[English] 日本語
Yorodumi
- EMDB-7968: Cryo-EM structure of human Ptch1 and ShhN complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7968
TitleCryo-EM structure of human Ptch1 and ShhN complex
Map data
Sample
  • Organelle or cellular component: Patch1
    • Protein or peptide: Protein patched homolog 1
  • Protein or peptide: Sonic hedgehog protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: SERINE
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
KeywordsReceptor / RND family / PROTEIN BINDING
Function / homology
Function and homology information


regulation of nodal signaling pathway / neural plate axis specification / 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 ...regulation of nodal signaling pathway / neural plate axis specification / 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 / hedgehog receptor activity / Formation of lateral plate mesoderm / epithelial-mesenchymal cell signaling / polarity specification of anterior/posterior axis / neural tube patterning / smoothened binding / ventral midline development / metanephric mesenchymal cell proliferation involved in metanephros development / hedgehog family protein binding / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / Ligand-receptor interactions / laminin-1 binding / neural tube formation / 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 / limb morphogenesis / stem cell development / negative regulation of cell division / 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 / pharyngeal system development / positive regulation of immature T cell proliferation in thymus / cellular response to cholesterol / 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 / response to alkaloid / commissural neuron axon guidance / positive regulation of smoothened signaling pathway / 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) / negative regulation of multicellular organism growth / 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 / cholesterol binding / midbrain development / forebrain development / ciliary membrane / heart looping / dendritic growth cone / oligodendrocyte differentiation / spermatid development / neuroblast proliferation / androgen metabolic process / protein autoprocessing / positive regulation of cell division / regulation of proteolysis / positive regulation of cholesterol efflux / negative regulation of cell differentiation / response to retinoic acid / vasculogenesis / response to mechanical stimulus / negative regulation of osteoblast differentiation / axonal growth cone / Hedgehog 'off' state / lung development / thymus development / liver regeneration
Similarity search - Function
Transformer protein 2 N-terminal domain / Transmembrane receptor, patched / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / : ...Transformer protein 2 N-terminal domain / Transmembrane receptor, patched / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / 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
Similarity search - Domain/homology
Protein patched homolog 1 / Sonic hedgehog protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYan N / Gong X
Funding support China, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31621092, 31630017, 31611130036 China
National Basic Research Program of China (973 Program)2015CB910101 China
CitationJournal: Science / Year: 2018
Title: Structural basis for the recognition of Sonic Hedgehog by human Patched1.
Authors: Xin Gong / Hongwu Qian / Pingping Cao / Xin Zhao / Qiang Zhou / Jianlin Lei / Nieng Yan /
Abstract: The Hedgehog (Hh) pathway involved in development and regeneration is activated by the extracellular binding of Hh to the membrane receptor Patched (Ptch). We report the structures of human Ptch1 ...The Hedgehog (Hh) pathway involved in development and regeneration is activated by the extracellular binding of Hh to the membrane receptor Patched (Ptch). We report the structures of human Ptch1 alone and in complex with the N-terminal domain of human Sonic hedgehog (ShhN) at resolutions of 3.9 and 3.6 angstroms, respectively, as determined by cryo-electron microscopy. Ptch1 comprises two interacting extracellular domains, ECD1 and ECD2, and 12 transmembrane segments (TMs), with TMs 2 to 6 constituting the sterol-sensing domain (SSD). Two steroid-shaped densities are resolved in both structures, one enclosed by ECD1/2 and the other in the membrane-facing cavity of the SSD. Structure-guided mutational analysis shows that interaction between ShhN and Ptch1 is steroid-dependent. The structure of a steroid binding-deficient Ptch1 mutant displays pronounced conformational rearrangements.
History
DepositionJun 5, 2018-
Header (metadata) releaseJul 11, 2018-
Map releaseJul 11, 2018-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6dmy
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7968.png

Downloads & links

-
Map

FileDownload / File: emd_7968.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 224 pix.
= 244.384 Å		1.09 Å/pix.
x 224 pix.
= 244.384 Å		1.09 Å/pix.
x 224 pix.
= 244.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.11725369 - 0.21128653
Average (Standard dev.)0.00041769576 (±0.0074620936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 244.38399 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z244.384244.384244.384
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.1170.2110.000

-
Supplemental data

-
Sample components

-
Entire : Patch1

EntireName: Patch1
Components
  • Organelle or cellular component: Patch1
    • Protein or peptide: Protein patched homolog 1
  • Protein or peptide: Sonic hedgehog protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: SERINE
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

-
Supramolecule #1: Patch1

SupramoleculeName: Patch1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Protein patched homolog 1

