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- PDB-1khu: Smad1 crystal structure reveals the details of BMP signaling pathway -

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Basic information

Entry
Database: PDB / ID: 1khu
TitleSmad1 crystal structure reveals the details of BMP signaling pathway
ComponentsSMAD1
KeywordsTRANSCRIPTION / beta-strand sandwich
Function / homology
Function and homology information


mesodermal cell fate commitment / homomeric SMAD protein complex / osteoblast fate commitment / SMAD protein complex / RUNX2 regulates bone development / co-SMAD binding / heteromeric SMAD protein complex / negative regulation of muscle cell differentiation / positive regulation of cartilage development / primary miRNA binding ...mesodermal cell fate commitment / homomeric SMAD protein complex / osteoblast fate commitment / SMAD protein complex / RUNX2 regulates bone development / co-SMAD binding / heteromeric SMAD protein complex / negative regulation of muscle cell differentiation / positive regulation of cartilage development / primary miRNA binding / DEAD/H-box RNA helicase binding / gamete generation / hindbrain development / cardiac conduction system development / primary miRNA processing / Signaling by BMP / embryonic pattern specification / SMAD protein signal transduction / I-SMAD binding / cartilage development / Cardiogenesis / 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 / anatomical structure morphogenesis / BMP signaling pathway / positive regulation of osteoblast differentiation / ossification / transforming growth factor beta receptor signaling pathway / bone development / positive regulation of miRNA transcription / MAPK cascade / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Tumour Suppressor Smad4 - #10 / 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 ...Tumour Suppressor Smad4 - #10 / 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 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mothers against decapentaplegic homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsQin, B.Y. / Lin, K.
CitationJournal: Mol.Cell / Year: 2001
Title: Structural basis of Smad1 activation by receptor kinase phosphorylation.
Authors: Qin, B.Y. / Chacko, B.M. / Lam, S.S. / de Caestecker, M.P. / Correia, J.J. / Lin, K.
History
DepositionDec 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMAD1
B: SMAD1
C: SMAD1
D: SMAD1


Theoretical massNumber of molelcules
Total (without water)98,1824
Polymers98,1824
Non-polymers00
Water10,557586
1
A: SMAD1
B: SMAD1
C: SMAD1


Theoretical massNumber of molelcules
Total (without water)73,6373
Polymers73,6373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-26 kcal/mol
Surface area24940 Å2
MethodPISA
2
D: SMAD1

D: SMAD1

D: SMAD1


Theoretical massNumber of molelcules
Total (without water)73,6373
Polymers73,6373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)138.129, 138.129, 199.340
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
SMAD1


Mass: 24545.607 Da / Num. of mol.: 4 / Fragment: DWB / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15797
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 3.73 Å3/Da / Density % sol: 66.99 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5 / Details: alcohol, pH 6.5, EVAPORATION, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMMES1reservoirpH6.0
26 %ethanol1reservoir
320 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 47621 / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 1.69 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.4
Reflection shellResolution: 2.5→2.57 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / Num. unique all: 4058 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 100 Å / % possible obs: 96.8 % / Num. measured all: 77509
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.351

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Smad4 active fragment homotrimer

Resolution: 2.5→38 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2297 -4.7
Rwork0.239 ---
all-45958 --
obs-45958 93.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.45 Å23.7 Å20 Å2
2---2.45 Å20 Å2
3---4.91 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6186 0 0 586 6772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00751
X-RAY DIFFRACTIONc_angle_d1.397
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 38 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS

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