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- EMDB-24617: Cryo-EM structure of murine Dispatched in complex with Sonic hedgehog -

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Basic information

Entry
Database: EMDB / ID: EMD-24617
TitleCryo-EM structure of murine Dispatched in complex with Sonic hedgehog
Map dataDISP1-A:ShhN complex - auto-sharpened map from cryoSPARC nonuniform refinement (paper version), units of standard deviation above mean density.
Sample
  • Complex: Dispatched protein complexed with Sonic hedgehog 26-189
    • Protein or peptide: x 2 types
  • Ligand: x 9 types
KeywordsRND transporter / Hedgehog binding / Sterol sensing domain / sodium binding / MEMBRANE PROTEIN
Function / homology
Function and homology information


forebrain regionalization / cell proliferation in external granule layer / zona limitans intrathalamica formation / positive regulation of neurotrophin production / positive regulation of photoreceptor cell differentiation / fungiform papilla development / Release of Hh-Np from the secreting cell / digestive tract mesoderm development / epithelial-mesenchymal signaling involved in prostate gland development / fungiform papilla morphogenesis ...forebrain regionalization / cell proliferation in external granule layer / zona limitans intrathalamica formation / positive regulation of neurotrophin production / positive regulation of photoreceptor cell differentiation / fungiform papilla development / Release of Hh-Np from the secreting cell / digestive tract mesoderm development / epithelial-mesenchymal signaling involved in prostate gland development / fungiform papilla morphogenesis / ventral spinal cord interneuron specification / tongue morphogenesis / respiratory tube development / Ligand-receptor interactions / patched ligand maturation / Activation of SMO / mesenchymal-epithelial cell signaling involved in prostate gland development / positive regulation of oligodendrocyte progenitor proliferation / trachea development / positive regulation of skeletal muscle cell proliferation / anatomical structure formation involved in morphogenesis / right lung development / left lung development / primary prostatic bud elongation / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of sclerotome development / tracheoesophageal septum formation / 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 / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / polarity specification of anterior/posterior axis / trunk neural crest cell migration / hindgut morphogenesis / striated muscle tissue development / negative regulation of alpha-beta T cell differentiation / regulation of glial cell proliferation / regulation of prostatic bud formation / metanephric mesenchymal cell proliferation involved in metanephros development / positive regulation of penile erection / neural tube formation / formation of anatomical boundary / lung epithelium development / positive regulation of striated muscle cell differentiation / myotube differentiation / trachea morphogenesis / regulation of epithelial cell proliferation involved in prostate gland development / cholesterol-protein transferase activity / bud outgrowth involved in lung branching / diaphragm development / telencephalon regionalization / epithelial-mesenchymal cell signaling / laminin-1 binding / vasculogenesis involved in coronary vascular morphogenesis / Hedgehog ligand biogenesis / salivary gland cavitation / negative regulation of cholesterol efflux / determination of left/right asymmetry in lateral mesoderm / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / positive regulation of cerebellar granule cell precursor proliferation / cell development / negative regulation of T cell differentiation in thymus / spinal cord motor neuron differentiation / positive regulation of T cell differentiation in thymus / cerebellar granule cell precursor proliferation / intermediate filament organization / mesenchymal cell apoptotic process / embryonic skeletal system development / male genitalia morphogenesis / limb bud formation / lung lobe morphogenesis / prostate gland development / skeletal muscle fiber differentiation / establishment of epithelial cell polarity / fungiform papilla formation / patched binding / thalamus development / embryonic digestive tract morphogenesis / embryonic foregut morphogenesis / somite development / epithelial cell proliferation involved in salivary gland morphogenesis / hindbrain development / positive regulation of skeletal muscle tissue development / animal organ formation / ectoderm development / neuron fate commitment / stem cell development / branching involved in prostate gland morphogenesis / dorsal/ventral neural tube patterning / negative regulation of dopaminergic neuron differentiation / mesenchymal cell proliferation involved in lung development / negative thymic T cell selection / skeletal muscle cell proliferation / positive regulation of immature T cell proliferation in thymus / lymphoid progenitor cell differentiation / mesenchymal cell proliferation
Similarity search - Function
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 / Protein patched/dispatched / Patched family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain ...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 / Protein patched/dispatched / Patched family / 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 dispatched homolog 1 / Sonic hedgehog protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsAsarnow D / Wang Q
Funding support United States, 5 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)R35GM140847 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020054 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD021741 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2021
Title: Dispatched uses Na flux to power release of lipid-modified Hedgehog.
Authors: Qianqian Wang / Daniel E Asarnow / Ke Ding / Randall K Mann / Jason Hatakeyama / Yunxiao Zhang / Yong Ma / Yifan Cheng / Philip A Beachy /
Abstract: The Dispatched protein, which is related to the NPC1 and PTCH1 cholesterol transporters and to H-driven transporters of the RND family, enables tissue-patterning activity of the lipid-modified ...The Dispatched protein, which is related to the NPC1 and PTCH1 cholesterol transporters and to H-driven transporters of the RND family, enables tissue-patterning activity of the lipid-modified Hedgehog protein by releasing it from tightly -localized sites of embryonic expression. Here we determine a cryo-electron microscopy structure of the mouse protein Dispatched homologue 1 (DISP1), revealing three Na ions coordinated within a channel that traverses its transmembrane domain. We find that the rate of Hedgehog export is dependent on the Na gradient across the plasma membrane. The transmembrane channel and Na binding are disrupted in DISP1-NNN, a variant with asparagine substitutions for three intramembrane aspartate residues that each coordinate and neutralize the charge of one of the three Na ions. DISP1-NNN and variants that disrupt single Na sites retain binding to, but are impaired in export of the lipid-modified Hedgehog protein to the SCUBE2 acceptor. Interaction of the amino-terminal signalling domain of the Sonic hedgehog protein (ShhN) with DISP1 occurs via an extensive buried surface area and contacts with an extended furin-cleaved DISP1 arm. Variability analysis reveals that ShhN binding is restricted to one extreme of a continuous series of DISP1 conformations. The bound and unbound DISP1 conformations display distinct Na-site occupancies, which suggests a mechanism by which transmembrane Na flux may power extraction of the lipid-linked Hedgehog signal from the membrane. Na-coordinating residues in DISP1 are conserved in PTCH1 and other metazoan RND family members, suggesting that Na flux powers their conformationally driven activities.
History
DepositionAug 3, 2021-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 2021-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rpk
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24617.png

