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- PDB-4c4m: Crystal structure of the Sonic Hedgehog-chondroitin-4-sulphate complex -

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Entry
Database: PDB / ID: 4c4m
TitleCrystal structure of the Sonic Hedgehog-chondroitin-4-sulphate complex
ComponentsSONIC HEDGEHOG PROTEINSonic hedgehog
KeywordsSIGNALING PROTEIN / HEDGEHOG SIGNALLING / MORPHOGENS / HEPARAN SULPHATE PROTEOGLYCANS / GLYCOSAMINOGLYCANS
Function / homologyHint domain N-terminal / Activation of SMO / Ligand-receptor interactions / Release of Hh-Np from the secreting cell / Hedgehog ligand biogenesis / Intein N-terminal splicing motif profile. / Hedgehog amino-terminal signalling domain / Hedgehog, N-terminal signalling domain / Intein N-terminal splicing region / Hedgehog protein ...Hint domain N-terminal / Activation of SMO / Ligand-receptor interactions / Release of Hh-Np from the secreting cell / Hedgehog ligand biogenesis / Intein N-terminal splicing motif profile. / Hedgehog amino-terminal signalling domain / Hedgehog, N-terminal signalling domain / Intein N-terminal splicing region / Hedgehog protein / Hint module / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hedgehog protein, Hint domain / Hint domain C-terminal / Hint domain superfamily / positive regulation of neurotrophin production / forebrain regionalization / zona limitans intrathalamica formation / fungiform papilla development / cell proliferation in external granule layer / positive regulation of photoreceptor cell differentiation / tongue morphogenesis / fungiform papilla morphogenesis / digestive tract mesoderm development / ventral spinal cord interneuron specification / mesenchymal cell proliferation / respiratory tube development / right lung development / positive regulation of skeletal muscle cell proliferation / positive regulation of sclerotome development / mesenchymal smoothened signaling pathway involved in prostate gland development / regulation of mesenchymal cell proliferation involved in prostate gland development / negative regulation of kidney smooth muscle cell differentiation / epithelial-mesenchymal cell signaling / primary prostatic bud elongation / epithelial-mesenchymal signaling involved in prostate gland development / tracheoesophageal septum formation / negative regulation of ureter smooth muscle cell differentiation / positive regulation of ureter smooth muscle cell differentiation / left lung development / positive regulation of kidney smooth muscle cell differentiation / regulation of prostatic bud formation / positive regulation of mesenchymal cell proliferation involved in ureter development / regulation of odontogenesis / spinal cord dorsal/ventral patterning / trachea development / polarity specification of anterior/posterior axis / hindgut morphogenesis / cerebellar granule cell precursor proliferation / striated muscle tissue development / positive regulation of oligodendrocyte progenitor proliferation / bud outgrowth involved in lung branching / positive regulation of cerebellar granule cell precursor proliferation / positive regulation of immature T cell proliferation in thymus / metanephric mesenchymal cell proliferation involved in metanephros development / positive regulation of striated muscle cell differentiation / positive regulation of penile erection / positive regulation of hh target transcription factor activity / negative regulation of alpha-beta T cell differentiation / determination of left/right asymmetry in lateral mesoderm / artery development / lung epithelium development / formation of anatomical boundary / smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation / trachea morphogenesis / telencephalon regionalization / neural tube formation / spinal cord motor neuron differentiation / laminin-1 binding / stem cell development / regulation of epithelial cell proliferation involved in prostate gland development / negative regulation of mesenchymal cell apoptotic process / myotube differentiation / salivary gland cavitation / intermediate filament organization / vasculogenesis involved in coronary vascular morphogenesis / fungiform papilla formation / positive regulation of T cell differentiation in thymus / negative regulation of cholesterol efflux / neuroblast proliferation / dorsal/ventral neural tube patterning / patched binding / embryonic morphogenesis / somite development / anatomical structure formation involved in morphogenesis / negative regulation of transcription elongation from RNA polymerase II promoter / lymphoid progenitor cell differentiation / embryonic digestive tract morphogenesis / embryonic foregut morphogenesis / branching involved in prostate gland morphogenesis / lung lobe morphogenesis / limb bud formation / epithelial cell proliferation involved in salivary gland morphogenesis / embryonic skeletal system development / negative thymic T cell selection / hindbrain development / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / thalamus development / dorsal/ventral pattern formation / mesenchymal cell proliferation involved in lung development
Function and homology information
Specimen sourceMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.74 Å resolution
AuthorsWhalen, D.M. / Malinauskas, T. / Gilbert, R.J.C. / Siebold, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural Insights Into Proteoglycan-Shaped Hedgehog Signaling.
Authors: Whalen, D.M. / Malinauskas, T. / Gilbert, R.J.C. / Siebold, C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 5, 2013 / Release: Oct 2, 2013
RevisionDateData content typeGroupProviderType
1.0Oct 2, 2013Structure modelrepositoryInitial release
1.1Oct 9, 2013Structure modelDatabase references
1.2Oct 30, 2013Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SONIC HEDGEHOG PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9639
Polyers18,7681
Non-polymers1,1958
Water2,324129
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)40.350, 55.660, 71.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide SONIC HEDGEHOG PROTEIN / Sonic hedgehog / SHH / HHG-1


