[English] 日本語
Yorodumi
- EMDB-24467: Cryo-EM structure of Xenopus Patched-1 in nanodisc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24467
TitleCryo-EM structure of Xenopus Patched-1 in nanodisc
Map data
Sample
  • Complex: patched
    • Protein or peptide: Patched-1
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordspatched / MEMBRANE PROTEIN
Function / homology
Function and homology information


hedgehog receptor activity / smoothened binding / hedgehog family protein binding / negative regulation of smoothened signaling pathway / 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
Patched 1 S homeolog
Similarity search - Component
Biological speciesXenopus calcaratus (Biafran clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHuang P / Lian T / Jiang J / Salic A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122920 United States
CitationJournal: Dev Cell / Year: 2022
Title: Structural basis for catalyzed assembly of the Sonic hedgehog-Patched1 signaling complex.
Authors: Pengxiang Huang / Bradley M Wierbowski / Tengfei Lian / Charlene Chan / Sara García-Linares / Jiansen Jiang / Adrian Salic /
Abstract: The dually lipidated Sonic hedgehog (SHH) morphogen signals through the tumor suppressor membrane protein Patched1 (PTCH1) to activate the Hedgehog pathway, which is fundamental in development and ...The dually lipidated Sonic hedgehog (SHH) morphogen signals through the tumor suppressor membrane protein Patched1 (PTCH1) to activate the Hedgehog pathway, which is fundamental in development and cancer. SHH engagement with PTCH1 requires the GAS1 coreceptor, but the mechanism is unknown. We demonstrate a unique role for GAS1, catalyzing SHH-PTCH1 complex assembly in vertebrate cells by direct SHH transfer from the extracellular SCUBE2 carrier to PTCH1. Structure of the GAS1-SHH-PTCH1 transition state identifies how GAS1 recognizes the SHH palmitate and cholesterol modifications in modular fashion and how it facilitates lipid-dependent SHH handoff to PTCH1. Structure-guided experiments elucidate SHH movement from SCUBE2 to PTCH1, explain disease mutations, and demonstrate that SHH-induced PTCH1 dimerization causes its internalization from the cell surface. These results define how the signaling-competent SHH-PTCH1 complex assembles, the key step triggering the Hedgehog pathway, and provide a paradigm for understanding morphogen reception and its regulation.
History
DepositionJul 18, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7rhr
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24467.png

Downloads & links

-
Map

FileDownload / File: emd_24467.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-5.2748656 - 8.198335
Average (Standard dev.)0.0061230958 (±0.13701193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z254.400254.400254.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-5.2758.1980.006

-
Supplemental data

-
Sample components

-
Entire : patched

EntireName: patched
Components
  • Complex: patched
    • Protein or peptide: Patched-1
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: patched

SupramoleculeName: patched / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Xenopus calcaratus (Biafran clawed frog)

-
Macromolecule #1: Patched-1

MacromoleculeName: Patched-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus calcaratus (Biafran clawed frog)
Molecular weightTheoretical: 134.622391 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString: MASAACAAEL GASGEAAAQP RVVRRRGRSR RVAPPDHDYL QRPSYCDANF ALQQISEGKA IGRKAPLWLR AFFQRQLFKL GCYIQKNCG KFLVVGLLIF GAFAVGLRAA NLETNVEELW VEVGGRVSRE LDYTRQKIGE EAMFNPQLMI QTPLEDGANV L TTEALLQH ...String:
MASAACAAEL GASGEAAAQP RVVRRRGRSR RVAPPDHDYL QRPSYCDANF ALQQISEGKA IGRKAPLWLR AFFQRQLFKL GCYIQKNCG KFLVVGLLIF GAFAVGLRAA NLETNVEELW VEVGGRVSRE LDYTRQKIGE EAMFNPQLMI QTPLEDGANV L TTEALLQH LHSALEATKV QVYMYNKPWK LEELCFKSGE LITEAVYVSQ IIDSMYPCLI ITPLDCFWEG AKLQSGMAYL PG KDILQWT NFDPLELLEE LKKGKLHIDI WEEMINKAEV GHGYMDRPCL NPSDKNCPYT APNKNSTKPV DVSLILSGGC YGL SKKYMH WQEELIIGGT VKNASGQIVS ALALQTMFQL MTPKQMYEHF KGHEVVSHMN WNEDKAAAIL EAWQRTYVQV VHQS VPQNS SQKVLPFTTT TLDDILKSFS DVSVIRVASG YLLMLAYACL TMLRWDCAKS QGAVGLAGVL LVALSVAAGL GLCSL IGIS FNAATTQVLP FLALGVGVDD VFLLAHAFSE TGQNKRIPFE DRTGECLKRT GASVALTSIS NVTAFFMAAL IPIPAL RAF SLQAAVVVVF NFAMVLLIFP AILSMDLYRR EVRRLDIFCC FSSPCVSRVI QIEPQAYTDN NDNTRYSLPP TYSSHSF AH ETQITMQSTV QLRTEYDPRT QLYYTTAQPR SEISVQPAAS TPQDVSGQTP ESTSSTRDLI SQFSVHGGSM QCTPDSKW T LSSFAEKHYA PFLLKPKTKV AVILGFLALL SVSLYGTTRV RDGLDLTDIV PRETREYDFI ATQFKYFSFY HMYVVTQKA DYPRAQRLLY ELHKSFVGVR YVLLEGNKQL PKMWLHYFRD WLQGLQDTFD HEWEAGKITR NDYRNASDDA VLAYKLLIQT GNSDKPINL NQLTKQRLVD ADGIIQPNAF YIYLTAWVSN DPVAYAASQA NIRPHPPEWL HDKADDRPET RTIRAAEPIE Y VQFPFYLN GLRETSDFVE AIEKVRAICN NYTSLGVSSY PNGYPFLFWE QYISLRHWLL LSISVVLACT FLVCALFLLN PW TAGIIVM VLALMTVELF GMMGLIGIKL SAVPVVILIA SVGIGVEFTV HVALAFLTAV GDKNRRAVLA LEHMFAPVLD GAV STLLGV LMLAGSEFDF IVRYFFAVLA ILTLLGVLNG LVLLPVLLSF FGPYPEVSPT NGSSSPAAAH HHHHHHHEDQ VDPR LIDGK

UniProtKB: Patched 1 S homeolog

-
Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 3 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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

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

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 71.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106749
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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