Downloads & links

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Map

FileDownload / File: emd_24617.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDISP1-A:ShhN complex - auto-sharpened map from cryoSPARC nonuniform refinement (paper version), units of standard deviation above mean density.
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-14.416078000000001 - 22.779126999999999
Average (Standard dev.)0.011065019 (±0.5738553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 240.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8350.8350.835
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z240.480240.480240.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-14.41622.7790.011

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Supplemental data

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Mask #1

Fileemd_24617_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_24617_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DISP1-A:ShhN complex - raw map from cryoSPARC nonuniform...

Fileemd_24617_additional_1.map
AnnotationDISP1-A:ShhN complex - raw map from cryoSPARC nonuniform refinement (paper version).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DISP1-A:ShhN complex - auto-sharpened map from cryoSPARC nonuniform...

Fileemd_24617_additional_2.map
AnnotationDISP1-A:ShhN complex - auto-sharpened map from cryoSPARC nonuniform refinement (paper version).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DISP1-A:ShhN complex - half map 1 from cryoSPARC...

Fileemd_24617_half_map_1.map
AnnotationDISP1-A:ShhN complex - half map 1 from cryoSPARC nonuniform refinement (paper version).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DISP1-A:ShhN complex - half map 2 from cryoSPARC...

Fileemd_24617_half_map_2.map
AnnotationDISP1-A:ShhN complex - half map 2 from cryoSPARC nonuniform refinement (paper version).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dispatched protein complexed with Sonic hedgehog 26-189

EntireName: Dispatched protein complexed with Sonic hedgehog 26-189
Components
  • Complex: Dispatched protein complexed with Sonic hedgehog 26-189
    • Protein or peptide: Protein dispatched homolog 1
    • Protein or peptide: Sonic hedgehog protein
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: SODIUM IONSodium
  • Ligand: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
  • Ligand: ZINC ION
  • Ligand: SULFATE IONSulfate
  • Ligand: water

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Supramolecule #1: Dispatched protein complexed with Sonic hedgehog 26-189

SupramoleculeName: Dispatched protein complexed with Sonic hedgehog 26-189
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 151.91493 KDa

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Macromolecule #1: Protein dispatched homolog 1

