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- PDB-6lph: the Sufu-Fu complex crystal structure -

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Basic information

Entry
Database: PDB / ID: 6lph
Titlethe Sufu-Fu complex crystal structure
Components
  • Serine/threonine-protein kinase fused
  • Suppressor of fused homolog
KeywordsPROTEIN BINDING / kinases / phosphorylation
Function / homology
Function and homology information


Hedgehog signaling complex / Assembly of the CI containing complexes / negative regulation of nucleocytoplasmic transport / Activation of CI / Activation of SMO / : / Hedgehog 'off' state / Phosphorylation of CI / germarium-derived egg chamber formation / Phosphorylation of SMO ...Hedgehog signaling complex / Assembly of the CI containing complexes / negative regulation of nucleocytoplasmic transport / Activation of CI / Activation of SMO / : / Hedgehog 'off' state / Phosphorylation of CI / germarium-derived egg chamber formation / Phosphorylation of SMO / Assembly of the 'signalling complexes' / Ubiquitination and proteolysis of phosphorylated CI / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / wing disc pattern formation / positive regulation of nucleocytoplasmic transport / smoothened binding / segment polarity determination / protein serine/threonine kinase activity => GO:0004674 / intraciliary transport / cytoplasmic sequestering of protein / molecular sequestering activity / nuclear localization sequence binding / smoothened signaling pathway / transcription factor binding / negative regulation of BMP signaling pathway / negative regulation of smoothened signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of protein ubiquitination / cilium / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / protein-containing complex / ATP binding / 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) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase fused / Suppressor of fused homolog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsHua, L. / Geng, W.
CitationJournal: To Be Published
Title: Structure of the Sufu-Fu complex at 1.9 Angstroms resolution.
Authors: Hua, L.
History
DepositionJan 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Suppressor of fused homolog
B: Serine/threonine-protein kinase fused


Theoretical massNumber of molelcules
Total (without water)32,3322
Polymers32,3322
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-10 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.145, 68.423, 56.144
Angle α, β, γ (deg.)90.000, 97.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Suppressor of fused homolog


Mass: 29311.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Su(fu) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VG38
#2: Protein/peptide Serine/threonine-protein kinase fused


Mass: 3021.368 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: fu / Production host: Escherichia coli (E. coli)
References: UniProt: P23647, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.16 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1% w/v Tryptone, 0.05M HEPES sodium pH7.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.91878 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91878 Å / Relative weight: 1
ReflectionResolution: 1.91→55.67 Å / Num. obs: 20919 / % possible obs: 99.7 % / Redundancy: 7.5 % / CC1/2: 0.893 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.3
Reflection shellResolution: 1.91→1.98 Å / Rmerge(I) obs: 0.639 / Num. unique obs: 20919 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMD
Resolution: 1.91→55.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.234 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.148
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 1056 5.2 %RANDOM
Rwork0.1476 ---
obs0.1513 19445 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.07 Å2 / Biso mean: 24.615 Å2 / Biso min: 8.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å2-0.98 Å2
2---0.33 Å20 Å2
3----1.27 Å2
Refinement stepCycle: final / Resolution: 1.91→55.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 0 145 2278
Biso mean---34.4 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022188
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9472983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3765270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.3624.955111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.215338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9341512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211726
X-RAY DIFFRACTIONr_rigid_bond_restr3.92532188
X-RAY DIFFRACTIONr_sphericity_free32.853542
X-RAY DIFFRACTIONr_sphericity_bonded17.50952236
LS refinement shellResolution: 1.913→1.963 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 52 -
Rwork0.153 1090 -
all-1142 -
obs--75.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.03150.0116-0.00950.05950.00750.1397-0.0006-0.001-0.004-0.0047-0.00370.0001-0.00460.0010.00430.00460.00050.00540.0193-0.00090.03350.847-14.69-21.808
21.99710.38960.35860.21380.36050.67720.038-0.1714-0.1150.022-0.0105-0.02470.03710.0231-0.02750.00680.00360.00080.02960.00260.037110.577-18.262-3.1
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 256
2X-RAY DIFFRACTION2B361 - 388

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