[English] 日本語
Yorodumi
- EMDB-18353: S. cerevisia Niemann-Pick type C protein NCR1 in Peptidisc at pH 7.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18353
TitleS. cerevisia Niemann-Pick type C protein NCR1 in Peptidisc at pH 7.5
Map data
Sample
  • Complex: NCR1 pH 7.5 in Peptidisc
    • Protein or peptide: NPC intracellular sterol transporter 1-related protein 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordssterol transport / vacuole / lysosome / LIPID TRANSPORT / membrane protein
Function / homology
Function and homology information


Intestinal lipid absorption / LDL clearance / sterol binding / sterol transport / sphingolipid metabolic process / fungal-type vacuole membrane / endoplasmic reticulum / membrane
Similarity search - Function
Niemann-Pick C1, N-terminal / Niemann-Pick C1 N terminus / Protein patched/dispatched / Patched family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
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: 2.43 Å
AuthorsFrain KM / Dedic E / Nel L / Olesen E / Stokes D / Panyella Pedersen B
Funding support United States, Denmark, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144109 United States
Danish Council for Independent Research0135-00032B Denmark
The Carlsberg FoundationCF19-0127 Denmark
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Conformational changes in the Niemann-Pick type C1 protein NCR1 drive sterol translocation.
Authors: Kelly M Frain / Emil Dedic / Lynette Nel / Anastasiia Bohush / Esben Olesen / Katja Thaysen / Daniel Wüstner / David L Stokes / Bjørn Panyella Pedersen /
Abstract: The membrane protein Niemann-Pick type C1 (NPC1, named NCR1 in yeast) is central to sterol homeostasis in eukaryotes. NCR1 is localized to the vacuolar membrane, where it is suggested to carry ...The membrane protein Niemann-Pick type C1 (NPC1, named NCR1 in yeast) is central to sterol homeostasis in eukaryotes. NCR1 is localized to the vacuolar membrane, where it is suggested to carry sterols across the protective glycocalyx and deposit them into the vacuolar membrane. However, documentation of a vacuolar glycocalyx in fungi is lacking, and the mechanism for sterol translocation has remained unclear. Here, we provide evidence supporting the presence of a glycocalyx in isolated vacuoles and report four cryo-EM structures of NCR1 in two distinct conformations, named tense and relaxed. These two conformations illustrate the movement of sterols through a tunnel formed by the luminal domains, thus bypassing the barrier presented by the glycocalyx. Based on these structures and on comparison with other members of the Resistance-Nodulation-Division (RND) superfamily, we propose a transport model that links changes in the luminal domains with a cycle of protonation and deprotonation within the transmembrane region of the protein. Our model suggests that NPC proteins work by a generalized RND mechanism where the proton motive force drives conformational changes in the transmembrane domains that are allosterically coupled to luminal/extracellular domains to promote sterol transport.
History
DepositionAug 31, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18353.png

Downloads & links

-
Map

FileDownload / File: emd_18353.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 440 pix.
= 284.68 Å		0.65 Å/pix.
x 440 pix.
= 284.68 Å		0.65 Å/pix.
x 440 pix.
= 284.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-2.719152 - 4.123805
Average (Standard dev.)-0.0008911134 (±0.065545335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 284.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18353_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18353_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18353_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NCR1 pH 7.5 in Peptidisc

EntireName: NCR1 pH 7.5 in Peptidisc
Components
  • Complex: NCR1 pH 7.5 in Peptidisc
    • Protein or peptide: NPC intracellular sterol transporter 1-related protein 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

-
Supramolecule #1: NCR1 pH 7.5 in Peptidisc

SupramoleculeName: NCR1 pH 7.5 in Peptidisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 132.6 KDa

-
Macromolecule #1: NPC intracellular sterol transporter 1-related protein 1

MacromoleculeName: NPC intracellular sterol transporter 1-related protein 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 132.755094 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MNVLWIIALV GQLMRLVQGT ATCAMYGNCG KKSVFGNELP CPVPRSFEPP VLSDETSKLL VEVCGEEWKE VRYACCTKDQ VVALRDNLQ KAQPLISSCP ACLKNFNNLF CHFTCAADQG RFVNITKVEK SKEDKDIVAE LDVFMNSSWA SEFYDSCKNI K FSATNGYA ...String:
MNVLWIIALV GQLMRLVQGT ATCAMYGNCG KKSVFGNELP CPVPRSFEPP VLSDETSKLL VEVCGEEWKE VRYACCTKDQ VVALRDNLQ KAQPLISSCP ACLKNFNNLF CHFTCAADQG RFVNITKVEK SKEDKDIVAE LDVFMNSSWA SEFYDSCKNI K FSATNGYA MDLIGGGAKN YSQFLKFLGD AKPMLGGSPF QINYKYDLAN EEKEWQEFND EVYACDDAQY KCACSDCQES CP HLKPLKD GVCKVGPLPC FSLSVLIFYT ICALFAFMWY YLCKRKKNGA MIVDDDIVPE SGSLDESETN VFESFNNETN FFN GKLANL FTKVGQFSVE NPYKILITTV FSIFVFSFII FQYATLETDP INLWVSKNSE KFKEKEYFDD NFGPFYRTEQ IFVV NETGP VLSYETLHWW FDVENFITEE LQSSENIGYQ DLCFRPTEDS TCVIESFTQY FQGALPNKDS WKRELQECGK FPVNC LPTF QQPLKTNLLF SDDDILNAHA FVVTLLLTNH TQSANRWEER LEEYLLDLKV PEGLRISFNT EISLEKELNN NNDIST VAI SYLMMFLYAT WALRRKDGKT RLLLGISGLL IVLASIVCAA GFLTLFGLKS TLIIAEVIPF LILAIGIDNI FLITHEY DR NCEQKPEYSI DQKIISAIGR MSPSILMSLL CQTGCFLIAA FVTMPAVHNF AIYSTVSVIF NGVLQLTAYV SILSLYEK R SNYKQITGNE ETKESFLKTF YFKMLTQKRL IIIIFSAWFF TSLVFLPEIQ FGLDQTLAVP QDSYLVDYFK DVYSFLNVG PPVYMVVKNL DLTKRQNQQK ICGKFTTCER DSLANVLEQE RHRSTITEPL ANWLDDYFMF LNPQNDQCCR LKKGTDEVCP PSFPSRRCE TCFQQGSWNY NMSGFPEGKD FMEYLSIWIN APSDPCPLGG RAPYSTALVY NETSVSASVF RTAHHPLRSQ K DFIQAYSD GVRISSSFPE LDMFAYSPFY IFFVQYQTLG PLTLKLIGSA IILIFFISSV FLQNIRSSFL LALVVTMIIV DI GALMALL GISLNAVSLV NLIICVGLGV EFCVHIVRSF TVVPSETKKD ANSRVLYSLN TIGESVIKGI TLTKFIGVCV LAF AQSKIF DVFYFRMWFT LIIVAALHAL LFLPALLSLF GGESYRDDSI EAED

UniProtKB: NPC intracellular sterol transporter 1-related protein 1

-
Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 130 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
50.0 mMNH2C(CH2OH)3.HClTris-HCl
0.5 mg/mlPeptidisc
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 5995 / Average electron dose: 60.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
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: 1868080
Startup modelType of model: NONE / Details: ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 232621
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6r4l


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 72.4
Output model

PDB-8qee:
S. cerevisia Niemann-Pick type C protein NCR1 in Peptidisc at pH 7.5

+
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