MacromoleculeName: Protein dispatched homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 152.071141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARPFKFPRS YAALLADWPV VVLGMCTLLI VVCALVGVLV PELPDFSDPL LGFEPRGTTI GQRLVTWNNM MRNTGYKATL ANYPYKYAE EQARSHRDDR WSDDHHERER REVDWNFQKD SFFCDVPSDG YSRVVFASAG GETLWNLPAI KSMCDVDNSR I RSHPQFSD ...String:
MARPFKFPRS YAALLADWPV VVLGMCTLLI VVCALVGVLV PELPDFSDPL LGFEPRGTTI GQRLVTWNNM MRNTGYKATL ANYPYKYAE EQARSHRDDR WSDDHHERER REVDWNFQKD SFFCDVPSDG YSRVVFASAG GETLWNLPAI KSMCDVDNSR I RSHPQFSD LCQRTTAVSC CPSWTLGNYI AILNNRSSCQ KIVERDVSHT LKLLRTCAKH YQNGTLGPDC WDKAARRKDQ LK CTNVPRK CTKYNAVYQI LHYLVDKDFM TPKTADYAVP ALKYSMLFSP TEKGESMMNI YLDNFENWNS SDGITTVTGI EFG IKHSLF QDYLLMDTVY PAIAIAIVLL IMCVYTKSMF ITLMTMFAII SSLIVSYFLY RVVFNFEFFP FMNLTALIIL VGIG ADDAF VLCDVWNYTK FDKPRAETSE AVSVTLQHAA LSMFVTSFTT AAAFYANYVS NITAIRCFGV YAGTAILVNY VLMVT WLPA VIVLHERYLL NIFTCFRKPQ PQAYDKSCWA VLCQKCRRVL FAVSEASRIF FEKVLPCIVI KFRYLWLIWF LALTVG GAY IVCVNPKMKL PSLELSEFQV FRSSHPFERY DAEFKKLFMF ERVHHGEELH MPITVIWGVS PEDSGDPLNP KSKGELT LD STFNIASPAS QAWILHFCQK LRNQTFFHQT EQQDFTSCFI ETFKQWMENQ DCDEPALYPC CSHCSFPYKQ EVFELCIK K AIMELDRSTG YHLNNKTPGP RFDINDTIRA VVLEFQSTFL FTLAYEKMQQ FYKEVDSWIS HELSSAPEGL SRGWFVSNL EFYDLQDSLS DGTLIAMGLS VAVAFSVMLL TTWNIIISLY AIVSIAGTIF VTVGSLVLLG WELNVLESVT ISVAVGLSVD FAVHYGVAY RLAPDPDREG KVIFSLSRMG SAIAMAALTT FVAGAMMMPS TVLAYTQLGT FMMLVMCVSW AFATFFFQCL C RCLGPQGT CGQIPFPTKL QCSPFSHTLS ARPGDRGPSK THAASAYSVD ARGQKSQLEH EFYELQPLAS HSCTSSEKTT YE EPHTCSE FFNGQAKNLR MPVPAAYSSE LTKSPSSEPG SALLQSCLEQ DTVCHFSLNP RCNCRDAYTH LQYGLPEIHC QQM GDSLCH KCASTAGGFV QIQSSVAPLK ASHQAAEGLL HPAQHMLPPG MQNSRPRNFF LHSVQHFQAQ ENLGRTSTHS TDER LPRTA ELSPPPSDSR STESFQRACC HPENNQRRLC KSRDPGDTEG SGGTKSKVSG LPNQTDKEEK QVEPSLLQTD ETVNS EHLN HNESNFTFSH LPGEAGCRSC PNSPQSCRSI MRSKCGTEDC QTPNLEANVP AVPTHSDLSG ESLLIKTL

UniProtKB: Protein dispatched homolog 1

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Macromolecule #2: Sonic hedgehog protein

MacromoleculeName: Sonic hedgehog protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.73209 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPGRGFGKRR HPKKLTPLAY KQFIPNVAEK TLGASGRYEG KITRNSERFK ELTPNYNPDI IFKDEENTGA DRLMTQRCKD KLNALAISV MNQWPGVKLR VTEGWDEDGH HSEESLHYEG RAVDITTSDR DRSKYGMLAR LAVEAGFDWV YYESKAHIHC S VKAE

UniProtKB: Sonic hedgehog protein

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 26 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #4: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 4 / Number of copies: 2 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #6: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoylo...

MacromoleculeName: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate
type: ligand / ID: 6 / Number of copies: 1 / Formula: 6OE
Molecular weightTheoretical: 411.428 Da
Chemical component information

ChemComp-6OE:
(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #8: CALCIUM ION

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

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #10: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION / Sulfate

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 42 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.56 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
300.0 mMNaClSodium chloridesodium chloride
0.012 % (w/v)C47H88O22lauryl maltoside neopentyl glycol
0.0025 % (w/v)C56H92O25glyo-diosgenin
0.0024 % (w/v)C31H50O4cholesteryl hemisuccinate
5.0 mMCaCl2calcium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: Wait time 20 seconds, blot time 4 seconds, blotting force 0.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 59880 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsAutomated data collection in SerialEM using 3x3 image shift pattern (one shot per hole), using beam tilt compensation.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1687 / Average electron dose: 66.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1406648
Startup modelType of model: OTHER / Details: Ab initio reconstruction from cryoSPARC
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 204786

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 69.9
Output model

PDB-7rpk:
Cryo-EM structure of murine Dispatched in complex with Sonic hedgehog

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