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- PDB-6rty: Crystal structure of the Patched ectodomain in complex with nanob... -

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Basic information

Entry
Database: PDB / ID: 6rty
TitleCrystal structure of the Patched ectodomain in complex with nanobody NB64
Components
  • Llama-derived nanobody NB64
  • Protein patched homolog 1
KeywordsMEMBRANE PROTEIN / ---- Hedgehog morphogen receptor / receptor-nanobody complex / cholesterol / palmitate / lipid-protein-modification
Function / homology
Function and homology information


neural plate axis specification / response to chlorate / cell differentiation involved in kidney development / hedgehog receptor activity / cell proliferation involved in metanephros development / neural tube patterning / smoothened binding / hedgehog family protein binding / hindlimb morphogenesis / Ligand-receptor interactions ...neural plate axis specification / response to chlorate / cell differentiation involved in kidney development / hedgehog receptor activity / cell proliferation involved in metanephros development / neural tube patterning / smoothened binding / hedgehog family protein binding / hindlimb morphogenesis / Ligand-receptor interactions / epidermal cell fate specification / spinal cord motor neuron differentiation / prostate gland development / Activation of SMO / limb morphogenesis / patched binding / negative regulation of cell division / somite development / dorsal/ventral neural tube patterning / smooth muscle tissue development / pharyngeal system development / cellular response to cholesterol / mammary gland duct morphogenesis / mammary gland epithelial cell differentiation / cell fate determination / commissural neuron axon guidance / metanephric collecting duct development / regulation of smoothened signaling pathway / dorsal/ventral pattern formation / Class B/2 (Secretin family receptors) / embryonic limb morphogenesis / negative regulation of multicellular organism growth / ciliary membrane / branching involved in ureteric bud morphogenesis / cholesterol binding / positive regulation of epidermal cell differentiation / dendritic growth cone / keratinocyte proliferation / positive regulation of cholesterol efflux / spermatid development / negative regulation of osteoblast differentiation / negative regulation of keratinocyte proliferation / embryonic organ development / response to mechanical stimulus / response to retinoic acid / axonal growth cone / heart morphogenesis / negative regulation of stem cell proliferation / Hedgehog 'off' state / liver regeneration / cyclin binding / regulation of mitotic cell cycle / animal organ morphogenesis / stem cell proliferation / protein localization to plasma membrane / Hedgehog 'on' state / negative regulation of smoothened signaling pathway / neural tube closure / brain development / caveola / protein processing / endocytic vesicle membrane / apical part of cell / glucose homeostasis / response to estradiol / heparin binding / regulation of protein localization / midbody / in utero embryonic development / postsynaptic membrane / response to xenobiotic stimulus / intracellular membrane-bounded organelle / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / plasma membrane
Similarity search - Function
Transmembrane receptor, patched / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
Protein patched homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsRudolf, A.F. / Kowatsch, C. / El Omari, K. / Malinauskas, T. / Kinnebrew, M. / Ansell, T.B. / Bishop, B. / Pardon, E. / Schwab, R.A. / Qian, M. ...Rudolf, A.F. / Kowatsch, C. / El Omari, K. / Malinauskas, T. / Kinnebrew, M. / Ansell, T.B. / Bishop, B. / Pardon, E. / Schwab, R.A. / Qian, M. / Duman, R. / Covey, D.F. / Steyaert, J. / Wagner, A. / Sansom, M.S.P. / Rohatgi, R. / Siebold, C.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKC20724/A14414 United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
European Research Council647278 United Kingdom
CitationJournal: Nat Chem Biol / Year: 2019
Title: The morphogen Sonic hedgehog inhibits its receptor Patched by a pincer grasp mechanism.
Authors: Amalie F Rudolf / Maia Kinnebrew / Christiane Kowatsch / T Bertie Ansell / Kamel El Omari / Benjamin Bishop / Els Pardon / Rebekka A Schwab / Tomas Malinauskas / Mingxing Qian / Ramona Duman ...Authors: Amalie F Rudolf / Maia Kinnebrew / Christiane Kowatsch / T Bertie Ansell / Kamel El Omari / Benjamin Bishop / Els Pardon / Rebekka A Schwab / Tomas Malinauskas / Mingxing Qian / Ramona Duman / Douglas F Covey / Jan Steyaert / Armin Wagner / Mark S P Sansom / Rajat Rohatgi / Christian Siebold /
Abstract: Hedgehog (HH) ligands, classical morphogens that pattern embryonic tissues in all animals, are covalently coupled to two lipids-a palmitoyl group at the N terminus and a cholesteroyl group at the C ...Hedgehog (HH) ligands, classical morphogens that pattern embryonic tissues in all animals, are covalently coupled to two lipids-a palmitoyl group at the N terminus and a cholesteroyl group at the C terminus. While the palmitoyl group binds and inactivates Patched 1 (PTCH1), the main receptor for HH ligands, the function of the cholesterol modification has remained mysterious. Using structural and biochemical studies, along with reassessment of previous cryo-electron microscopy structures, we find that the C-terminal cholesterol attached to Sonic hedgehog (Shh) binds the first extracellular domain of PTCH1 and promotes its inactivation, thus triggering HH signaling. Molecular dynamics simulations show that this interaction leads to the closure of a tunnel through PTCH1 that serves as the putative conduit for sterol transport. Thus, Shh inactivates PTCH1 by grasping its extracellular domain with two lipidic pincers, the N-terminal palmitate and the C-terminal cholesterol, which are both inserted into the PTCH1 protein core.
History
DepositionMay 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Protein patched homolog 1
B: Llama-derived nanobody NB64
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8465
Polymers48,1822
Non-polymers6643
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint5 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.718, 65.873, 150.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein patched homolog 1 / PTC1


Mass: 34138.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human PTCH1-ECD1 residues 139-423, containing three N-terminal additional residues derived from the expression vector pHLsec, and a C-terminal His6-Tag for IMAC purification.
Source: (gene. exp.) Homo sapiens (human) / Gene: PTCH1, PTCH / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13635
#2: Antibody Llama-derived nanobody NB64


Mass: 14043.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Nanobody NB64 containing a C-terminal His6-Tag for purification
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMES4y / Production host: Escherichia coli (E. coli)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES/imidazole pH 6.5, 0.02M of each amino acid (L-glutamate, alanine, glycine, lysine, serine), 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→150.54 Å / Num. obs: 27821 / % possible obs: 97.5 % / Redundancy: 11.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Net I/σ(I): 16.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1068 / CC1/2: 0.521 / Rpim(I) all: 0.696 / % possible all: 75.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
xia2data reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.902 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25498 1372 5 %RANDOM
Rwork0.21577 ---
obs0.21771 25995 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.261 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 42 79 3248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133278
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172930
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.6624459
X-RAY DIFFRACTIONr_angle_other_deg1.2451.5866836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7815397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87523.374163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08815545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6581514
X-RAY DIFFRACTIONr_chiral_restr0.0570.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023647
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02661
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3387.2841591
X-RAY DIFFRACTIONr_mcbond_other5.337.2821590
X-RAY DIFFRACTIONr_mcangle_it7.35710.8941987
X-RAY DIFFRACTIONr_mcangle_other7.35610.8961988
X-RAY DIFFRACTIONr_scbond_it5.3667.7241687
X-RAY DIFFRACTIONr_scbond_other5.3647.7271688
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.89911.4142473
X-RAY DIFFRACTIONr_long_range_B_refined11.57712876
X-RAY DIFFRACTIONr_long_range_B_other11.58612840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 76 -
Rwork0.411 1423 -
obs--72.38 %

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