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

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Basic information

Entry
Database: PDB / ID: 4c4m
TitleCrystal structure of the Sonic Hedgehog-chondroitin-4-sulphate complex
ComponentsSONIC HEDGEHOG PROTEIN
KeywordsSIGNALING PROTEIN / HEDGEHOG SIGNALLING / MORPHOGENS / HEPARAN SULPHATE PROTEOGLYCANS / GLYCOSAMINOGLYCANS
Function / homology
Function and homology information


positive regulation of skeletal muscle cell proliferation / lateral motor column neuron differentiation / forebrain regionalization / cell proliferation in external granule layer / zona limitans intrathalamica formation / respiratory tube development / positive regulation of neurotrophin production / positive regulation of photoreceptor cell differentiation / right lung development / left lung development ...positive regulation of skeletal muscle cell proliferation / lateral motor column neuron differentiation / forebrain regionalization / cell proliferation in external granule layer / zona limitans intrathalamica formation / respiratory tube development / positive regulation of neurotrophin production / positive regulation of photoreceptor cell differentiation / right lung development / left lung development / primary prostatic bud elongation / mesenchymal-epithelial cell signaling / : / mesenchymal smoothened signaling pathway involved in prostate gland development / fungiform papilla development / tracheoesophageal septum formation / Release of Hh-Np from the secreting cell / digestive tract mesoderm development / fungiform papilla morphogenesis / striated muscle tissue development / ventral spinal cord interneuron specification / formation of anatomical boundary / bud outgrowth involved in lung branching / negative regulation of mesenchymal cell apoptotic process / hindgut morphogenesis / mesenchymal cell proliferation / positive regulation of cerebellar granule cell precursor proliferation / Ligand-receptor interactions / negative regulation of alpha-beta T cell differentiation / animal organ formation / regulation of prostatic bud formation / tongue morphogenesis / male genitalia morphogenesis / positive regulation of striated muscle cell differentiation / regulation of epithelial cell proliferation involved in prostate gland development / trachea morphogenesis / salivary gland cavitation / Activation of SMO / telencephalon regionalization / digestive tract morphogenesis / positive regulation of epithelial cell proliferation involved in prostate gland development / alpha-tubulin acetylation / anatomical structure formation involved in morphogenesis / trachea development / ectoderm development / dorsal/ventral neural tube patterning / positive regulation of sclerotome development / negative regulation of ureter smooth muscle cell differentiation / positive regulation of ureter smooth muscle cell differentiation / negative regulation of kidney smooth muscle cell differentiation / positive regulation of kidney smooth muscle cell differentiation / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / embryonic foregut morphogenesis / cerebellar granule cell precursor proliferation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / epithelial-mesenchymal cell signaling / polarity specification of anterior/posterior axis / spinal cord motor neuron differentiation / lung epithelium development / neural tube formation / spinal cord dorsal/ventral patterning / positive regulation of penile erection / metanephric mesenchymal cell proliferation involved in metanephros development / neuron fate specification / cholesterol-protein transferase activity / positive regulation of oligodendrocyte progenitor proliferation / epithelial tube branching involved in lung morphogenesis / negative thymic T cell selection / vasculogenesis involved in coronary vascular morphogenesis / laminin-1 binding / prostate epithelial cord elongation / myotube differentiation / positive regulation of T cell differentiation in thymus / stem cell development / lung lobe morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / negative regulation of T cell differentiation in thymus / tongue development / determination of left/right asymmetry in lateral mesoderm / negative regulation of cholesterol efflux / lymphoid progenitor cell differentiation / embryonic skeletal system development / branching involved in salivary gland morphogenesis / mesenchymal cell proliferation involved in lung development / lung-associated mesenchyme development / Hedgehog ligand biogenesis / intermediate filament organization / metanephric collecting duct development / embryonic hindlimb morphogenesis / cell development / limb bud formation / fungiform papilla formation / positive regulation of skeletal muscle tissue development / embryonic forelimb morphogenesis / embryonic digestive tract morphogenesis / somite development / prostate gland development / male genitalia development / Bergmann glial cell differentiation
Similarity search - Function
Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal ...Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Sonic hedgehog protein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
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.
History
DepositionSep 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _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_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: SONIC HEDGEHOG PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9096
Polymers18,7681
Non-polymers1,1415
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
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-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein SONIC HEDGEHOG PROTEIN / SHH / HHG-1


Mass: 18768.016 Da / Num. of mol.: 1 / Fragment: N-TEMINAL SIGNALLING DOMAIN, RESIDUES 40-195
Source method: isolated from a genetically manipulated source
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
#2: Polysaccharide beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta- ...beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 936.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAb1-3DGalpNAc[4S]b1-4DGlcpAb1-3DGalpNAc[4S]b1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2112h-1b_1-5_2*NCC/3=O_4*OSO/3=O/3=O][a2122A-1b_1-5]/1-2-1-2/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc4SO3]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][b-D-4-deoxy-GlcpA]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 133 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % 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 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorDate: Jul 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.74→43.8 Å / Num. obs: 17037 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 17.84 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.3
Reflection shellResolution: 1.74→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→43.828 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1934 861 5.1 %
Rwork0.1602 --
obs0.1618 16992 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→43.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 67 129 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
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.8490.27781500.20052608X-RAY DIFFRACTION100
1.849-1.99180.21861480.17582647X-RAY DIFFRACTION100
1.9918-2.19220.19561290.15622665X-RAY DIFFRACTION100
2.1922-2.50940.18311650.15742665X-RAY DIFFRACTION100
2.5094-3.16150.20251350.17482699X-RAY DIFFRACTION100
3.1615-43.84150.17091340.14472847X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.7888 Å / Origin y: -3.2345 Å / Origin z: -13.019 Å
111213212223313233
T0.0505 Å2-0.0033 Å20.001 Å2-0.0465 Å20.0113 Å2--0.0539 Å2
L0.6269 °2-0.2437 °20.0228 °2-0.6131 °2-0.4125 °2--0.8462 °2
S-0.0113 Å °0.016 Å °-0.0071 Å °-0.0126 Å °-0.0649 Å °-0.1002 Å °0.0253 Å °0.042 Å °-0.2067 Å °
Refinement TLS groupSelection details: ALL

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