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- PDB-1vhh: A POTENTIAL CATALYTIC SITE WITHIN THE AMINO-TERMINAL SIGNALLING D... -

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Basic information

Entry
Database: PDB / ID: 1vhh
TitleA POTENTIAL CATALYTIC SITE WITHIN THE AMINO-TERMINAL SIGNALLING DOMAIN OF SONIC HEDGEHOG
ComponentsSONIC HEDGEHOG
KeywordsSIGNALLING PROTEIN
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 / epithelial-mesenchymal signaling involved in prostate gland development / fungiform papilla development / Release of Hh-Np from the secreting cell / digestive tract mesoderm 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 / epithelial-mesenchymal signaling involved in prostate gland development / fungiform papilla development / Release of Hh-Np from the secreting cell / digestive tract mesoderm development / fungiform papilla morphogenesis / ventral spinal cord interneuron specification / tongue morphogenesis / respiratory tube development / Ligand-receptor interactions / Activation of SMO / positive regulation of oligodendrocyte progenitor proliferation / trachea development / 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 / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / mesenchymal-epithelial cell signaling involved in prostate gland development / trunk neural crest cell migration / hindgut morphogenesis / polarity specification of anterior/posterior axis / anatomical structure formation involved in 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 / neural tube formation / trachea morphogenesis / cholesterol-protein transferase activity / positive regulation of penile erection / bud outgrowth involved in lung branching / regulation of epithelial cell proliferation involved in prostate gland development / myotube differentiation / telencephalon regionalization / epithelial-mesenchymal cell signaling / laminin-1 binding / limb bud formation / lung lobe morphogenesis / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of cholesterol efflux / Hedgehog ligand biogenesis / salivary gland cavitation / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / determination of left/right asymmetry in lateral mesoderm / embryonic digestive tract morphogenesis / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of T cell differentiation in thymus / epithelial cell proliferation involved in salivary gland morphogenesis / spinal cord motor neuron differentiation / cell development / positive regulation of T cell differentiation in thymus / branching involved in prostate gland morphogenesis / mesenchymal cell proliferation involved in lung development / intermediate filament organization / prostate gland development / cerebellar granule cell precursor proliferation / male genitalia morphogenesis / embryonic skeletal system development / establishment of epithelial cell polarity / skeletal muscle fiber differentiation / mesenchymal cell apoptotic process / fungiform papilla formation / patched binding / somite development / animal organ formation / embryonic foregut morphogenesis / hindbrain development / neuron fate commitment / ectoderm development / positive regulation of skeletal muscle tissue development / stem cell development / thalamus development / negative regulation of dopaminergic neuron differentiation / branching involved in salivary gland morphogenesis / skeletal muscle cell proliferation / lymphoid progenitor cell differentiation / positive regulation of immature T cell proliferation in thymus / dorsal/ventral neural tube patterning / negative thymic T cell selection / mesenchymal cell proliferation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment
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 ...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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sonic hedgehog protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsHall, T.M.T. / Porter, J.A. / Beachy, P.A. / Leahy, D.J.
CitationJournal: Nature / Year: 1995
Title: A potential catalytic site revealed by the 1.7-A crystal structure of the amino-terminal signalling domain of Sonic hedgehog.
Authors: Hall, T.M. / Porter, J.A. / Beachy, P.A. / Leahy, D.J.
History
DepositionOct 3, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7063
Polymers18,5451
Non-polymers1612
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.700, 79.000, 35.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 50

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Components

#1: Protein SONIC HEDGEHOG / HHG-1 / VHH-1


Mass: 18544.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: POTENTIAL / Plasmid: PGEX2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q62226
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Source detailsTHE AMINO-TERMINAL DOMAIN OF MURINE SONIC HEDGEHOG WAS EXPRESSED AS A GLUTATHIONE S-TRANSFERASE ...THE AMINO-TERMINAL DOMAIN OF MURINE SONIC HEDGEHOG WAS EXPRESSED AS A GLUTATHIONE S-TRANSFERASE FUSION PROTEIN USING THE PGEX2T VECTOR. THE FUSION PROTEIN WAS CLEAVED WITH THROMBIN TO RELEASE THE SONIC HEDGEHOG FRAGMENT.

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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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal
*PLUS
Density % sol: 35 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.4 mg/mlprotein1drop
21.4 mMbeta-mercaptoethanol1drop
330 %PEG80001reservoir
40.12 Mammonium sulfate1reservoir
510 mMsodium cacodylate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9686, 0.9792, 0.9793, 0.9879
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 6, 1995
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97921
30.97931
40.98791
ReflectionResolution: 1.7→30 Å / Num. obs: 14968 / % possible obs: 86.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.7→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.261 -5 %
Rwork0.191 --
obs0.191 14783 83.4 %
Displacement parametersBiso mean: 10.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 0 6 360 1926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.968
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.42
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.385
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.42
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.385
X-RAY DIFFRACTIONx_mcbond_it1.51
X-RAY DIFFRACTIONx_scbond_it2.77
X-RAY DIFFRACTIONx_mcangle_it1.56
X-RAY DIFFRACTIONx_scangle_it2.98

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