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- EMDB-4343: Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC... -

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Basic information

Entry
Database: EMDB / ID: EMD-4343
TitleFilament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) core at 4.6 A resolution
Map data
Sample
  • Complex: Multienzyme core
    • Protein or peptide: Acetyl-CoA carboxylase 1
Function / homology
Function and homology information


fatty-acyl-CoA biosynthetic process / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / acetyl-CoA carboxylase / Fatty acyl-CoA biosynthesis / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / ChREBP activates metabolic gene expression / tissue homeostasis ...fatty-acyl-CoA biosynthetic process / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / acetyl-CoA carboxylase / Fatty acyl-CoA biosynthesis / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / ChREBP activates metabolic gene expression / tissue homeostasis / Carnitine metabolism / protein metabolic process / lipid homeostasis / Activation of gene expression by SREBF (SREBP) / fibrillar center / cellular response to prostaglandin E stimulus / fatty acid biosynthetic process / actin cytoskeleton / protein homotetramerization / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase ...Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Rudiment single hybrid motif / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Acetyl-CoA carboxylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsHunkeler M / Hagmann A / Stuttfeld E / Chami M / Stahlberg H / Maier T
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation138262 Switzerland
Swiss National Science Foundation164074 Switzerland
Swiss National Science Foundation15696 Switzerland
CitationJournal: Nature / Year: 2018
Title: Structural basis for regulation of human acetyl-CoA carboxylase.
Authors: Moritz Hunkeler / Anna Hagmann / Edward Stuttfeld / Mohamed Chami / Yakir Guri / Henning Stahlberg / Timm Maier /
Abstract: Acetyl-CoA carboxylase catalyses the ATP-dependent carboxylation of acetyl-CoA, a rate-limiting step in fatty acid biosynthesis. Eukaryotic acetyl-CoA carboxylases are large, homodimeric multienzymes. ...Acetyl-CoA carboxylase catalyses the ATP-dependent carboxylation of acetyl-CoA, a rate-limiting step in fatty acid biosynthesis. Eukaryotic acetyl-CoA carboxylases are large, homodimeric multienzymes. Human acetyl-CoA carboxylase occurs in two isoforms: the metabolic, cytosolic ACC1, and ACC2, which is anchored to the outer mitochondrial membrane and controls fatty acid β-oxidation. ACC1 is regulated by a complex interplay of phosphorylation, binding of allosteric regulators and protein-protein interactions, which is further linked to filament formation. These filaments were discovered in vitro and in vivo 50 years ago, but the structural basis of ACC1 polymerization and regulation remains unknown. Here, we identify distinct activated and inhibited ACC1 filament forms. We obtained cryo-electron microscopy structures of an activated filament that is allosterically induced by citrate (ACC-citrate), and an inactivated filament form that results from binding of the BRCT domains of the breast cancer type 1 susceptibility protein (BRCA1). While non-polymeric ACC1 is highly dynamic, filament formation locks ACC1 into different catalytically competent or incompetent conformational states. This unique mechanism of enzyme regulation via large-scale conformational changes observed in ACC1 has potential uses in engineering of switchable biosynthetic systems. Dissecting the regulation of acetyl-CoA carboxylase opens new paths towards counteracting upregulation of fatty acid biosynthesis in disease.
History
DepositionMar 23, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseJun 13, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6g2h
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4343.png

Downloads & links

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Map

FileDownload / File: emd_4343.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.058 Å
Density
Contour LevelBy EMDB: 0.014 / Movie #1: 0.018
Minimum - Maximum-0.04452072 - 0.09092379
Average (Standard dev.)0.0003105495 (±0.0028422684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 397.80798 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z376376376
origin x/y/z0.0000.0000.000
length x/y/z397.808397.808397.808
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS376376376
D min/max/mean-0.0450.0910.000

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Supplemental data

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Sample components

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Entire : Multienzyme core

EntireName: Multienzyme core
Components
  • Complex: Multienzyme core
    • Protein or peptide: Acetyl-CoA carboxylase 1

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Supramolecule #1: Multienzyme core

SupramoleculeName: Multienzyme core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Acetyl-CoA carboxylase 1

