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- EMDB-4771: S. cerevisiae Niemann-Pick type C Related Protein 1 (NCR1) -

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Basic information

Entry
Database: EMDB / ID: EMD-4771
TitleS. cerevisiae Niemann-Pick type C Related Protein 1 (NCR1)
Map datapost-processed map
Sample
  • Organelle or cellular component: NCR1
    • Protein or peptide: Niemann-Pick type C-related protein 1
Function / homology
Function and homology information


Intestinal lipid absorption / LDL clearance / sterol binding / sterol transport / sphingolipid metabolic process / fungal-type vacuole membrane / transmembrane transporter activity / endoplasmic reticulum / membrane
Similarity search - Function
Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Acriflavin resistance protein / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
NPC intracellular sterol transporter 1-related protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsRawson S / Kidmose RT / Muench SP / Pedersen BP
Funding support Denmark, United Kingdom, 5 items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-4002-0052 Denmark
Other privateCarlsberg Foundation CF17-0180 Denmark
European Research Council637372
Wellcome Trust108466/Z/15/Z United Kingdom
Other governmentAIAS fellowship Denmark
CitationJournal: Cell / Year: 2019
Title: Structural Insight into Eukaryotic Sterol Transport through Niemann-Pick Type C Proteins.
Authors: Mikael B L Winkler / Rune T Kidmose / Maria Szomek / Katja Thaysen / Shaun Rawson / Stephen P Muench / Daniel Wüstner / Bjørn Panyella Pedersen /
Abstract: Niemann-Pick type C (NPC) proteins are essential for sterol homeostasis, believed to drive sterol integration into the lysosomal membrane before redistribution to other cellular membranes. Here, ...Niemann-Pick type C (NPC) proteins are essential for sterol homeostasis, believed to drive sterol integration into the lysosomal membrane before redistribution to other cellular membranes. Here, using a combination of crystallography, cryo-electron microscopy, and biochemical and in vivo studies on the Saccharomyces cerevisiae NPC system (NCR1 and NPC2), we present a framework for sterol membrane integration. Sterols are transferred between hydrophobic pockets of vacuolar NPC2 and membrane-protein NCR1. NCR1 has its N-terminal domain (NTD) positioned to deliver a sterol to a tunnel connecting NTD to the luminal membrane leaflet 50 Å away. A sterol is caught inside this tunnel during transport, and a proton-relay network of charged residues in the transmembrane region is linked to this tunnel supporting a proton-driven transport mechanism. We propose a model for sterol integration that clarifies the role of NPC proteins in this essential eukaryotic pathway and that rationalizes mutations in patients with Niemann-Pick disease type C.
History
DepositionApr 4, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4771.png

Downloads & links

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Map

FileDownload / File: emd_4771.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost-processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 220 pix.
= 230.34 Å		1.05 Å/pix.
x 220 pix.
= 230.34 Å		1.05 Å/pix.
x 220 pix.
= 230.34 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0468 / Movie #1: 0.04
Minimum - Maximum-0.058619715 - 0.12875955
Average (Standard dev.)0.0013118687 (±0.007214644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 230.34001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0471.0471.047
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z230.340230.340230.340
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0590.1290.001

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Supplemental data

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Additional map: local resolution filtered.

Fileemd_4771_additional.map
Annotationlocal resolution filtered.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: local resolution filtered.

Fileemd_4771_additional_1.map
Annotationlocal resolution filtered.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_4771_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_4771_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NCR1

EntireName: NCR1
Components
  • Organelle or cellular component: NCR1
    • Protein or peptide: Niemann-Pick type C-related protein 1

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Supramolecule #1: NCR1

SupramoleculeName: NCR1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 133 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Niemann-Pick type C-related protein 1

MacromoleculeName: Niemann-Pick type C-related protein 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MNVLWIIALV GQLMRLVQGT ATCAMYGNCG KKSVFGNELP CPVPRSFEPP VLSDETSKLL VEVCGEEWKE VRYACCTKDQ VVALRDNLQK AQPLISSCPA CLKNFNNLFC HFTCAADQGR FVNITKVEKS KEDKDIVAEL DVFMNSSWAS EFYDSCKNIK FSATNGYAMD ...String:
MNVLWIIALV GQLMRLVQGT ATCAMYGNCG KKSVFGNELP CPVPRSFEPP VLSDETSKLL VEVCGEEWKE VRYACCTKDQ VVALRDNLQK AQPLISSCPA CLKNFNNLFC HFTCAADQGR FVNITKVEKS KEDKDIVAEL DVFMNSSWAS EFYDSCKNIK FSATNGYAMD LIGGGAKNYS QFLKFLGDAK PMLGGSPFQI NYKYDLANEE KEWQEFNDEV YACDDAQYKC ACSDCQESCP HLKPLKDGVC KVGPLPCFSL SVLIFYTICA LFAFMWYYLC KRKKNGAMIV DDDIVPESGS LDESETNVFE SFNNETNFFN GKLANLFTKV GQFSVENPYK ILITTVFSIF VFSFIIFQYA TLETDPINLW VSKNSEKFKE KEYFDDNFGP FYRTEQIFVV NETGPVLSYE TLHWWFDVEN FITEELQSSE NIGYQDLCFR PTEDSTCVIE SFTQYFQGAL PNKDSWKREL QECGKFPVNC LPTFQQPLKT NLLFSDDDIL NAHAFVVTLL LTNHTQSANR WEERLEEYLL DLKVPEGLRI SFNTEISLEK ELNNNNDIST VAISYLMMFL YATWALRRKD GKTRLLLGIS GLLIVLASIV CAAGFLTLFG LKSTLIIAEV IPFLILAIGI DNIFLITHEY DRNCEQKPEY SIDQKIISAI GRMSPSILMS LLCQTGCFLI AAFVTMPAVH NFAIYSTVSV IFNGVLQLTA YVSILSLYEK RSNYKQITGN EETKESFLKT FYFKMLTQKR LIIIIFSAWF FTSLVFLPEI QFGLDQTLAV PQDSYLVDYF KDVYSFLNVG PPVYMVVKNL DLTKRQNQQK ICGKFTTCER DSLANVLEQE RHRSTITEPL ANWLDDYFMF LNPQNDQCCR LKKGTDEVCP PSFPSRRCET CFQQGSWNYN MSGFPEGKDF MEYLSIWINA PSDPCPLGGR APYSTALVYN ETSVSASVFR TAHHPLRSQK DFIQAYSDGV RISSSFPELD MFAYSPFYIF FVQYQTLGPL TLKLIGSAII LIFFISSVFL QNIRSSFLLA LVVTMIIVDI GALMALLGIS LNAVSLVNLI ICVGLGVEFC VHIVRSFTVV PSETKKDANS RVLYSLNTIG ESVIKGITLT KFIGVCVLAF AQSKIFDVFY FRMWFTLIIV AALHALLFLP ALLSLFGGES YRDDSIEAED LVPRGSGGGG SGGGGSGGHH HHHHHHHH

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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 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / 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: COUNTING / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20535
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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