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- PDB-4bl9: Crystal structure of full-length human Suppressor of fused (SUFU)... -

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Basic information

Entry
Database: PDB / ID: 4bl9
TitleCrystal structure of full-length human Suppressor of fused (SUFU) mutant lacking a regulatory subdomain (crystal form I)
ComponentsMALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
KeywordsSIGNALING PROTEIN / SUGAR BINDING PROTEIN-SIGNALING PROTEIN COMPLEX / HEDGEHOG GENE REGULATION / SIGNAL TRANSDUCTION / GLI / TRANSCRIPTION FACTOR / CHIMERA / FUSION
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 / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / spermatid development / maltose transport / maltodextrin transmembrane transport / negative regulation of osteoblast differentiation / Hedgehog 'off' state / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of smoothened signaling pathway / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / cytoplasm / cytosol
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: 2.8 Å
AuthorsCherry, A.L. / Finta, C. / Karlstrom, M. / 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 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_validate_close_contact / 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 / _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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
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
C: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
D: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,5888
Polymers336,2194
Non-polymers1,3694
Water00
1
A: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3972
Polymers84,0551
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)84,3972
Polymers84,0551
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3972
Polymers84,0551
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3972
Polymers84,0551
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.430, 103.280, 111.510
Angle α, β, γ (deg.)63.67, 81.13, 76.03
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 84054.734 Da / Num. of mol.: 4
Fragment: MBPP RESIDUES 29-387,SUFUH RESIDUES 32-278,361-483
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DELETION OF RESIDUES 279-360 AND REPLACEMENT WITH PSRGEDP LINKER
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.: 4
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 372-618 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32-278. RESIDUES 619- ...RESIDUES 372-618 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32-278. RESIDUES 619-625 REPRESENT AN ARTIFICIAL LINKER. RESIDUES 626-748 REPRESENT UNIPROT Q9UMX1 RESIDUES 361-483.

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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: 2.79 Å3/Da / Density % sol: 55.89 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PROTEIN (6.5 MG/ML IN 10 MM TRIS-HCL PH 7.5, 50 MM NACL, 1 MM DTT, 1 MM MALTOSE) WAS CRYSTALLISED AT 4C BY HANGING DROP VAPOUR DIFFUSION WITH 0.08 M NA-CACODYLATE (PH 6.6), 20% (V/V) ...Details: PROTEIN (6.5 MG/ML IN 10 MM TRIS-HCL PH 7.5, 50 MM NACL, 1 MM DTT, 1 MM MALTOSE) WAS CRYSTALLISED AT 4C BY HANGING DROP VAPOUR DIFFUSION WITH 0.08 M NA-CACODYLATE (PH 6.6), 20% (V/V) GLYCEROL, 160 MM CA(OAC)2 AND 9% (V/V) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 87954 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 59.163 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2 / % possible all: 98.1

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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 4BL8 AND 1OMP

4bl8

1omp


Resolution: 2.8→29.476 Å / SU ML: 0.36 / σ(F): 1.97 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 2191 2.5 %
Rwork0.2002 --
obs0.2011 87940 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.344 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22691 0 92 0 22783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623390
X-RAY DIFFRACTIONf_angle_d0.8531824
X-RAY DIFFRACTIONf_dihedral_angle_d12.528521
X-RAY DIFFRACTIONf_chiral_restr0.0463459
X-RAY DIFFRACTIONf_plane_restr0.0054128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.86080.38341370.335328X-RAY DIFFRACTION98
2.8608-2.92730.3271310.29525354X-RAY DIFFRACTION98
2.9273-3.00050.34281380.27395311X-RAY DIFFRACTION98
3.0005-3.08150.28571490.26895323X-RAY DIFFRACTION98
3.0815-3.17210.31761310.26735346X-RAY DIFFRACTION98
3.1721-3.27430.29991340.25825353X-RAY DIFFRACTION98
3.2743-3.39120.27271350.23115331X-RAY DIFFRACTION98
3.3912-3.52680.26821190.21995384X-RAY DIFFRACTION99
3.5268-3.6870.27871380.20945364X-RAY DIFFRACTION99
3.687-3.8810.2261340.19355370X-RAY DIFFRACTION99
3.881-4.12350.22451380.18225360X-RAY DIFFRACTION99
4.1235-4.44090.18681470.15715378X-RAY DIFFRACTION99
4.4409-4.8860.17471410.14915383X-RAY DIFFRACTION99
4.886-5.58880.20921340.17235390X-RAY DIFFRACTION99
5.5888-7.02560.23751430.20275386X-RAY DIFFRACTION99
7.0256-29.47730.18131420.17355388X-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)
11.6599-0.5366-0.05011.5803-0.5022.2201-0.076-0.04970.05830.164-0.0623-0.22660.09780.3049-0.00210.35470.03060.00260.47440.10190.4011-54.4532-38.6735-23.8313
23.40260.5889-0.34461.5135-0.07471.8691-0.1967-0.01180.0215-0.0710.1039-0.1604-0.07770.129700.3386-0.0101-0.02660.43670.00450.3384-31.6484-28.071-53.7978
32.10710.074-0.32131.23490.16721.65140.1247-0.0172-0.251-0.2737-0.1147-0.4821-0.00770.1643-00.4901-0.11010.11430.49880.00360.727-4.3877-30.621-80.2709
43.69080.81030.50122.25350.53712.22640.10910.8352-0.2242-0.2441-0.15350.2662-0.04790.02080.00120.7490.1737-0.2120.7428-0.20670.7904-51.9387-84.5921-34.6034
53.02990.70560.15720.37470.01560.38350.27750.3672-0.52540.0843-0.1169-0.08220.14630.166400.73540.1469-0.17180.6109-0.18680.6679-18.4023-81.985-14.8703
61.997-0.65790.78771.4957-0.56931.32630.1728-0.0830.1569-0.2165-0.161-0.264-0.08880.233400.45990.02480.03710.52630.03350.494314.3735-69.18331.2348
71.1192-0.1145-0.0412.0357-0.00511.2844-0.02660.2075-0.0415-0.1767-0.06780.08890.1784-0.0395-00.348-0.0127-0.0010.4107-0.00110.302-1.7591-40.0915-28.0606
83.23170.5604-0.9061.3549-0.10181.54440.0199-0.1827-0.01550.215-0.05570.13820.0497-0.098800.4691-0.03390.06740.27210.01710.3626-18.35-51.209511.3145
91.31920.13-0.24140.83990.06151.41610.381-0.2607-0.2906-0.1654-0.08680.38470.365-0.6520.00010.6128-0.1862-0.09590.67150.07640.6419-45.9343-77.834212.0396
103.1508-0.6133-0.91272.24510.56351.9767-0.4257-0.9786-0.1750.8460.42190.03040.64820.69370.00960.98850.26380.04370.91440.03640.444-5.0955-131.184724.795
113.5711-0.31-1.37971.6946-0.01171.62940.1332-0.17170.466-0.17210.07360.2837-0.03450.00190.00980.6256-0.09150.12610.2806-0.07650.733-39.1125-111.916120.6962
122.6538-0.31230.43951.16560.16081.5060.0554-0.3008-0.29440.2161-0.00120.07480.0486-0.440600.3898-0.0831-0.03860.51880.04730.5634-72.0362-93.870929.7582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:371)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 372:606)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 607:742)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 5:371)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 372:606)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 607:746)
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 3:371)
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 372:606)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 607:742)
10X-RAY DIFFRACTION10CHAIN D AND (RESSEQ 8:371)
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 372:606)
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 607:746)

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