2643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092781
X-RAY DIFFRACTIONf_angle_d1.3553876
X-RAY DIFFRACTIONf_chiral_restr0.085407
X-RAY DIFFRACTIONf_plane_restr0.006388
X-RAY DIFFRACTIONf_dihedral_angle_d20.6581103
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A164X-RAY DIFFRACTIONPOSITIONAL0.049
12B164X-RAY DIFFRACTIONPOSITIONAL0.049
21A630X-RAY DIFFRACTIONPOSITIONAL0.041
22B630X-RAY DIFFRACTIONPOSITIONAL0.041
31A181X-RAY DIFFRACTIONPOSITIONAL0.042
32B181X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.9080.3931380.27525372675100
2.908-3.20.3081370.24525762713100
3.2-3.6620.3061560.22525422698100
3.662-4.6080.2071210.1842609273099
4.608-23.4140.1861310.1652676280798
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)
12.5468-1.1374-1.5782.5250.21730.2591-0.3086-0.1348-0.06060.49480.18620.26060.2390.07070.13090.45390.00230.06280.35840.05620.2922-6.1101-9.4663-4.7637
22.68721.2968-0.90090.9739-0.31622.01880.0913-0.30270.49570.0001-0.05260.4205-0.02040.0639-0.01460.30220.01860.05860.2753-0.10590.4423-16.891431.8765-17.0281
34.241.33462.42464.2151.41211.3401-0.2174-0.3059-0.3056-0.40810.3653-0.2543-0.6785-0.2628-0.06150.2774-0.00310.08660.3503-0.07160.2114-13.870513.6852-7.7842
42.1053-0.31011.51453.50941.59233.78510.1797-0.4447-0.5719-0.01250.1555-0.4897-0.4322-0.0561-0.44250.1331-0.0628-0.0040.37360.05970.3029-15.06498.577-8.7586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA9 - 132
2X-RAY DIFFRACTION2CHAIN BB10 - 132
3X-RAY DIFFRACTION3CHAIN CC1 - 15
4X-RAY DIFFRACTION4CHAIN DD2 - 16

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