[English] 日本語
Yorodumi
- EMDB-23408: Chicken Scap D435V L1-L7 domain / Fab complex focused map -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23408
TitleChicken Scap D435V L1-L7 domain / Fab complex focused map
Map dataMap of L1L7/Fab domain from focused classification
Sample
  • Complex: Ternary complex of Scap with Fab fragment
    • Complex: Scap L1-L7 domain
      • Protein or peptide: Sterol regulatory element-binding protein cleavage-activating protein
    • Complex: 4G10 Fab
      • Protein or peptide: 4G10 Fab heavy chain
      • Protein or peptide: 4G10 Fab kappa chain
Function / homology
Function and homology information


Regulation of cholesterol biosynthesis by SREBP (SREBF) / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / SREBP signaling pathway / cellular lipid metabolic process / sterol binding / regulation of fatty acid biosynthetic process / positive regulation of cholesterol biosynthetic process / cholesterol metabolic process / response to insulin ...Regulation of cholesterol biosynthesis by SREBP (SREBF) / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / SREBP signaling pathway / cellular lipid metabolic process / sterol binding / regulation of fatty acid biosynthetic process / positive regulation of cholesterol biosynthetic process / cholesterol metabolic process / response to insulin / ER to Golgi transport vesicle membrane / membrane => GO:0016020 / response to hypoxia / immune response / Golgi membrane / endoplasmic reticulum membrane
Similarity search - Function
Sterol regulatory element-binding protein cleavage-activating protein / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Quinoprotein alcohol dehydrogenase-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...Sterol regulatory element-binding protein cleavage-activating protein / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Quinoprotein alcohol dehydrogenase-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Sterol regulatory element-binding protein cleavage-activating protein
Similarity search - Component
Biological speciesGallus gallus (chicken) / Mus musculus (house mouse) / Mouse (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKober DL / Radhakrishnan A / Goldstein JL / Brown MS / Clark LD / Bai X-C / Rosenbaum DM
Funding support United States, France, 11 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM116387 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL020948 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM136976 United States
Welch FoundationI-1770 United States
Welch FoundationI-1793 United States
Welch FoundationI-1944 United States
Mallinckrodt Foundation United States
Leducq Foundation19CVD04 France
Cancer Prevention and Research Institute of Texas (CPRIT)RR160082 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
American Heart Association18POST34080141 United States
CitationJournal: Cell / Year: 2021
Title: Scap structures highlight key role for rotation of intertwined luminal loops in cholesterol sensing.
Authors: Daniel L Kober / Arun Radhakrishnan / Joseph L Goldstein / Michael S Brown / Lindsay D Clark / Xiao-Chen Bai / Daniel M Rosenbaum /
Abstract: The cholesterol-sensing protein Scap induces cholesterol synthesis by transporting membrane-bound transcription factors called sterol regulatory element-binding proteins (SREBPs) from the endoplasmic ...The cholesterol-sensing protein Scap induces cholesterol synthesis by transporting membrane-bound transcription factors called sterol regulatory element-binding proteins (SREBPs) from the endoplasmic reticulum (ER) to the Golgi apparatus for proteolytic activation. Transport requires interaction between Scap's two ER luminal loops (L1 and L7), which flank an intramembrane sterol-sensing domain (SSD). Cholesterol inhibits Scap transport by binding to L1, which triggers Scap's binding to Insig, an ER retention protein. Here we used cryoelectron microscopy (cryo-EM) to elucidate two structures of full-length chicken Scap: (1) a wild-type free of Insigs and (2) mutant Scap bound to chicken Insig without cholesterol. Strikingly, L1 and L7 intertwine tightly to form a globular domain that acts as a luminal platform connecting the SSD to the rest of Scap. In the presence of Insig, this platform undergoes a large rotation accompanied by rearrangement of Scap's transmembrane helices. We postulate that this conformational change halts Scap transport of SREBPs and inhibits cholesterol synthesis.
History
DepositionFeb 2, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0561
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0561
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7lkh
  • Surface level: 0.0561
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23408.png

Downloads & links

-
Map

FileDownload / File: emd_23408.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of L1L7/Fab domain from focused classification
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.0561 / Movie #1: 0.0561
Minimum - Maximum-0.3095082 - 0.27011514
Average (Standard dev.)-7.1311704e-05 (±0.004649391)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 291.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z291.600291.600291.600
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.3100.270-0.000

-
Supplemental data

-
Sample components

-
Entire : Ternary complex of Scap with Fab fragment

EntireName: Ternary complex of Scap with Fab fragment
Components
  • Complex: Ternary complex of Scap with Fab fragment
    • Complex: Scap L1-L7 domain
      • Protein or peptide: Sterol regulatory element-binding protein cleavage-activating protein
    • Complex: 4G10 Fab
      • Protein or peptide: 4G10 Fab heavy chain
      • Protein or peptide: 4G10 Fab kappa chain

-
Supramolecule #1: Ternary complex of Scap with Fab fragment

SupramoleculeName: Ternary complex of Scap with Fab fragment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Fab fragment generated by proteolytic cleavage of IgG antibody
Molecular weightTheoretical: 50 KDa

-
Supramolecule #2: Scap L1-L7 domain

SupramoleculeName: Scap L1-L7 domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)
Recombinant expressionOrganism: Homo sapiens (human)

-
Supramolecule #3: 4G10 Fab

SupramoleculeName: 4G10 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Details: Fab fragment generated by proteolytic cleavage of IgG antibody
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Sterol regulatory element-binding protein cleavage-activating protein

