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- PDB-1m1l: Human Suppressor of Fused (N-terminal domain) -

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Basic information

Entry
Database: PDB / ID: 1m1l
TitleHuman Suppressor of Fused (N-terminal domain)
ComponentsSuppressor of Fused
KeywordsSIGNALING PROTEIN / Gene regulation / Hedgehog signaling / signal transduction / fused
Function / homology
Function and homology information


smoothened signaling pathway involved in ventral spinal cord interneuron specification / smoothened signaling pathway involved in spinal cord motor neuron cell fate specification / positive regulation of cellular response to drug / GLI-SUFU complex / ciliary tip / coronary vasculature development / aorta development / ventricular septum development / negative regulation of protein import into nucleus / skin development ...smoothened signaling pathway involved in ventral spinal cord interneuron specification / smoothened signaling pathway involved in spinal cord motor neuron cell fate specification / positive regulation of cellular response to drug / GLI-SUFU complex / ciliary tip / coronary vasculature development / aorta development / ventricular septum development / negative regulation of protein import into nucleus / skin development / ciliary base / spermatid development / heart looping / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of osteoblast differentiation / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / negative regulation of DNA-binding transcription factor activity / neural tube closure / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / beta-catenin binding / transcription corepressor activity / cilium / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Suppressor of fused / Suppressor of fused, eukaryotic / Suppressor of fused C-terminal / Suppressor of fused, N-terminal / Suppressor of fused, C-terminal domain superfamily / Suppressor of Fused Gli/Ci N terminal binding domain / Suppressor of fused-like domain / Suppressor of fused protein (SUFU)
Similarity search - Domain/homology
Suppressor of fused homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsMerchant, M. / Vajdos, F.F. / Ultsch, M. / Maun, H.R. / Wendt, U. / Cannon, J. / Lazarus, R.A. / de Vos, A.M. / de Sauvage, F.J.
CitationJournal: Mol.Cell.Biol. / Year: 2004
Title: Suppressor of fused regulates Gli activity through a dual binding mechanism
Authors: Merchant, M. / Vajdos, F.F. / Ultsch, M. / Maun, H.R. / Wendt, U. / Cannon, J. / Desmarais, W. / Lazarus, R.A. / de Vos, A.M. / de Sauvage, F.J.
History
DepositionJun 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 4 CHAIN(S). AUTHOR STATES THAT BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Suppressor of Fused
B: Suppressor of Fused
C: Suppressor of Fused
D: Suppressor of Fused


Theoretical massNumber of molelcules
Total (without water)106,3714
Polymers106,3714
Non-polymers00
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.025, 173.025, 290.833
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Suppressor of Fused


Mass: 26592.730 Da / Num. of mol.: 4 / Fragment: N-terminal domain (Residues 27-262)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pST-239 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UMX1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 3.94 Å3/Da / Density % sol: 68.77 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1 M LiCl, 0.1 M NaCitrate pH 5.0- 6.0, 10% w/v PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 mg/mlprotein1drop
225 mMTris1droppH7.5
310 mMdithiothreitol1drop
41 M1reservoirLiCl
50.1 Msodium citrate1reservoirpH5.0-6.0
610 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→29.81 Å / Num. all: 48643 / Num. obs: 48643 / % possible obs: 99.2 % / Observed criterion σ(I): -3
Reflection
*PLUS
Lowest resolution: 99 Å / Redundancy: 9.1 % / Num. measured all: 441505 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Highest resolution: 2.65 Å / Lowest resolution: 2.7 Å / % possible obs: 100 % / Rmerge(I) obs: 0.362

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.65→29.81 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2564 -Thin shells
Rwork0.2235 --
obs-48273 -
Refinement stepCycle: LAST / Resolution: 2.65→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7486 0 0 346 7832
Refinement
*PLUS
% reflection Rfree: 8 % / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.01
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.5

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