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- PDB-3d1m: Crystal Structure of Sonic Hedgehog Bound to the third FNIII doma... -

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Basic information

Entry
Database: PDB / ID: 3d1m
TitleCrystal Structure of Sonic Hedgehog Bound to the third FNIII domain of CDO
Components
  • Cell adhesion molecule
  • Sonic hedgehog protein
Keywordssignaling protein / cell adhesion / Fibronectin Protein-Protein Complex / Autocatalytic cleavage / Developmental protein / Glycoprotein / Hydrolase / Lipoprotein / Membrane / Palmitate / Protease / Secreted / Immunoglobulin domain / Transmembrane / signaling protein - cell adhesion COMPLEX
Function / homology
Function and homology information


forebrain regionalization / cell proliferation in external granule layer / zona limitans intrathalamica formation / positive regulation of neurotrophin production / positive regulation of photoreceptor cell differentiation / fungiform papilla development / Release of Hh-Np from the secreting cell / digestive tract mesoderm development / epithelial-mesenchymal signaling involved in prostate gland development / fungiform papilla morphogenesis ...forebrain regionalization / cell proliferation in external granule layer / zona limitans intrathalamica formation / positive regulation of neurotrophin production / positive regulation of photoreceptor cell differentiation / fungiform papilla development / Release of Hh-Np from the secreting cell / digestive tract mesoderm development / epithelial-mesenchymal signaling involved in prostate gland development / fungiform papilla morphogenesis / ventral spinal cord interneuron specification / skeletal muscle satellite cell differentiation / tongue morphogenesis / respiratory tube development / Ligand-receptor interactions / Activation of SMO / mesenchymal-epithelial cell signaling involved in prostate gland development / positive regulation of oligodendrocyte progenitor proliferation / embryonic body morphogenesis / embryonic retina morphogenesis in camera-type eye / trachea development / positive regulation of skeletal muscle cell proliferation / anatomical structure formation involved in morphogenesis / right lung development / left lung development / primary prostatic bud elongation / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of sclerotome development / tracheoesophageal septum formation / 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 / polarity specification of anterior/posterior axis / trunk neural crest cell migration / hindgut morphogenesis / striated muscle tissue development / negative regulation of alpha-beta T cell differentiation / regulation of glial cell proliferation / regulation of prostatic bud formation / metanephric mesenchymal cell proliferation involved in metanephros development / positive regulation of penile erection / formation of anatomical boundary / lung epithelium development / positive regulation of striated muscle cell differentiation / neural tube formation / trachea morphogenesis / myotube differentiation / regulation of epithelial cell proliferation involved in prostate gland development / cholesterol-protein transferase activity / bud outgrowth involved in lung branching / telencephalon regionalization / epithelial-mesenchymal cell signaling / laminin-1 binding / Ligand-receptor interactions / vasculogenesis involved in coronary vascular morphogenesis / Hedgehog ligand biogenesis / salivary gland cavitation / negative regulation of cholesterol efflux / determination of left/right asymmetry in lateral mesoderm / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / cell development / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of T cell differentiation in thymus / spinal cord motor neuron differentiation / positive regulation of T cell differentiation in thymus / intermediate filament organization / cerebellar granule cell precursor proliferation / mesenchymal cell apoptotic process / embryonic skeletal system development / male genitalia morphogenesis / limb bud formation / lung lobe morphogenesis / prostate gland development / Activation of SMO / skeletal muscle fiber differentiation / establishment of epithelial cell polarity / fungiform papilla formation / thalamus development / embryonic digestive tract morphogenesis / embryonic foregut morphogenesis / somite development / patched binding / epithelial cell proliferation involved in salivary gland morphogenesis / hindbrain development / positive regulation of skeletal muscle tissue development / animal organ formation / ectoderm development / neuron fate commitment / branching involved in prostate gland morphogenesis / stem cell development / dorsal/ventral neural tube patterning / negative regulation of dopaminergic neuron differentiation / mesenchymal cell proliferation involved in lung development / negative thymic T cell selection / skeletal muscle cell proliferation
Similarity search - Function
Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / 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 / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cell adhesion molecule-related/down-regulated by oncogenes / Sonic hedgehog protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsMcLellan, J.S. / Leahy, D.J.
CitationJournal: Nature / Year: 2008
Title: The mode of Hedgehog binding to Ihog homologues is not conserved across different phyla.
Authors: McLellan, J.S. / Zheng, X. / Hauk, G. / Ghirlando, R. / Beachy, P.A. / Leahy, D.J.
History
DepositionMay 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_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.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sonic hedgehog protein
B: Sonic hedgehog protein
C: Cell adhesion molecule
D: Cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,67410
Polymers61,3824
Non-polymers2916
Water7,386410
1
A: Sonic hedgehog protein
D: Cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8375
Polymers30,6912
Non-polymers1463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sonic hedgehog protein
C: Cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8375
Polymers30,6912
Non-polymers1463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.179, 98.582, 144.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sonic hedgehog protein / SHH / HHG-1 / Sonic hedgehog protein N-product / Sonic hedgehog protein C-product