MacromoleculeName: Sterol regulatory element-binding protein cleavage-activating protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 148.364828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PAMTLTEKLR ERISRAFYNH GLLCASYPIP IILFTGLCIL ACCYPLLKLP LPGTGPVEFS TPVKDYFPPS PDVVSQQGDL SERPDWYVG APVAYIQQIF VKATVSPWQK NFLAVDVFRS PLSRVFQLVE EIRNHALRDS SGVKSLEEVC LQVTDLLPGL K KLRNLLPE ...String:
PAMTLTEKLR ERISRAFYNH GLLCASYPIP IILFTGLCIL ACCYPLLKLP LPGTGPVEFS TPVKDYFPPS PDVVSQQGDL SERPDWYVG APVAYIQQIF VKATVSPWQK NFLAVDVFRS PLSRVFQLVE EIRNHALRDS SGVKSLEEVC LQVTDLLPGL K KLRNLLPE HGCLLLSPGN FWQNDRERFN ADPDIIKTIH QHEPKALQTS ATLKDLLFGL PGKYSGVNLY NRKRVVSYTV TL GLQRYDS RFLSSLRSRL KLLHPSPNCT LREDSIVHVH FKEEIGIAEL IPLVTTYIIL FAYIYFSTRK IDMVKSKWGL ALA AVVTVL SSLLMSVGLC TLFGLTPTLN GGEIFPYLVV VIGLENVLVL TKSVVSTPVD LEVKLRIAQG LSNESWSIMK NMAT ELGII LIGYFTLVPA IQEFCLFAVV GLVSVFFLQM LFFTTVLSID IRRMELADLN KRLPAEACLP PAKPASRSQR YERQP AVRP ATPHTITLQP SSFRNLRLPK RLRVIYFFAR TRLAQRLIMA GTVIWIGILV YTDPAGLRTY LTSQVTEQSP LGEAGL PPM PVPGGVLPAG DPKIDLSVFP SDPIQLSENQ TQQREQQAGL EPLGRLETNQ HSWAQGPEGR GNGQTELGTE AEVTWGA ED EEIWRKLSFR HWPSLFSYYN ITLAKRYISI LPAIPVTLYL NPQEALEVRH PQEANRYHPF LSSSGGKLNA EAQPDQTS S RLQGHRDVTL YKVAALGLAS GILLVLLLFC LYRLLCPKNY GQNGLSHSRR RRGDLPCDDY GYSPPETEIV PLVLRGHLM DIECLASDGM LLVSCCLVGQ IRVWDAQTGD CLTVIPKPRL RRDSSGIFDY QESWDHSPDG KTGLDDSFES SHQLKRMLSP PQPPLFCDQ PDLTSLIDTN FSEQVKVAES EPRLRAVGGR QKEAGYDFSS LVGKVYEEHS TSNCMNFGGL SAPHGQAGFC V GGSTARSL GCGSEEGGCG GRRRSLGDES LSGFDKSSPL PSWGGDFESS VWSLDLQGNL IVAGRSNGKL EVWDAIEGTL RS SNDESQS GITALVFLNN RIVAARLNGS LDFFSLETHT SLNHLQFRGA PSRSSIPSSP LFSSSDVIVC QLTHTVSCAH QKP ITALKA AAGRLVTGSQ DHTLRVFRLE DSCCLFTLQG HSGAITAVYI DQTMVLASGG QDGAICLWDV LTGSKVSHMY AHRG DVTSL TCTTSCVISS GLDDVISIWD RSSGIKLYSI QQEMGCGSSL GVISDNLLVT GGQGCVSFWD IGYGDLLQTV YLGKS NESQ PARQILVLEN AAIVCNFGSE LSLVYVPSVL EKLDDYKDDD DKGSDYKDDD DKGSDYKDDD DK

-
Macromolecule #2: 4G10 Fab heavy chain

MacromoleculeName: 4G10 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 24.94266 KDa
SequenceString: TGVHSEVQLQ QSGAELVRPG ASVKLSCTAS GFKIKDDYIH WVKQRPEQGL EWIGRIDPAN GHTRYAPKFQ DKATITADTS SNTAYLQLS SLTSEDTAVY YCTRYNDYDA FYFDYWGQGT TLTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
TGVHSEVQLQ QSGAELVRPG ASVKLSCTAS GFKIKDDYIH WVKQRPEQGL EWIGRIDPAN GHTRYAPKFQ DKATITADTS SNTAYLQLS SLTSEDTAVY YCTRYNDYDA FYFDYWGQGT TLTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DKT

-
Macromolecule #3: 4G10 Fab kappa chain

MacromoleculeName: 4G10 Fab kappa chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 23.667178 KDa
SequenceString: DIQMTQTTSS LSASLGDRVT ISCRASQDIR NYLNWYQQKP DGTVKLLIYY TSRLHSGVPS RFSGSGSGTD YSLTISNLEQ EDIATYFCQ QTNTLPWTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQTTSS LSASLGDRVT ISCRASQDIR NYLNWYQQKP DGTVKLLIYY TSRLHSGVPS RFSGSGSGTD YSLTISNLEQ EDIATYFCQ QTNTLPWTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMHEPES
0.004 %glyco-diosgenin
0.0004 %cholestoryl hemisuccinate
0.5 mMTris(2-carboxyethyl)phosphine hydrochloride
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 9052025
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155187
FSC plot (resolution estimation)

+
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