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- EMDB-31595: Cryo-EM structure of the hedgehog release protein Disp from water... -

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Basic information

Entry
Database: EMDB / ID: EMD-31595
TitleCryo-EM structure of the hedgehog release protein Disp from water bear (Hypsibius dujardini)
Map data
Sample
  • Complex: Dispatched
    • Protein or peptide: Protein dispatched-like protein 1
Keywordscryo-EM / Dispatched / Hedgehog release / Hedgehog signaling / membrane protein / setrol sensing domain / water bear
Function / homologyMembrane transport protein MMPL domain / MMPL family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / membrane => GO:0016020 / plasma membrane / Protein dispatched-like protein 1
Function and homology information
Biological speciesHypsibius dujardini (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsLuo Y / Wan G
Funding support China, 6 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020204 China
Chinese Academy of SciencesXDB19020100 China
Chinese Academy of SciencesQYZDB SSW SMC037 China
National Natural Science Foundation of China (NSFC)31870726 China
National Natural Science Foundation of China (NSFC)31630047 China
National Natural Science Foundation of China (NSFC)31771610 China
CitationJournal: Front Mol Biosci / Year: 2021
Title: Architecture of Dispatched, a Transmembrane Protein Responsible for Hedgehog Release.
Authors: Yitian Luo / Guoyue Wan / Xuan Zhou / Qiuwen Wang / Yunbin Zhang / Juan Bao / Yao Cong / Yun Zhao / Dianfan Li /
Abstract: The evolutionarily conserved Hedgehog (Hh) signaling pathway is crucial for programmed cell differentiation and proliferation. Dispatched (Disp) is a 12-transmembrane protein that plays a critical ...The evolutionarily conserved Hedgehog (Hh) signaling pathway is crucial for programmed cell differentiation and proliferation. Dispatched (Disp) is a 12-transmembrane protein that plays a critical role in the Hedgehog (Hh) signaling pathway by releasing the dually lipidated ligand HhN from the membrane, a prerequisite step to the downstream signaling cascade. In this study, we focus on the Disp from water bear, a primitive animal known as the most indestructible on Earth. Using a zebrafish model, we show that the water bear homolog possesses the function of Disp. We have solved its structure to a 6.5-Å resolution using single-particle cryogenic electron microscopy. Consistent with the evolutional conservation of the pathway, the water bear Disp structure is overall similar to the previously reported structures of the fruit fly and human homologs. Although not revealing much detail at this resolution, the water bear Disp shows a different conformation compared to published structures, suggesting that they represent different functional snapshots.
History
DepositionJul 31, 2021-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7fif
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31595.png

Downloads & links

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Map

FileDownload / File: emd_31595.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.023
Minimum - Maximum-0.056659244 - 0.08685326
Average (Standard dev.)0.00023536137 (±0.002803333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z208208208
origin x/y/z0.0000.0000.000
length x/y/z208.000208.000208.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-113-15
NX/NY/NZ10616274
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS208208208
D min/max/mean-0.0570.0870.000

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Supplemental data

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Half map: #1

Fileemd_31595_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_31595_half_map_2.map
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

EntireName: Dispatched
Components
  • Complex: Dispatched
    • Protein or peptide: Protein dispatched-like protein 1

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Supramolecule #1: Dispatched

SupramoleculeName: Dispatched / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hypsibius dujardini (invertebrata)
Molecular weightTheoretical: 130 kDa/nm

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Macromolecule #1: Protein dispatched-like protein 1

MacromoleculeName: Protein dispatched-like protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hypsibius dujardini (invertebrata)
Molecular weightTheoretical: 124.943414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSHHHHHHH HHHHHGSPRQ LVRRRKKTVM QRYAHFLAHH PFLILTLTFC ANIVLLLVIV CTDSLPAFDD PQAGFEPRGS LINQRAQAW RNFLERDGVV QPSTRRKATT TKPVAARQNA PVQEIGTGLR NSTVKENVFS SSGMASLGPI TQPRGFFCSR P LLGHAKLI ...String:
MGSHHHHHHH HHHHHGSPRQ LVRRRKKTVM QRYAHFLAHH PFLILTLTFC ANIVLLLVIV CTDSLPAFDD PQAGFEPRGS LINQRAQAW RNFLERDGVV QPSTRRKATT TKPVAARQNA PVQEIGTGLR NSTVKENVFS SSGMASLGPI TQPRGFFCSR P LLGHAKLI LRRKDAGNLL NLEGIRELCQ LDADIRRLDE FQSCSEESAD TGRLCRTWNL PNYVAVLAGK TSCHQLEEHD IR NVLNLTA TCLPFYRSGQ LKADCSTSED DGKTMQEDTI TCPGVPTDCI KDSSIYHLLY FISDKESRET GYSSMKHTLA VLP VWSSPA ALPLYRALQW GNFTRPDDDG PIQVIGMEMG LGDRLFNTAL LEDTLYVGVA AGVVVVVLWL YTGSLFVTLM NLMA IFFSL VVSYFLYVFV FRLTFFPFMN LLTCVIIVAI GADALVIFAR LWHLAKTEKD DGRFEKVVHA TFRHAAQAIL VSSLT ASAA LFSDIVNPII AIRCFSIFAG LTVLVHLFFA VTWMPACFVV ADKWGSSVYV CTKSPVCRLL YRCRCLHSGL RQYCDY FRI FFEKLLPCLV IRLKWMWMAS FVLLTVGACV VVFVFPGLQL ASGRTFSLWN SGHPSEQYRL LKDRFAFEEN RNLNNNE KV SLHFVWGVLA LNQAALLDPT DTGITTMDGR FNMSDPLSQI WMLKFCADLR QQTFFDNSTQ SDNACYFDSF MLWMETGA C SGHSQFPYPP ATFIRCVHTF SNSFPQAKHF GPNFNSLHQI DSFVLRLQTS QLFSHSYTAM QQLHQHVDQW FTAALRTAP PSLQGAWFTG DFAFFDLQQS LISGTALSLI VSLFVAFLVL FFTTLNVGVS LIAITVIAGI MLATTAALVL MEWQLSVFES TIIGLAIGL SVDFTLHYAV SYCCAESYEE RELKTNIVIS EMASCVTMSA VTTFLAGALM IPSDILFYRQ LGLFIITVTA I SLLYATIF LPACLAVLGP QGAFLQFHYP SCRPLCCRPD PSKLVEKSMH SSAEFDTTYT TGGTYDHHRE TKQCFHQSIN QP YQGKALR SPSAAANNHH VVVISATPEQ PPKTHPALLL DVDPDLADEE TDSVGELGSV PTSRGPSRGT SLIGTLEVLF Q

UniProtKB: Protein dispatched-like protein 1

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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

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
0.1 %C56H92O29digitonin
0.5 mMEDTAEthylenediaminetetraacetic acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 3 / Number real images: 5380 / Average exposure time: 7.6 sec. / Average electron dose: 60.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 62850
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 1
Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 31425 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6tbu


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7fif:
Cryo-EM structure of the hedgehog release protein Disp from water bear (Hypsibius dujardini)

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