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- EMDB-21414: Trimeric Complex of Them1 Negative Stain Map -

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Basic information

Entry
Database: EMDB / ID: EMD-21414
TitleTrimeric Complex of Them1 Negative Stain Map
Map dataNegative stain structure of Them1 trimer
Sample
  • Complex: Trimer complex of Them1
    • Protein or peptide: Thioesterase Superfamily Member 1
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsTillman MC / Imai N / Li Y / Khadka M / Okafor CD / Juneja P / Adhiyaman A / Hagen SJ / Cohen DE / Ortlund EA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK103046-06 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008602 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Allosteric regulation of thioesterase superfamily member 1 by lipid sensor domain binding fatty acids and lysophosphatidylcholine.
Authors: Matthew C Tillman / Norihiro Imai / Yue Li / Manoj Khadka / C Denise Okafor / Puneet Juneja / Akshitha Adhiyaman / Susan J Hagen / David E Cohen / Eric A Ortlund /
Abstract: Nonshivering thermogenesis occurs in brown adipose tissue to generate heat in response to cold ambient temperatures. Thioesterase superfamily member 1 (Them1) is transcriptionally up-regulated in ...Nonshivering thermogenesis occurs in brown adipose tissue to generate heat in response to cold ambient temperatures. Thioesterase superfamily member 1 (Them1) is transcriptionally up-regulated in brown adipose tissue upon exposure to the cold and suppresses thermogenesis in order to conserve energy reserves. It hydrolyzes long-chain fatty acyl-CoAs that are derived from lipid droplets, preventing their use as fuel for thermogenesis. In addition to its enzymatic domains, Them1 contains a C-terminal StAR-related lipid transfer (START) domain with unknown ligand or function. By complementary biophysical approaches, we show that the START domain binds to long-chain fatty acids, products of Them1's enzymatic reaction, as well as lysophosphatidylcholine (LPC), lipids shown to activate thermogenesis in brown adipocytes. Certain fatty acids stabilize the START domain and allosterically enhance Them1 catalysis of acyl-CoA, whereas 18:1 LPC destabilizes and inhibits activity, which we verify in cell culture. Additionally, we demonstrate that the START domain functions to localize Them1 near lipid droplets. These findings define the role of the START domain as a lipid sensor that allosterically regulates Them1 activity and spatially localizes it in proximity to the lipid droplet.
History
DepositionFeb 19, 2020-
Header (metadata) releaseMar 18, 2020-
Map releaseAug 19, 2020-
UpdateSep 23, 2020-
Current statusSep 23, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0097
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0097
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21414.png

Downloads & links

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Map

FileDownload / File: emd_21414.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain structure of Them1 trimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 256 pix.
= 399.36 Å		1.56 Å/pix.
x 256 pix.
= 399.36 Å		1.56 Å/pix.
x 256 pix.
= 399.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0097 / Movie #1: 0.0097
Minimum - Maximum-0.02302197 - 0.062241305
Average (Standard dev.)0.00001846106 (±0.002436477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 399.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.561.561.56
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z399.360399.360399.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0230.0620.000

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Supplemental data

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Sample components

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Entire : Trimer complex of Them1

EntireName: Trimer complex of Them1
Components
  • Complex: Trimer complex of Them1
    • Protein or peptide: Thioesterase Superfamily Member 1

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Supramolecule #1: Trimer complex of Them1

SupramoleculeName: Trimer complex of Them1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F
Molecular weightExperimental: 197 KDa

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Macromolecule #1: Thioesterase Superfamily Member 1

MacromoleculeName: Thioesterase Superfamily Member 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHSSG VDLGTENLYF QSNAYRNPTE VQMSQLVLPC HTNHRGELSI GQLLKWIDTT ACLSAERHAG CPCVTASMDD IYFDHTISVG QVVNIKAKVN RAFNSSMEVG IQVVSEDLCS EKQWSVCKAL ATFVAHRELS KVKLKQVIPL TEEEKTEHGV AAERRRMRLV ...String:
MHHHHHHSSG VDLGTENLYF QSNAYRNPTE VQMSQLVLPC HTNHRGELSI GQLLKWIDTT ACLSAERHAG CPCVTASMDD IYFDHTISVG QVVNIKAKVN RAFNSSMEVG IQVVSEDLCS EKQWSVCKAL ATFVAHRELS KVKLKQVIPL TEEEKTEHGV AAERRRMRLV YADTIKDLLT HCVIQDDLDK DCSNMVPAEK TRVESVELVL PPHANHQGNT FGGQIMAWME NVATIAASRL CHAHPTLKAI EMFHFRGPSQ VGDRLVLKAI VNNAFKHSME VGVCVEAYRQ EAETQRRHIN SAFMTFVVLD KDDQPQKLPW IRPQPGEGER RYREASARKK IRLDRKYLVS CKQAEVALSV PWDPSNQVYL SYYNVSSLKT LMAKDNWVLS VEISEVRLYI LEEDFLSFHL EMVVNVDAAQ VFQLLSDLRR RPEWDKHYRS VELVQQVDED DAIYHVISPA LSGNTKPQDF VILASRRKPC DNGDPYVIAL RSVTLPTHHE TPEYQRGETL CSGFCLWREG DQMTKVSYYN QATPGFLNYV TTNVSGLSSE FYNTFKACES FLLDNRNDLA PSLQTL

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl formate

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 4457
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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