Mass: 18768.016 Da / Num. of mol.: 1 / Fragment: N-TEMINAL SIGNALLING DOMAIN, RESIDUES 40-195 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q62226

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Non-polymers , 6 types, 137 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#4: Chemical ChemComp-ASG / 2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE


Mass: 301.271 Da / Num. of mol.: 2 / Formula: C8H15NO9S
#5: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 2 / Formula: C6H10O7 / Glucuronic acid
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Formula: C2H3O2 / Acetate
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Formula: H2O / Water

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Details

Nonpolymer detailsBETA-D-GLUCOPYRANURONIC ACID (BDP): THE OLIGOSACCHARIDE CHAIN BDP-ASG IS CONTINUOUS RUNNING THROUGH ...BETA-D-GLUCOPYRANURONIC ACID (BDP): THE OLIGOSACCHARIDE CHAIN BDP-ASG IS CONTINUOUS RUNNING THROUGH SEVERAL UNIT CELLS.
Sequence detailsCONSTRUCT CONTAINS TWO ADDITIONAL N-TERMINAL RESIDUES (MA) AND 6 ADDITIONAL C-TERMINAL RESIDUES (HHHHHH)

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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: 2.13 / Density percent sol: 42.17 % / Description: NONE
Crystal growpH: 7.5 / Details: 25% (W/V) PEG 3350, 100 MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: DIAMOND BEAMLINE I03 / Synchrotron site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorCollection date: Jul 8, 2012
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 17.84 Å2 / D resolution high: 1.74 Å / D resolution low: 43.8 Å / Number obs: 17037 / Observed criterion sigma I: 0 / Rmerge I obs: 0.08 / NetI over sigmaI: 15.3 / Redundancy: 6.9 % / Percent possible obs: 99.9
Reflection shellRmerge I obs: 0.7 / Highest resolution: 1.74 Å / Lowest resolution: 1.79 Å / MeanI over sigI obs: 2.7 / Redundancy: 7 % / Percent possible all: 1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.18 / Sigma F: 1.35 / Overall phase error: 18.04 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.1934 / R factor R work: 0.1602 / R factor obs: 0.1618 / Highest resolution: 1.74 Å / Lowest resolution: 43.828 Å / Number reflection R free: 861 / Number reflection obs: 16992 / Percent reflection R free: 5.1 / Percent reflection obs: 99.88
Refine hist #LASTHighest resolution: 1.74 Å / Lowest resolution: 43.828 Å
Number of atoms included #LASTProtein: 1228 / Nucleic acid: 0 / Ligand: 67 / Solvent: 129 / Total: 1424
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061320
X-RAY DIFFRACTIONf_angle_d1.1181792
X-RAY DIFFRACTIONf_dihedral_angle_d20.064512
X-RAY DIFFRACTIONf_chiral_restr0.076196
X-RAY DIFFRACTIONf_plane_restr0.004232
Refine LS shell

Refine ID: X-RAY DIFFRACTION / Percent reflection obs: 1

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R work
1.74000.27780.20051.84901502608
1.84900.21860.17581.99181482647
1.99180.19560.15622.19221292665
2.19220.18310.15742.50941652665
2.50940.20250.17483.16151352699
3.16150.17090.144743.84151342847
Refine TLSMethod: refined / L11: 0.6269 deg.2 / L12: -0.2437 deg.2 / L13: 0.0228 deg.2 / L22: 0.6131 deg.2 / L23: -0.4125 deg.2 / L33: 0.8462 deg.2 / S11: -0.0113 Å deg. / S12: 0.016 Å deg. / S13: -0.0071 Å deg. / S21: -0.0126 Å deg. / S22: -0.0649 Å deg. / S23: -0.1002 Å deg. / S31: 0.0253 Å deg. / S32: 0.042 Å deg. / S33: -0.2067 Å deg. / T11: 0.0505 Å2 / T12: -0.0033 Å2 / T13: 0.001 Å2 / T22: 0.0465 Å2 / T23: 0.0113 Å2 / T33: 0.0539 Å2 / Origin x: 8.7888 Å / Origin y: -3.2345 Å / Origin z: -13.019 Å
Refine TLS groupSelection details: ALL

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