[English] 日本語
Yorodumi
- EMDB-22689: Hedgehog receptor Patched (PTCH1) in complex with conformation se... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22689
TitleHedgehog receptor Patched (PTCH1) in complex with conformation selective nanobody TI23
Map dataSharpened map of Patched in complex with nanobody TI23
Sample
  • Complex: Complex between Hedgehog receptor PTCH1 and nanobody TI23
    • Complex: Hedgehog receptor Patched PTCH1
      • Protein or peptide: Protein patched homolog 1
    • Complex: nanobody TI23
      • Protein or peptide: nanobody TI23
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Ligand-receptor interactions / Activation of SMO / neural plate axis specification / cell differentiation involved in kidney development / hedgehog receptor activity / response to chlorate / cell proliferation involved in metanephros development / smoothened binding / neural tube formation / hedgehog family protein binding ...Ligand-receptor interactions / Activation of SMO / neural plate axis specification / cell differentiation involved in kidney development / hedgehog receptor activity / response to chlorate / cell proliferation involved in metanephros development / smoothened binding / neural tube formation / hedgehog family protein binding / hindlimb morphogenesis / Hedgehog 'on' state / epidermal cell fate specification / spinal cord motor neuron differentiation / prostate gland development / Hedgehog 'off' state / patched binding / negative regulation of cell division / somite development / cellular response to cholesterol / dorsal/ventral neural tube patterning / smooth muscle tissue development / pattern specification process / pharyngeal system development / mammary gland duct morphogenesis / mammary gland epithelial cell differentiation / mammary gland development / cell fate determination / commissural neuron axon guidance / metanephric collecting duct development / dorsal/ventral pattern formation / regulation of growth / embryonic limb morphogenesis / cholesterol binding / negative regulation of multicellular organism growth / branching involved in ureteric bud morphogenesis / positive regulation of epidermal cell differentiation / dendritic growth cone / keratinocyte proliferation / spermatid development / positive regulation of cholesterol efflux / negative regulation of keratinocyte proliferation / epidermis development / negative regulation of osteoblast differentiation / embryonic organ development / axonal growth cone / response to retinoic acid / negative regulation of stem cell proliferation / heart morphogenesis / response to mechanical stimulus / negative regulation of smoothened signaling pathway / regulation of mitotic cell cycle / cyclin binding / stem cell proliferation / epithelial cell proliferation / protein localization to plasma membrane / neural tube closure / liver regeneration / animal organ morphogenesis / brain development / caveola / protein processing / cilium / negative regulation of epithelial cell proliferation / apical part of cell / response to estradiol / glucose homeostasis / regulation of protein localization / heparin binding / regulation of cell population proliferation / midbody / in utero embryonic development / response to xenobiotic stimulus / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / protein-containing complex binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / signal transduction / zinc ion binding / extracellular region / plasma membrane
Similarity search - Function
Transmembrane receptor, patched / : / Sterol-sensing domain of SREBP cleavage-activation / Protein patched/dispatched / Patched family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
Protein patched homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang Y / Bulkley DP
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102498 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098672 United States
National Institutes of Health/Office of the DirectorDP5OD023048 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Hedgehog pathway activation through nanobody-mediated conformational blockade of the Patched sterol conduit.
Authors: Yunxiao Zhang / Wan-Jin Lu / David P Bulkley / Jiahao Liang / Arthur Ralko / Shuo Han / Kelsey J Roberts / Anping Li / Wonhwa Cho / Yifan Cheng / Aashish Manglik / Philip A Beachy /
Abstract: Activation of the Hedgehog pathway may have therapeutic value for improved bone healing, taste receptor cell regeneration, and alleviation of colitis or other conditions. Systemic pathway activation, ...Activation of the Hedgehog pathway may have therapeutic value for improved bone healing, taste receptor cell regeneration, and alleviation of colitis or other conditions. Systemic pathway activation, however, may be detrimental, and agents amenable to tissue targeting for therapeutic application have been lacking. We have developed an agonist, a conformation-specific nanobody against the Hedgehog receptor Patched1 (PTCH1). This nanobody potently activates the Hedgehog pathway in vitro and in vivo by stabilizing an alternative conformation of a Patched1 "switch helix," as revealed by our cryogenic electron microscopy structure. Nanobody-binding likely traps Patched in one stage of its transport cycle, thus preventing substrate movement through the Patched1 sterol conduit. Unlike the native Hedgehog ligand, this nanobody does not require lipid modifications for its activity, facilitating mechanistic studies of Hedgehog pathway activation and the engineering of pathway activating agents for therapeutic use. Our conformation-selective nanobody approach may be generally applicable to the study of other PTCH1 homologs.
History
DepositionSep 18, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 4.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7k65
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22689.png

Downloads & links

-
Map

FileDownload / File: emd_22689.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of Patched in complex with nanobody TI23
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.8 / Movie #1: 4.8
Minimum - Maximum-14.967468 - 25.975850999999999
Average (Standard dev.)-0.021284537 (±0.87775165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.104 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.104271.104271.104
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-14.96725.976-0.021

-
Supplemental data

-
Half map: half map 1

Fileemd_22689_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_22689_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex between Hedgehog receptor PTCH1 and nanobody TI23

EntireName: Complex between Hedgehog receptor PTCH1 and nanobody TI23
Components
  • Complex: Complex between Hedgehog receptor PTCH1 and nanobody TI23
    • Complex: Hedgehog receptor Patched PTCH1
      • Protein or peptide: Protein patched homolog 1
    • Complex: nanobody TI23
      • Protein or peptide: nanobody TI23
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside

