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- EMDB-22144: Structure of Human Dispatched-1 (DISP1) -

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Basic information

Entry
Database: EMDB / ID: EMD-22144
TitleStructure of Human Dispatched-1 (DISP1)
Map dataStructure of Human Dispatched-1 (DISP1)
Sample
  • Organelle or cellular component: Human dispatched-1 in complex with dual-lipidated SHH-N
    • Protein or peptide: Protein dispatched homolog 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshedgehog / secretion / sterol binding / Sterol-sensing domain / MEMBRANE PROTEIN
Function / homology
Function and homology information


patched ligand maturation / diaphragm development / molecular carrier activity / embryonic pattern specification / dorsal/ventral pattern formation / peptide transport / determination of left/right symmetry / smoothened signaling pathway / regulation of protein secretion / protein homotrimerization ...patched ligand maturation / diaphragm development / molecular carrier activity / embryonic pattern specification / dorsal/ventral pattern formation / peptide transport / determination of left/right symmetry / smoothened signaling pathway / regulation of protein secretion / protein homotrimerization / basolateral plasma membrane / membrane
Similarity search - Function
: / Membrane transport protein MMPL domain / MMPL family / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
Protein dispatched homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.53 Å
AuthorsChen H / Liu Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01 HL020948 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM135343 United States
CitationJournal: Life Sci Alliance / Year: 2020
Title: Structure of human Dispatched-1 provides insights into Hedgehog ligand biogenesis.
Authors: Hongwen Chen / Yang Liu / Xiaochun Li /
Abstract: Hedgehog (HH) signaling is essential for metazoan development. The HH ligand is secreted into the extracellular space by a cell surface protein named Dispatched-1 (DISP1). Here, we report the cryo-EM ...Hedgehog (HH) signaling is essential for metazoan development. The HH ligand is secreted into the extracellular space by a cell surface protein named Dispatched-1 (DISP1). Here, we report the cryo-EM structure of human DISP1 protein. DISP1 contains 12 transmembrane helices (TMs) and two extracellular domains (ECDs). Its ECDs reveal an open state, in contrast to its structural homologues PTCH1 and NPC1, whose extracellular/luminal domains adopt a closed state. The low-resolution structure of the DISP1 complex with dual lipid-modified HH ligand reveals how the ECDs of DISP1 engage with HH ligand. Moreover, several cholesterol-like molecules are found in the TMs, implying a transport-like function of DISP1.
History
DepositionJun 12, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xe6
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22144.png

Downloads & links

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Map

FileDownload / File: emd_22144.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Human Dispatched-1 (DISP1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 213.248 Å		0.83 Å/pix.
x 256 pix.
= 213.248 Å		0.83 Å/pix.
x 256 pix.
= 213.248 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0175 / Movie #1: 0.0175
Minimum - Maximum-0.04732763 - 0.06743968
Average (Standard dev.)0.00004338323 (±0.0027684553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 213.248 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8330.8330.833
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z213.248213.248213.248
α/β/γ90.00090.00090.000
start NX/NY/NZ777686
NX/NY/NZ10710993
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0470.0670.000

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Supplemental data

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Sample components

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Entire : Human dispatched-1 in complex with dual-lipidated SHH-N

EntireName: Human dispatched-1 in complex with dual-lipidated SHH-N
Components
  • Organelle or cellular component: Human dispatched-1 in complex with dual-lipidated SHH-N
    • Protein or peptide: Protein dispatched homolog 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human dispatched-1 in complex with dual-lipidated SHH-N

SupramoleculeName: Human dispatched-1 in complex with dual-lipidated SHH-N
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 124.49875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAWSHPQFEK SRPFKLPKSY AALIADWPVV VLGMCTMFIV VCALVGVLVP ELPDFSDPLL GFEPRGTAIG QRLVTWNNMV KNTGYKATL ANYPFKYADE QAKSHRDDRW SDDHYEREKR EVDWNFHKDS FFCDVPSDRY SRVVFTSSGG ETLWNLPAIK S MCNVDNSR ...String:
MAWSHPQFEK SRPFKLPKSY AALIADWPVV VLGMCTMFIV VCALVGVLVP ELPDFSDPLL GFEPRGTAIG QRLVTWNNMV KNTGYKATL ANYPFKYADE QAKSHRDDRW SDDHYEREKR EVDWNFHKDS FFCDVPSDRY SRVVFTSSGG ETLWNLPAIK S MCNVDNSR IRSHPQFGDL CQRTTAASCC PSWTLGNYIA ILNNRSSCQK IVERDVSHTL KLLRTCAKHY QNGTLGPDCW DM AARRKDQ LKCTNVPRKC TKYNAVYQIL HYLVDKDFMT PKTADYATPA LKYSMLFSPT EKGESMMNIY LDNFENWNSS DGV TTITGI EFGIKHSLFQ DYLLMDTVYP AIAIVIVLLV MCVYTKSMFI TLMTMFAIIS SLIVSYFLYR VVFHFEFFPF MNLT ALIIL VGIGADDAFV LCDVWNYTKF DKPHAETSET VSITLQHAAL SMFVTSFTTA AAFYANYVSN ITAIRCFGVY AGTAI LVNY VLMVTWLPAV VVLHERYLLN IFTCFKKPQQ QIYDNKSCWT VACQKCHKVL FAISEASRIF FEKVLPCIVI KFRYLW LFW FLALTVGGAY IVCINPKMKL PSLELSEFQV FRSSHPFERY DAEYKKLFMF ERVHHGEELH MPITVIWGVS PEDNGNP LN PKSKGKLTLD SSFNIASPAS QAWILHFCQK LRNQTFFYQT DEQDFTSCFI ETFKQWMENQ DCDEPALYPC CSHWSFPY K QEIFELCIKR AIMELERSTG YHLDSKTPGP RFDINDTIRA VVLEFQSTYL FTLAYEKMHQ FYKEVDSWIS SELSSAPEG LSNGWFVSNL EFYDLQDSLS DGTLIAMGLS VAVAFSVMLL TTWNIIISLY AIISIAGTIF VTVGSLVLLG WELNVLESVT ISVAVGLSV DFAVHYGVAY RLAPDPDREG KVIFSLSRVG SAMAMAALTT FVAGAMMMPS TVLAYTQLGT FMMLIMCISW A FATFFFQC MCRCLGPQGT CGQIPLPKKL QCSAFSHALS TSPSDKGQSK THTINAYHLD PRGPKSELEH EFYELEPLAS HS CTAPEKT TYEETHICSE FFNSQAKNLG MPVHAAYNSE LSKSTESDAG SDYKDDDDK

UniProtKB: Protein dispatched homolog 1

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

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

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

Concentration6 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
0.06 %C56H92O29digitonin
0.002 %C31H50O4Cholesteryl Hemisuccinate Tris Salt
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionNumber classes used: 2 / Resolution.type: BY AUTHOR / Resolution: 4.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 400432
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationSoftware - Name: RELION

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