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Yorodumi- PDB-4blb: Crystal structure of a human Suppressor of fused (SUFU)-GLI1p complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4blb | |||||||||
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Title | Crystal structure of a human Suppressor of fused (SUFU)-GLI1p complex | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / SUGAR BINDING PROTEIN-SIGNALING PROTEIN COMPLEX / CHIMERA / FUSION PROTEIN / HEDGEHOG SIGNALING / GENE REGULATION / TRANSCRIPTION FACTOR | |||||||||
Function / homology | Function and homology information notochord regression / GLI proteins bind promoters of Hh responsive genes to promote transcription / 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 / regulation of hepatocyte proliferation / GLI-SUFU complex / ventral midline development / epidermal cell differentiation / digestive tract morphogenesis ...notochord regression / GLI proteins bind promoters of Hh responsive genes to promote transcription / 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 / regulation of hepatocyte proliferation / GLI-SUFU complex / ventral midline development / epidermal cell differentiation / digestive tract morphogenesis / pituitary gland development / prostate gland development / proximal/distal pattern formation / ciliary tip / positive regulation of cell cycle G1/S phase transition / cerebellar cortex morphogenesis / coronary vasculature development / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / dorsal/ventral pattern formation / aorta development / ventricular septum development / regulation of osteoblast differentiation / skin development / ciliary base / negative regulation of protein import into nucleus / smoothened signaling pathway / negative regulation of osteoblast differentiation / detection of maltose stimulus / positive regulation of DNA replication / maltose transport complex / heart looping / axoneme / carbohydrate transport / carbohydrate transmembrane transporter activity / spermatid development / maltose binding / maltose transport / maltodextrin transmembrane transport / Hedgehog 'off' state / negative regulation of ubiquitin-dependent protein catabolic process / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of smoothened signaling pathway / positive regulation of cardiac muscle cell proliferation / liver regeneration / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / lung development / neural tube closure / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / response to wounding / beta-catenin binding / osteoblast differentiation / transcription corepressor activity / outer membrane-bounded periplasmic space / DNA-binding transcription activator activity, RNA polymerase II-specific / microtubule binding / sequence-specific DNA binding / transcription cis-regulatory region binding / periplasmic space / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / positive regulation of cell population proliferation / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Cherry, A.L. / Finta, C. / Karlstrom, M. / De Sanctis, D. / Toftgard, R. / Jovine, L. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural Basis of Sufu-GLI Interaction in Hedgehog Signalling Regulation Authors: Cherry, A.L. / Finta, C. / Karlstrom, M. / Jin, Q. / Schwend, T. / Astorga-Wells, J. / Zubarev, R.A. / Del Campo, M. / Criswell, A.R. / De Sanctis, D. / Jovine, L. / Toftgard, R. #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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4blb.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4blb.ent.gz | 986 KB | Display | PDB format |
PDBx/mmJSON format | 4blb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4blb_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4blb_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4blb_validation.xml.gz | 93.7 KB | Display | |
Data in CIF | 4blb_validation.cif.gz | 129 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/4blb ftp://data.pdbj.org/pub/pdb/validation_reports/bl/4blb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 83634.141 Da / Num. of mol.: 4 Fragment: MBPP RESIDUES 29-392,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. DELETION OF RESIDUES 454-456. W61D, L62S, G63F, P453A, K457A 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) / References: UniProt: P0AEX9, UniProt: Q9UMX1 #2: Protein/peptide | Mass: 1649.803 Da / Num. of mol.: 4 / Fragment: RESIDUES 332-338 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P08151 #3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose #4: Chemical | ChemComp-ZN / Sequence details | RESIDUES 216 AND 220 OF MALTOSE-BINDING PERIPLASMIC PROTEIN ARE MUTATED TO HISTIDINES. RESIDUES 372- ...RESIDUES 216 AND 220 OF MALTOSE-BINDING PERIPLASMI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.36 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PROTEIN (10 MG/ML IN 10 MM TRIS-HCL PH 7.5, 50 MM NACL, 1 MM DTT, 1 MM MALTOSE) WAS MIXED IN A 1:1 MOLAR RATIO WITH ZN(OAC)2 AND A 1:4 MOLAR RATIO WITH GLI1 PEPTIDE. THE COMPLEX WAS ...Details: PROTEIN (10 MG/ML IN 10 MM TRIS-HCL PH 7.5, 50 MM NACL, 1 MM DTT, 1 MM MALTOSE) WAS MIXED IN A 1:1 MOLAR RATIO WITH ZN(OAC)2 AND A 1:4 MOLAR RATIO WITH GLI1 PEPTIDE. THE COMPLEX WAS CRYSTALLISED BY HANGING DROP VAPOUR DIFFUSION AT 4C WITH 1:1 OR 2:1 DROPS OF PROTEIN:WELL SOLUTION (14-18% (V/V) PEG 3350, AND 0.2 M NA FORMATE) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→62.73 Å / Num. obs: 85233 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 79.984 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.4 / % possible all: 98.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB SUBMISSION 56660 Resolution: 2.8→19.985 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 28.38 / Stereochemistry target values: ML Details: RESIDUES 372-618 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32-278. RESIDUES 619-625 REPRESENT AN ARTIFICIAL LINKER. RESIDUES 626-718 REPRESENT UNIPROT Q9UMX1 RESIDUES 361- ...Details: RESIDUES 372-618 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32-278. RESIDUES 619-625 REPRESENT AN ARTIFICIAL LINKER. RESIDUES 626-718 REPRESENT UNIPROT Q9UMX1 RESIDUES 361-453. RESIDUES 719-745 REPRESENT UNIPROT Q9UMX1 RESIDUES 457-483. THEREFORE, TO OBTAIN THE CORRECT NUMBERING, 340 SHOULD BE SUBTRACTED FROM RESIDUES 372-618, 265 SHOULD BE SUBTRACTED FROM RESIDUES 626-718 AND 262 SHOULD BE SUBTRACTED FROM RESIDUES 719-745.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.384 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.985 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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