Mass: 19030.389 Da / Num. of mol.: 2
Fragment: N-terminal Domain, Sonic hedgehog protein N-product, residues 26-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shh, Hhg1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62226
#2: Protein Cell adhesion molecule


Mass: 11660.819 Da / Num. of mol.: 2 / Fragment: Fibronectin type-III domain 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDON, CDO / Production host: Escherichia coli (E. coli) / References: UniProt: Q4KMG0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 28% PEG 3350, 200 mM MgCl2, 100 mM Tris pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97893 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 24, 2007
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 55705 / % possible obs: 99 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.086 / Χ2: 0.942 / Net I/σ(I): 10.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.471 / Num. unique all: 5054 / Χ2: 0.805 / % possible all: 91.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.545 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2693 4.9 %RANDOM
Rwork0.186 ---
obs0.189 55421 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.158 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2---0.87 Å20 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 6 410 4327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214003
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9385412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5924.369206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75915689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3161524
X-RAY DIFFRACTIONr_chiral_restr0.1020.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023094
X-RAY DIFFRACTIONr_nbd_refined0.2110.22014
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22760
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2362
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.217
X-RAY DIFFRACTIONr_mcbond_it0.7991.52469
X-RAY DIFFRACTIONr_mcangle_it1.25123881
X-RAY DIFFRACTIONr_scbond_it2.03131773
X-RAY DIFFRACTIONr_scangle_it2.9854.51531
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 182 -
Rwork0.259 3455 -
all-3637 -
obs--89.36 %
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)
12.4525-0.33690.07641.8413-0.31310.7613-0.01730.2467-0.3038-0.08680.03580.06840.0540.1351-0.0185-0.1622-0.0212-0.0098-0.14-0.0179-0.135851.031-39.49418.529
21.63170.4235-0.19421.91060.06171.0982-0.00280.19640.1183-0.1412-0.0272-0.0423-0.1132-0.15130.03-0.1251-0.0073-0.0291-0.1110.0168-0.137448.59620.67416.238
32.2960.63520.05834.1223-0.36121.8607-0.08470.1753-0.2779-0.160.0077-0.73640.18970.01050.077-0.1523-0.01640.0527-0.1839-0.00630.014559.562-1.07919.163
42.6828-0.5269-0.04912.1534-0.38632.1044-0.05760.39270.2019-0.0220.09310.2157-0.1982-0.0918-0.0355-0.1213-0.0285-0.0394-0.12790.0785-0.072539.118-16.90217.165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 188
2X-RAY DIFFRACTION2B40 - 189
3X-RAY DIFFRACTION3C829 - 924
4X-RAY DIFFRACTION4D826 - 924

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