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- PDB-6pjv: Structure of Human Sonic Hedgehog in complex with Zinc and Magnesium -

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Basic information

Entry
Database: PDB / ID: 6pjv
TitleStructure of Human Sonic Hedgehog in complex with Zinc and Magnesium
ComponentsSonic hedgehog protein
KeywordsSIGNALING PROTEIN / HEDGEHOG PROTEINS / SIGNALING / ZINC IONS / Magnesium ions / AUTOCATALYTIC CLEAVAGE DEVELOPMENTAL / PROTEIN / HOLOPROSENCEPHALY / SECRETED / sonic hedgehog / SHH / SHH-N
Function / homology
Function and homology information


regulation of nodal signaling pathway / 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 / morphogen activity / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / Formation of lateral plate mesoderm ...regulation of nodal signaling pathway / 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 / morphogen activity / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / Formation of lateral plate mesoderm / epithelial-mesenchymal cell signaling / polarity specification of anterior/posterior axis / ventral midline development / metanephric mesenchymal cell proliferation involved in metanephros development / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / Ligand-receptor interactions / laminin-1 binding / determination of left/right asymmetry in lateral mesoderm / negative regulation of cholesterol efflux / positive regulation of T cell differentiation in thymus / cerebellar granule cell precursor proliferation / cell development / prostate gland development / stem cell development / patched binding / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / somite development / hindbrain development / neuron fate commitment / Activation of SMO / pattern specification process / self proteolysis / smooth muscle tissue development / negative thymic T cell selection / negative regulation of dopaminergic neuron differentiation / male genitalia development / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / dopaminergic neuron differentiation / positive regulation of immature T cell proliferation in thymus / lymphoid progenitor cell differentiation / Release of Hh-Np from the secreting cell / glycosaminoglycan binding / embryonic pattern specification / positive regulation of alpha-beta T cell differentiation / Formation of axial mesoderm / positive thymic T cell selection / metanephros development / intein-mediated protein splicing / metanephric collecting duct development / positive regulation of smoothened signaling pathway / dorsal/ventral pattern formation / regulation of protein localization to nucleus / embryonic limb morphogenesis / cell fate specification / Class B/2 (Secretin family receptors) / neural crest cell migration / embryonic digit morphogenesis / smoothened signaling pathway / branching involved in ureteric bud morphogenesis / branching involved in blood vessel morphogenesis / branching morphogenesis of an epithelial tube / midbrain development / forebrain development / heart looping / oligodendrocyte differentiation / neuroblast proliferation / androgen metabolic process / protein autoprocessing / positive regulation of cell division / regulation of proteolysis / negative regulation of cell differentiation / vasculogenesis / lung development / thymus development / negative regulation of cell migration / axon guidance / central nervous system development / apoptotic signaling pathway / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Hedgehog 'on' state / T cell differentiation in thymus / peptidase activity / cell-cell signaling / regulation of cell population proliferation / heart development / extracellular matrix / regulation of gene expression / endopeptidase activity / Hydrolases; Acting on ester bonds / membrane raft / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription
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
Sonic hedgehog protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å
AuthorsBonn-Breach, R.B. / Jenkins, J.L. / Wedekind, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM123864 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structure of Sonic Hedgehog protein in complex with zinc(II) and magnesium(II) reveals ion-coordination plasticity relevant to peptide drug design.
Authors: Bonn-Breach, R. / Gu, Y. / Jenkins, J. / Fasan, R. / Wedekind, J.
History
DepositionJun 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)19,63410
Polymers19,1221
Non-polymers5119
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.728, 118.728, 118.728
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sonic hedgehog protein / SHH / HHG-1 / Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains / ShhNC


Mass: 19122.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q15465

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Non-polymers , 6 types, 261 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24% (w/v) polyethylene glycol 8000, 0.10 M TRIS pH 7.0, and 0.24 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.43→37.545 Å / Num. obs: 51261 / % possible obs: 99.9 % / Redundancy: 19.6 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 20
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2488 / CC1/2: 0.593 / Rpim(I) all: 0.462 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSJanuary 26, 2018data reduction
Aimless0.7.3data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vhh

1vhh


Resolution: 1.43→37.5 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.67
RfactorNum. reflection% reflection
Rfree0.1391 2297 4.48 %
Rwork0.1237 --
obs0.1244 51261 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.54 Å2 / Biso mean: 21.6788 Å2 / Biso min: 11.38 Å2
Refinement stepCycle: final / Resolution: 1.43→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 49 256 1524
Biso mean--73.17 32.71 -
Num. residues----152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4304-1.46150.26921390.2193303999
1.4615-1.49550.20741440.17213006100
1.4955-1.53290.17161450.14063037100
1.5329-1.57430.14231420.11793040100
1.5743-1.62060.12871430.11053017100
1.6206-1.67290.14671400.10493051100
1.6729-1.73270.13561440.10763039100
1.7327-1.80210.12741460.11123067100
1.8021-1.88410.12151410.10623056100
1.8841-1.98340.10151420.10863042100
1.9834-2.10770.11631460.10643064100
2.1077-2.27040.12231420.1083061100
2.2704-2.49890.12021470.11473067100
2.4989-2.86030.14931390.12433083100
2.8603-3.60330.15641450.12353110100
3.6033-37.50.14161520.14243185100

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