-
Supramolecule #1: Complex between Hedgehog receptor PTCH1 and nanobody TI23

SupramoleculeName: Complex between Hedgehog receptor PTCH1 and nanobody TI23
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

-
Supramolecule #2: Hedgehog receptor Patched PTCH1

SupramoleculeName: Hedgehog receptor Patched PTCH1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

-
Supramolecule #3: nanobody TI23

SupramoleculeName: nanobody TI23 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Lama glama (llama)

-
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: Mus musculus (house mouse)
Molecular weightTheoretical: 142.619938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASAGNAAGA LGRQAGGGRR RRTGGPHRAA PDRDYLHRPS YCDAAFALEQ ISKGKATGRK APLWLRAKFQ RLLFKLGCYI QKNCGKFLV VGLLIFGAFA VGLKAANLET NVEELWVEVG GRVSRELNYT RQKIGEEAMF NPQLMIQTPK EEGANVLTTE A LLQHLDSA ...String:
MASAGNAAGA LGRQAGGGRR RRTGGPHRAA PDRDYLHRPS YCDAAFALEQ ISKGKATGRK APLWLRAKFQ RLLFKLGCYI QKNCGKFLV VGLLIFGAFA VGLKAANLET NVEELWVEVG GRVSRELNYT RQKIGEEAMF NPQLMIQTPK EEGANVLTTE A LLQHLDSA LQASRVHVYM YNRQWKLEHL CYKSGELITE TGYMDQIIEY LYPCLIITPL DCFWEGAKLQ SGTAYLLGKP PL RWTNFDP LEFLEELKKI NYQVDSWEEM LNKAEVGHGY MDRPCLNPAD PDCPATAPNK NSTKPLDVAL VLNGGCQGLS RKY MHWQEE LIVGGTVKNA TGKLVSAHAL QTMFQLMTPK QMYEHFRGYD YVSHINWNED RAAAILEAWQ RTYVEVVHQS VAPN STQKV LPFTTTTLDD ILKSFSDVSV IRVASGYLLM LAYACLTMLR WDCSKSQGAV GLAGVLLVAL SVAAGLGLCS LIGIS FNAA TTQVLPFLAL GVGVDDVFLL AHAFSETGQN KRIPFEDRTG ECLKRTGASV ALTSISNVTA FFMAALIPIP ALRAFS LQA AVVVVFNFAM VLLIFPAILS MDLYRREDRR LDIFCCFTSP CVSRVIQVEP QAYTEPMQST VQLRTEYDPH THVYYTT AE PRSEISVQPV TVTQDNLSCQ SPESTSSTRD LLSQFSDSSL HCLEPPCTKW TLSSFAEKHY APFLLKPKAK VVVILLFL G LLGVSLYGTT RVRDGLDLTD IVPRETREYD FIAAQFKYFS FYNMYIVTQK ADYPNIQHLL YDLHKSFSNV KYVMLEENK QLPQMWLHYF RDWLQGLQDA FDSDWETGRI MPNNYKNGSD DGVLAYKLLV QTGSRDKPID ISQLTKQRLV DADGIINPSA FYIYLTAWV SNDPVAYAAS QANIRPHRPE WVHDKADYMP ETRLRIPAAE PIEYAQFPFY LNGLRDTSDF VEAIEKVRVI C NNYTSLGL SSYPNGYPFL FWEQYISLRH WLLLSISVVL ACTFLVCAVF LLNPWTAGII VMVLALMTVE LFGMMGLIGI KL SAVPVVI LIASVGIGVE FTVHVALAFL TAIGDKNHRA MLALEHMFAP VLDGAVSTLL GVLMLAGSEF DFIVRYFFAV LAI LTVLGV LNGLVLLPVL LSFFGPCPEV SPANGLNRLP TPSPEPPPSV VRFAVPPGHT NNGSDSSDSE YSSQTTVSGI SEEL RQYEA QQGAGGPAHQ VIVEATENPV FARSTVVHPD SRHQPPLTPR QQPHLDSGSL SPGRQGQQPR RDMDEKTTGW RGGHV V

UniProtKB: Protein patched homolog 1

-
Macromolecule #2: nanobody TI23

MacromoleculeName: nanobody TI23 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.821417 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCAASGNIFA YYIMGWYRQA PGKERELVAT IDIGGNTNYA DSVKGRFTIS RDNAKNNVYL QMNSLKPED TAVYYCAVQA VPIRYRRYWG QGTQVTVSSH HHHHH

-
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: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl...

MacromoleculeName: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
type: ligand / ID: 5 / Number of copies: 4 / Formula: Q7G
Molecular weightTheoretical: 1.165315 KDa
Chemical component information

ChemComp-Q7G:
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
0.02 %GDNglycol-diosgenin
GridModel: Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number real images: 7046 / Average exposure time: 12.0 sec. / Average electron dose: 85.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3621265
Details: Particles were picked first using a Gaussian blob as the template and then were re-picked using the 2D classes generated from the first round.
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1) / Number images used: 307652
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 307652 / Software - Name: cryoSPARC (ver. 2)

-
Atomic model buiding 1

Initial modelPDB ID:

6mg8


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7k65:
Hedgehog receptor Patched (PTCH1) in complex with conformation selective nanobody TI23

+
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