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- PDB-4bl8: Crystal structure of full-length human Suppressor of fused (SUFU) -

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Entry
Database: PDB / ID: 4bl8
TitleCrystal structure of full-length human Suppressor of fused (SUFU)
ComponentsMALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
KeywordsSIGNALING PROTEIN / SUGAR BINDING PROTEIN-SIGNALING PROTEIN COMPLEX / CHIMERA / FUSION / HEDGEHOG GENE REGULATION / SIGNAL TRANSDUCTION / GLI / TRANSCRIPTION FACTOR
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 / skin 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 / aorta development / ventricular septum development / skin development / ciliary base / negative regulation of protein import into nucleus / detection of maltose stimulus / maltose transport complex / heart looping / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / spermatid development / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of osteoblast differentiation / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / 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 / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / membrane / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Suppressor of fused homolog
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsKarlstrom, M. / Finta, C. / Cherry, A.L. / Toftgard, R. / Jovine, L.
Citation
#1: Journal: Nat.Cell Biol. / Year: 1999
Title: Mammalian Suppressor-of-Fused Modulates Nuclear-Cytoplasmic Shuttling of GLI-1.
Authors: Kogerman, P. / Grimm, T. / Kogerman, L. / Krause, D. / Unden, A.B. / Sandstedt, B. / Toftgard, R. / Zaphiropoulos, P.G.
#2: Journal: J.Biol.Chem. / Year: 2003
Title: Characterization of the Physical Interaction of GLI Proteins with Sufu Proteins.
Authors: Dunaeva, M. / Michelson, P. / Kogerman, P. / Toftgard, R.
#3: Journal: 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.
#4: Journal: Dev.Cell / Year: 2006
Title: Genetic Elimination of Suppressor of Fused Reveals an Essential Repressor Function in the Mammalian Hedgehog Signaling Pathway.
Authors: Svard, J. / Heby-Henricson, K. / Persson-Lek, M. / Rozell, B. / Lauth, M. / Bergstrom, A. / Ericson, J. / Toftgard, R. / Teglund, S.
History
DepositionMay 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
B: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,6694
Polymers184,9842
Non-polymers6852
Water0
1
A: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8342
Polymers92,4921
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8342
Polymers92,4921
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.320, 99.550, 192.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG


Mass: 92492.172 Da / Num. of mol.: 2
Fragment: MBPP RESIDUES 29-387,SUFUH RESIDUES 32-278,361-483
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli), (gene. exp.) HOMO SAPIENS (human)
Plasmid: PLJMBP4C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): JM109(DE3) / References: UniProt: P0AEX9, UniProt: Q9UMX1
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
Sequence detailsRESIDUES 372-748 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32-483.

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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: 2.53 Å3/Da / Density % sol: 51.47 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.6
Details: PROTEIN (12 MG/ML IN 10 MM TRIS-HCL PH 7.5, 50 MM NACL, 1 MM DTT, 1 MM MALTOSE) WAS CRYSTALLISED AT 4OC BY HANGING DROP VAPOUR DIFFUSION WITH 0.2 M K/NA TARTRATE, 0.1 M BIS-TRIS PROPANE PH 8. ...Details: PROTEIN (12 MG/ML IN 10 MM TRIS-HCL PH 7.5, 50 MM NACL, 1 MM DTT, 1 MM MALTOSE) WAS CRYSTALLISED AT 4OC BY HANGING DROP VAPOUR DIFFUSION WITH 0.2 M K/NA TARTRATE, 0.1 M BIS-TRIS PROPANE PH 8.5 AND 16% (V/V) PEG 3350 (AT A PROTEIN:MOTHER LIQUOR RATIO OF 2:1)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.04→49.78 Å / Num. obs: 36846 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 90.064 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17
Reflection shellResolution: 3.04→3.2 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3D4G AND 1M1L

3d4g

1m1l


Resolution: 3.04→48.666 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 26.36 / Stereochemistry target values: ML
Details: RESIDUES 372-748 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32-483. THEREFORE, TO OBTAIN THE CORRECT NUMBERING, 340 SHOULD BE SUBTRACTED FROM RESIDUE NUMBERS.
RfactorNum. reflection% reflection
Rfree0.2465 2198 6 %
Rwork0.2002 --
obs0.2029 36780 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.608 Å2
Refinement stepCycle: LAST / Resolution: 3.04→48.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11449 0 46 0 11495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611800
X-RAY DIFFRACTIONf_angle_d0.916050
X-RAY DIFFRACTIONf_dihedral_angle_d13.3864303
X-RAY DIFFRACTIONf_chiral_restr0.0551742
X-RAY DIFFRACTIONf_plane_restr0.0042083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.10610.4061230.34772139X-RAY DIFFRACTION100
3.1061-3.17830.35441360.29892106X-RAY DIFFRACTION100
3.1783-3.25780.3541480.28242126X-RAY DIFFRACTION100
3.2578-3.34590.31041360.27572136X-RAY DIFFRACTION100
3.3459-3.44430.31981360.24752125X-RAY DIFFRACTION100
3.4443-3.55540.31181250.23082168X-RAY DIFFRACTION100
3.5554-3.68250.25731330.21862137X-RAY DIFFRACTION100
3.6825-3.82990.27641390.20922136X-RAY DIFFRACTION100
3.8299-4.00410.24711400.20942137X-RAY DIFFRACTION100
4.0041-4.21510.24411470.19152139X-RAY DIFFRACTION100
4.2151-4.4790.21211340.17062174X-RAY DIFFRACTION100
4.479-4.82450.20241410.15512168X-RAY DIFFRACTION100
4.8245-5.30950.19281440.15992163X-RAY DIFFRACTION100
5.3095-6.07660.23211290.18852206X-RAY DIFFRACTION100
6.0766-7.6510.23811450.20142215X-RAY DIFFRACTION100
7.651-48.66620.22981420.18692307X-RAY DIFFRACTION99
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)
12.9369-0.85350.53072.71721.17313.45820.0814-0.07270.06570.34970.0332-0.12560.1268-0.029900.6089-0.0423-0.02060.45590.00570.67161.3155-12.158257.6394
25.53171.70160.63193.4578-0.15141.79950.05740.17320.1035-0.0911-0.01560.1210.1733-0.1637-00.5848-0.0443-0.00420.59710.02420.464429.2383-21.234537.2333
33.40830.2862-0.53432.65510.17113.71420.12230.2074-0.0637-0.4437-0.0520.8186-0.3138-0.335-00.7735-0.01-0.26270.7854-0.10870.8812-4.3294-19.722819.4932
43.3162-1.6586-0.33496.85370.83382.4981-0.2503-0.87920.2852-0.42910.5335-0.9197-0.10621.06480.020.87480.11570.08931.2936-0.15820.845710.9265-21.086466.9225
58.7546-1.1624-0.32392.1047-0.31881.29970.9752-1.01870.8670.3923-0.49090.3113-0.27260.02940.00541.2536-0.1840.29340.8117-0.12370.9387-19.645-39.73583.0535
64.24390.353-0.2113.75440.07162.9750.18430.18120.109-0.0171-0.20830.6778-0.0787-0.498800.81590.00560.2120.93550.01440.7887-52.9937-57.246786.64
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND (RESID 5:371 OR RESID 900))
2X-RAY DIFFRACTION2(CHAIN A AND RESID 372:605)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 606:818)
4X-RAY DIFFRACTION4(CHAIN B AND (RESID 1:371 OR RESID 900))
5X-RAY DIFFRACTION5(CHAIN B AND RESID 372:605)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 606:820)

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