MacromoleculeName: Acetyl-CoA carboxylase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: acetyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 272.632844 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAHHHHHHHH HHGSTSGSGE QKLISEEDLG STSGSGDYKD DDDKLTSLYK KAGLENLYFQ GMDEPSPLAQ PLELNQHSRF IIGSVSEDN SEDEISNLVK LDLLEEKEGS LSPASVGSDT LSDLGISSLQ DGLALHIRSS MSGLHLVKQG RDRKKIDSQR D FTVASPAE ...String:
MAHHHHHHHH HHGSTSGSGE QKLISEEDLG STSGSGDYKD DDDKLTSLYK KAGLENLYFQ GMDEPSPLAQ PLELNQHSRF IIGSVSEDN SEDEISNLVK LDLLEEKEGS LSPASVGSDT LSDLGISSLQ DGLALHIRSS MSGLHLVKQG RDRKKIDSQR D FTVASPAE FVTRFGGNKV IEKVLIANNG IAAVKCMRSI RRWSYEMFRN ERAIRFVVMV TPEDLKANAE YIKMADHYVP VP GGPNNNN YANVELILDI AKRIPVQAVW AGWGHASENP KLPELLLKNG IAFMGPPSQA MWALGDKIAS SIVAQTAGIP TLP WSGSGL RVDWQENDFS KRILNVPQEL YEKGYVKDVD DGLQAAEEVG YPVMIKASEG GGGKGIRKVN NADDFPNLFR QVQA EVPGS PIFVMRLAKQ SRHLEVQILA DQYGNAISLF GRDCSVQRRH QKIIEEAPAT IATPAVFEHM EQCAVKLAKM VGYVS AGTV EYLYSQDGSF YFLELNPRLQ VEHPCTEMVA DVNLPAAQLQ IAMGIPLYRI KDIRMMYGVS PWGDSPIDFE DSAHVP CPR GHVIAARITS ENPDEGFKPS SGTVQELNFR SNKNVWGYFS VAAAGGLHEF ADSQFGHCFS WGENREEAIS NMVVALK EL SIRGDFRTTV EYLIKLLETE SFQMNRIDTG WLDRLIAEKV QAERPDTMLG VVCGALHVAD VSLRNSVSNF LHSLERGQ V LPAHTLLNTV DVELIYEGVK YVLKVTRQSP NSYVVIMNGS CVEVDVHRLS DGGLLLSYDG SSYTTYMKEE VDRYRITIG NKTCVFEKEN DPSVMRSPSA GKLIQYIVED GGHVFAGQCY AEIEVMKMVM TLTAVESGCI HYVKRPGAAL DPGCVLAKMQ LDNPSKVQQ AELHTGSLPR IQSTALRGEK LHRVFHYVLD NLVNVMNGYC LPDPFFSSKV KDWVERLMKT LRDPSLPLLE L QDIMTSVS GRIPPNVEKS IKKEMAQYAS NITSVLCQFP SQQIANILDS HAATLNRKSE REVFFMNTQS IVQLVQRYRS GI RGHMKAV VMDLLRQYLR VETQFQNGHY DKCVFALREE NKSDMNTVLN YIFSHAQVTK KNLLVTMLID QLCGRDPTLT DEL LNILTE LTQLSKTTNA KVALRARQVL IASHLPSYEL RHNQVESIFL SAIDMYGHQF CIENLQKLIL SETSIFDVLP NFFY HSNQV VRMAALEVYV RRAYIAYELN SVQHRQLKDN TCVVEFQFML PTSHPNRGNI PTLNRMSFSS NLNHYGMTHV ASVSD VLLD NSFTPPCQRM GGMVSFRTFE DFVRIFDEVM GCFSDSPPQS PTFPEAGHTS LYDEDKVPRD EPIHILNVAI KTDCDI EDD RLAAMFREFT QQNKATLVDH GIRRLTFLVA QKDFRKQVNY EVDRRFHREF PKFFTFRARD KFEEDRIYRH LEPALAF QL ELNRMRNFDL TAIPCANHKM HLYLGAAKVE VGTEVTDYRF FVRAIIRHSD LVTKEASFEY LQNEGERLLL EAMDELEV A FNNTNVRTDC NHIFLNFVPT VIMDPSKIEE SVRSMVMRYG SRLWKLRVLQ AELKINIRLT PTGKAIPIRL FLTNESGYY LDISLYKEVT DSRTAQIMFQ AYGDKQGPLH GMLINTPYVT KDLLQSKRFQ AQSLGTTYIY DIPEMFRQSL IKLWESMSTQ AFLPSPPLP SDMLTYTELV LDDQGQLVHM NRLPGGNEIG MVAWKMTFKS PEYPEGRDII VIGNDITYRI GSFGPQEDLL F LRASELAR AEGIPRIYVS ANSGARIGLA EEIRHMFHVA WVDPEDPYKG YRYLYLTPQD YKRVSALNSV HCEHVEDEGE SR YKITDII GKEEGIGPEN LRGSGMIAGE SSLAYNEIIT ISLVTCRAIG IGAYLVRLGQ RTIQVENSHL ILTGAGALNK VLG REVYTS NNQLGGIQIM HNNGVTHCTV CDDFEGVFTV LHWLSYMPKS VHSSVPLLNS KDPIDRIIEF VPTKTPYDPR WMLA GRPHP TQKGQWLSGF FDYGSFSEIM QPWAQTVVVG RARLGGIPVG VVAVETRTVE LSIPADPANL DSEAKIIQQA GQVWF PDSA FKTYQAIKDF NREGLPLMVF ANWRGFSGGM KDMYDQVLKF GAYIVDGLRE CCQPVLVYIP PQAELRGGSW VVIDSS INP RHMEMYADRE SRGSVLEPEG TVEIKFRRKD LVKTMRRVDP VYIHLAERLG TPELSTAERK ELENKLKERE EFLIPIY HQ VAVQFADLHD TPGRMQEKGV ISDILDWKTS RTFFYWRLRR LLLEDLVKKK IHNANPELTD GQIQAMLRRW FVEVEGTV K AYVWDNNKDL AEWLEKQLTE EDGVHSVIEE NIKCISRDYV LKQIRSLVQA NPEVAMDSII HMTQHISPTQ RAEVIRILS TMDSPST

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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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 K2 SUMMIT (4k x 4k) / Average electron dose: 80.0 e/Å2
Details: Collected in movie-mode with total dose of 80 e-/A2 for a total of 80 frames. Frames 3-22 were used for final reconstruction.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Initial model was generated form 2D class averages using e2initialmodel.py in EMAN2
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.01) / Number images used: 48483

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