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- PDB-4km9: Crystal structure of human Suppressor of Fused -

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Basic information

Entry
Database: PDB / ID: 4km9
TitleCrystal structure of human Suppressor of Fused
ComponentsSuppressor of fused homolog
KeywordsPROTEIN BINDING / Suppressor of 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 / Hedgehog 'off' state / aorta development / ventricular septum development / ciliary base ...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 / Hedgehog 'off' state / aorta development / ventricular septum development / ciliary base / skin development / negative regulation of protein import into nucleus / heart looping / spermatid development / negative regulation of osteoblast differentiation / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of smoothened signaling pathway / 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 / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription corepressor activity / 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
Sufu, C-terminal domain / 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) / Gyrase A; domain 2 ...Sufu, C-terminal domain / 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) / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Suppressor of fused homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.19 Å
AuthorsZhang, Y. / Qi, X. / Zhang, Z. / Wu, G.
CitationJournal: Nat Commun / Year: 2013
Title: Structural insight into the mutual recognition and regulation between Suppressor of Fused and Gli/Ci.
Authors: Zhang, Y. / Fu, L. / Qi, X. / Zhang, Z. / Xia, Y. / Jia, J. / Jiang, J. / Zhao, Y. / Wu, G.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Experimental preparation
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Suppressor of fused homolog


Theoretical massNumber of molelcules
Total (without water)54,4511
Polymers54,4511
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.875, 120.940, 117.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

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Components

#1: Protein Suppressor of fused homolog / SUFUH


Mass: 54451.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUFU, UNQ650/PRO1280 / Cell (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UMX1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.41 Å3/Da / Density % sol: 49 % / Mosaicity: 0.836 °
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2M Potassium chloride, vapor diffusion, hanging drop, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorDetector: CCD / Date: May 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.19→63.04 Å / Num. obs: 8956 / % possible obs: 99.1 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.127 / Χ2: 1.002 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.318.60.4928641.0081100
3.31-3.458.80.398881.0061100
3.45-3.68.90.2838901.0041100
3.6-3.798.80.228851.0011100
3.79-4.038.70.1698890.9981100
4.03-4.348.60.1239110.993199.7
4.34-4.788.20.0978881.005199.2
4.78-5.478.20.1079011198.4
5.47-6.898.10.1019101199.7
6.89-507.20.1039301.005194.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KM8

4km8


Resolution: 3.19→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.849 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 59.121 / SU ML: 0.471 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.589 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3053 426 4.8 %RANDOM
Rwork0.2434 ---
obs0.2462 8939 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 120.57 Å2 / Biso mean: 109.491 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--3.58 Å20 Å2
3----3.71 Å2
Refinement stepCycle: LAST / Resolution: 3.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 0 7 2988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223063
X-RAY DIFFRACTIONr_angle_refined_deg0.971.9484173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.925379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54823.551138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68215469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0541518
X-RAY DIFFRACTIONr_chiral_restr0.0640.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212372
X-RAY DIFFRACTIONr_mcbond_it1.0081.51902
X-RAY DIFFRACTIONr_mcangle_it1.49423057
X-RAY DIFFRACTIONr_scbond_it0.36731161
X-RAY DIFFRACTIONr_scangle_it0.6694.51116
LS refinement shellResolution: 3.193→3.276 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 29 -
Rwork0.262 571 -
all-600 -
obs--95.39 %
Refinement TLS params.Method: refined / Origin x: -24.446 Å / Origin y: -15.776 Å / Origin z: -5.631 Å
111213212223313233
T0.2784 Å20.0403 Å20.0684 Å2-0.0306 Å2-0.0056 Å2--0.0334 Å2
L0.8689 °2-0.1928 °2-0.7737 °2-0.8016 °2-0.0039 °2--4.8377 °2
S-0.1376 Å °0.0399 Å °-0.0416 Å °0.1023 Å °-0.0567 Å °0.0054 Å °0.5009 Å °0.2534 Å °0.1943 Å °

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