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- PDB-3mxw: Crystal structure Sonic hedgehog bound to the 5E1 fab fragment -

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Basic information

Entry
Database: PDB / ID: 3mxw
TitleCrystal structure Sonic hedgehog bound to the 5E1 fab fragment
Components
  • 5E1 heavy chain
  • 5E1 light chain
  • Sonic hedgehog protein
KeywordsSIGNALING PROTEIN / antibody complex / fab fragment / metalloprotease / calcium binding / zinc hydrolase / development / morphogen
Function / homology
Function and homology information


Formation of lateral plate mesoderm / positive regulation of skeletal muscle cell proliferation / 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 ...Formation of lateral plate mesoderm / positive regulation of skeletal muscle cell proliferation / 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 / morphogen activity / 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 / formation of anatomical boundary / lung epithelium development / positive regulation of striated muscle cell differentiation / ventral midline development / trachea morphogenesis / cholesterol-protein transferase activity / bud outgrowth involved in lung branching / HHAT G278V doesn't palmitoylate Hh-Np / telencephalon regionalization / epithelial-mesenchymal cell signaling / laminin-1 binding / Ligand-receptor interactions / 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 / positive regulation of cerebellar granule cell precursor proliferation / cell development / negative regulation of T cell differentiation in thymus / spinal cord motor neuron differentiation / positive regulation of T cell differentiation in thymus / cerebellar granule cell precursor proliferation / intermediate filament organization / mesenchymal cell apoptotic process / embryonic skeletal system development / limb bud formation / lung lobe morphogenesis / prostate gland development / Activation of SMO / skeletal muscle fiber differentiation / establishment of epithelial cell polarity / patched binding / thalamus development / embryonic digestive tract morphogenesis / embryonic foregut morphogenesis / somite development / 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 / 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 / positive regulation of immature T cell proliferation in thymus / lymphoid progenitor cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / smooth muscle tissue development / regulation of stem cell proliferation / pattern specification process / male genitalia development / oligodendrocyte development / artery development / positive regulation of astrocyte differentiation / epithelial cell proliferation involved in prostate gland development / self proteolysis / branching involved in salivary gland morphogenesis / positive regulation of epithelial cell proliferation involved in prostate gland development / embryonic pattern specification / Release of Hh-Np from the secreting cell / lung-associated mesenchyme development / Formation of axial mesoderm / dopaminergic neuron differentiation / regulation of proteolysis / positive thymic T cell selection / metanephros development / intein-mediated protein splicing / glycosaminoglycan binding / metanephric collecting duct development / camera-type eye development / positive regulation of smoothened signaling pathway
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sonic hedgehog protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsHymowitz, S.G. / Maun, H.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Hedgehog pathway antagonist 5E1 binds hedgehog at the pseudo-active site.
Authors: Maun, H.R. / Wen, X. / Lingel, A. / de Sauvage, F.J. / Lazarus, R.A. / Scales, S.J. / Hymowitz, S.G.
History
DepositionMay 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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_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_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_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
L: 5E1 light chain
H: 5E1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8809
Polymers66,4463
Non-polymers4346
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-112 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.306, 90.544, 111.672
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 , 1 types, 1 molecules A

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


Mass: 19122.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHH / Plasmid: PET101/D-TOPO (INVITROGEN) WITH T7 promoter / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta 2 / References: UniProt: Q15465

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Antibody , 2 types, 2 molecules LH

#2: Antibody 5E1 light chain


Mass: 23507.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody 5E1 heavy chain


Mass: 23816.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 429 molecules

#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: protein solution (20 mM Hepes, pH 7.2, 0.1 M NaCl, 5 mM CaCl2) was mixed with equal volume of well solution (0.2 M lithium sulfate, 100 mM Hepes, pH 7.5, and 22% w/v PEG 4000), VAPOR ...Details: protein solution (20 mM Hepes, pH 7.2, 0.1 M NaCl, 5 mM CaCl2) was mixed with equal volume of well solution (0.2 M lithium sulfate, 100 mM Hepes, pH 7.5, and 22% w/v PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 28, 2009 / Details: Single crystal, cylindrically bent, Si(220)
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 54683 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.068 / Net I/σ(I): 16.4
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4917 / Rsym value: 0.464 / % possible all: 90.7

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VHH, refined fab

1vhh


Resolution: 1.83→47.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.323 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21844 5441 10.1 %RANDOM
Rwork0.17639 ---
all0.18056 ---
obs0.18056 54255 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.797 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2--0.54 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.83→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4537 0 18 423 4978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224708
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9516389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74324.554202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53815772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8951520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023553
X-RAY DIFFRACTIONr_nbd_refined0.1960.22029
X-RAY DIFFRACTIONr_nbtor_refined0.30.23175
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2408
X-RAY DIFFRACTIONr_metal_ion_refined0.150.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3620.225
X-RAY DIFFRACTIONr_mcbond_it2.5962.53035
X-RAY DIFFRACTIONr_mcangle_it3.4654752
X-RAY DIFFRACTIONr_scbond_it3.0632.51945
X-RAY DIFFRACTIONr_scangle_it4.44651630
LS refinement shellResolution: 1.83→1.868 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.338 269 -
Rwork0.246 2548 -
obs--87.84 %
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)
10.61290.06670.16831.1798-0.0411.93870.0018-0.0258-0.05470.08880.01760.0564-0.0582-0.1463-0.0194-0.08850.0076-0.0083-0.03410.0099-0.085-15.2285-20.122327.7473
20.6747-0.1009-0.24430.9126-0.06770.9875-0.00040.1492-0.0604-0.1818-0.0341-0.01530.0127-0.06980.0345-0.0948-0.0061-0.0112-0.0339-0.0317-0.0689-11.8841-24.7752-5.6774
32.2798-0.244-0.22112.4476-0.54941.44230.0077-0.01670.03840.0704-0.1018-0.3257-0.11180.10310.094-0.124-0.0096-0.0231-0.09760.046-0.0793-0.643-13.896750.9946
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION1H1 - 110
3X-RAY DIFFRACTION2L108 - 212
4X-RAY DIFFRACTION2H111 - 214
5X-RAY DIFFRACTION3A39 - 191

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