MacromoleculeName: Protein patched homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150.189578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGPDEVDASG RMASAGNAAE PQDRGGGGSG CIGAPGRPAG GGRRRRTGGL RRAAAPDRDY LHRPSYCDAA FALEQISKG KATGRKAPLW LRAKFQRLLF KLGCYIQKNC GKFLVVGLLI FGAFAVGLKA ANLETNVEEL WVEVGGRVSR E LNYTRQKI ...String:
MADYKDDDDK SGPDEVDASG RMASAGNAAE PQDRGGGGSG CIGAPGRPAG GGRRRRTGGL RRAAAPDRDY LHRPSYCDAA FALEQISKG KATGRKAPLW LRAKFQRLLF KLGCYIQKNC GKFLVVGLLI FGAFAVGLKA ANLETNVEEL WVEVGGRVSR E LNYTRQKI GEEAMFNPQL MIQTPKEEGA NVLTTEALLQ HLDSALQASR VHVYMYNRQW KLEHLCYKSG ELITETGYMD QI IEYLYPC LIITPLDCFW EGAKLQSGTA YLLGKPPLRW TNFDPLEFLE ELKKINYQVD SWEEMLNKAE VGHGYMDRPC LNP ADPDCP ATAPNKNSTK PLDMALVLNG GCHGLSRKYM HWQEELIVGG TVKNSTGKLV SAHALQTMFQ LMTPKQMYEH FKGY EYVSH INWNEDKAAA ILEAWQRTYV EVVHQSVAQN STQKVLSFTT TTLDDILKSF SDVSVIRVAS GYLLMLAYAC LTMLR WDCS KSQGAVGLAG VLLVALSVAA GLGLCSLIGI SFNAATTQVL PFLALGVGVD DVFLLAHAFS ETGQNKRIPF EDRTGE CLK RTGASVALTS ISNVTAFFMA ALIPIPALRA FSLQAAVVVV FNFAMVLLIF PAILSMDLYR REDRRLDIFC CFTSPCV SR VIQVEPQAYT DTHDNTRYSP PPPYSSHSFA HETQITMQST VQLRTEYDPH THVYYTTAEP RSEISVQPVT VTQDTLSC Q SPESTSSTRD LLSQFSDSSL HCLEPPCTKW TLSSFAEKHY APFLLKPKAK VVVIFLFLGL LGVSLYGTTR VRDGLDLTD IVPRETREYD FIAAQFKYFS FYNMYIVTQK ADYPNIQHLL YDLHRSFSNV KYVMLEENKQ LPKMWLHYFR DWLQGLQDAF DSDWETGKI MPNNYKNGSD DGVLAYKLLV QTGSRDKPID ISQLTKQRLV DADGIINPSA FYIYLTAWVS NDPVAYAASQ A NIRPHRPE WVHDKADYMP ETRLRIPAAE PIEYAQFPFY LNGLRDTSDF VEAIEKVRTI CSNYTSLGLS SYPNGYPFLF WE QYIGLRH WLLLFISVVL ACTFLVCAVF LLNPWTAGII VMVLALMTVE LFGMMGLIGI KLSAVPVVIL IASVGIGVEF TVH VALAFL TAIGDKNRRA VLALEHMFAP VLDGAVSTLL GVLMLAGSEF DFIVRYFFAV LAILTILGVL NGLVLLPVLL SFFG PYPEV SPANGLNRLP TPSPEPPPSV VRFAMPPGHT HSGSDSSDSE YSSQTTVSGL SEELRHYEAQ QGAGGPAHQV IVEAT ENPV FAHSTVVHPE SRHHPPSNPR QQPHLDSGSL PPGRQGQQPR RDLEGSDEVD AVEGSHHHHH HHHHH

UniProtKB: Protein patched homolog 1

-
Macromolecule #2: Sonic hedgehog protein

MacromoleculeName: Sonic hedgehog protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.934461 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
AHMCGPGRGF GKRRHPKKLT PLAYKQFIPN VAEKTLGASG RYEGKISRNS ERFKELTPNY NPDIIFKDEE NTGADRLMTQ RCKDKLNAL AISVMNQWPG VKLRVTEGWD EDGHHSEESL HYEGRAVDIT TSDRDRSKYG MLARLAVEAG FDWVYYESKA H IHCSVKAE NSVAAKSGG

UniProtKB: Sonic hedgehog protein

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Macromolecule #6: SERINE

MacromoleculeName: SERINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: SER
Molecular weightTheoretical: 105.093 Da
Chemical component information

ChemComp-SER:
SERINE

-
Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration15 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: Gctf / Type: NONE
Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 137823
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more