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- EMDB-4344: Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC... -

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Basic information

Entry
Database: EMDB / ID: EMD-4344
TitleFilament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution
Map data
Sample
  • Complex: acetyl-CoA carboxylase and BRCT
    • Complex: Acetyl-CoA carboxylase 1
      • Protein or peptide: Acetyl-CoA carboxylase 1
    • Complex: Breast cancer type 1 susceptibility protein
      • Protein or peptide: Breast cancer type 1 susceptibility protein
KeywordsFilament / Helical / Multienzyme / Ligase / Biotin-dependent carboxylase
Function / homology
Function and homology information


histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / acetyl-CoA carboxylase / BRCA1-B complex / BRCA1-A complex / BRCA1-C complex / Defective HLCS causes multiple carboxylase deficiency ...histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / acetyl-CoA carboxylase / BRCA1-B complex / BRCA1-A complex / BRCA1-C complex / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / negative regulation of centriole replication / fatty-acyl-CoA biosynthetic process / sex-chromosome dosage compensation / random inactivation of X chromosome / malonyl-CoA biosynthetic process / Fatty acyl-CoA biosynthesis / ubiquitin-modified histone reader activity / nuclear ubiquitin ligase complex / acetyl-CoA carboxylase activity / chordate embryonic development / cellular response to indole-3-methanol / gamma-tubulin ring complex / negative regulation of intracellular estrogen receptor signaling pathway / ChREBP activates metabolic gene expression / DNA strand resection involved in replication fork processing / negative regulation of fatty acid biosynthetic process / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / homologous recombination / acetyl-CoA metabolic process / tissue homeostasis / protein K6-linked ubiquitination / Carnitine shuttle / lateral element / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / mitotic G2/M transition checkpoint / RNA polymerase binding / DNA damage tolerance / DNA repair complex / centrosome cycle / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / intracellular membraneless organelle / HDR through Single Strand Annealing (SSA) / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to RAD51 / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / lipid homeostasis / negative regulation of cell cycle / negative regulation of reactive oxygen species metabolic process / positive regulation of vascular endothelial growth factor production / Presynaptic phase of homologous DNA pairing and strand exchange / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of DNA repair / protein autoubiquitination / tubulin binding / Meiotic synapsis / Activation of gene expression by SREBF (SREBP) / positive regulation of DNA repair / cellular response to ionizing radiation / male germ cell nucleus / chromosome segregation / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / negative regulation of cell growth / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / Meiotic recombination / Metalloprotease DUBs / fibrillar center / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / ubiquitin-protein transferase activity / fatty acid biosynthetic process / cellular response to tumor necrosis factor / p53 binding / KEAP1-NFE2L2 pathway / cellular response to prostaglandin E stimulus / double-strand break repair / actin cytoskeleton / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / Neddylation / Processing of DNA double-strand break ends / protein homotetramerization / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity
Similarity search - Function
Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal ...Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / 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 / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / ATP-grasp fold, subdomain 1 / BRCA1 C Terminus (BRCT) domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / breast cancer carboxy-terminal domain / ClpP/crotonase-like domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Carbamoyl-phosphate synthase subdomain signature 2. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Breast cancer type 1 susceptibility protein / Acetyl-CoA carboxylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsHunkeler M / Hagmann A
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation138262 Switzerland
Swiss National Science Foundation15696 Switzerland
Swiss National Science Foundation164074 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-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6g2i
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4344.png

Downloads & links

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Map

FileDownload / File: emd_4344.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 376 pix.
= 397.808 Å		1.06 Å/pix.
x 376 pix.
= 397.808 Å		1.06 Å/pix.
x 376 pix.
= 397.808 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.015 / Movie #1: 0.011
Minimum - Maximum-0.033335805 - 0.08117923
Average (Standard dev.)0.0006214671 (±0.0031576413)
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-0.0330.0810.001

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Supplemental data

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Sample components

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Entire : acetyl-CoA carboxylase and BRCT

EntireName: acetyl-CoA carboxylase and BRCT
Components
  • Complex: acetyl-CoA carboxylase and BRCT
    • Complex: Acetyl-CoA carboxylase 1
      • Protein or peptide: Acetyl-CoA carboxylase 1
    • Complex: Breast cancer type 1 susceptibility protein
      • Protein or peptide: Breast cancer type 1 susceptibility protein

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Supramolecule #1: acetyl-CoA carboxylase and BRCT

SupramoleculeName: acetyl-CoA carboxylase and BRCT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Acetyl-CoA carboxylase 1

SupramoleculeName: Acetyl-CoA carboxylase 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Breast cancer type 1 susceptibility protein

SupramoleculeName: Breast cancer type 1 susceptibility protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Acetyl-CoA carboxylase 1

MacromoleculeName: Acetyl-CoA carboxylase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: acetyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 265.949344 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDEPSPLAQP LELNQHSRFI IGSVSEDNSE DEISNLVKLD LLEEKEGSLS PASVGSDTLS DLGISSLQDG LALHIRSSMS GLHLVKQGR DRKKIDSQRD FTVASPAEFV TRFGGNKVIE KVLIANNGIA AVKCMRSIRR WSYEMFRNER AIRFVVMVTP E DLKANAEY ...String:
MDEPSPLAQP LELNQHSRFI IGSVSEDNSE DEISNLVKLD LLEEKEGSLS PASVGSDTLS DLGISSLQDG LALHIRSSMS GLHLVKQGR DRKKIDSQRD FTVASPAEFV TRFGGNKVIE KVLIANNGIA AVKCMRSIRR WSYEMFRNER AIRFVVMVTP E DLKANAEY IKMADHYVPV PGGPNNNNYA NVELILDIAK RIPVQAVWAG WGHASENPKL PELLLKNGIA FMGPPSQAMW AL GDKIASS IVAQTAGIPT LPWSGSGLRV DWQENDFSKR ILNVPQELYE KGYVKDVDDG LQAAEEVGYP VMIKASEGGG GKG IRKVNN ADDFPNLFRQ VQAEVPGSPI FVMRLAKQSR HLEVQILADQ YGNAISLFGR DCSVQRRHQK IIEEAPATIA TPAV FEHME QCAVKLAKMV GYVSAGTVEY LYSQDGSFYF LELNPRLQVE HPCTEMVADV NLPAAQLQIA MGIPLYRIKD IRMMY GVSP WGDSPIDFED SAHVPCPRGH VIAARITSEN PDEGFKPSSG TVQELNFRSN KNVWGYFSVA AAGGLHEFAD SQFGHC FSW GENREEAISN MVVALKELSI RGDFRTTVEY LIKLLETESF QMNRIDTGWL DRLIAEKVQA ERPDTMLGVV CGALHVA DV SLRNSVSNFL HSLERGQVLP AHTLLNTVDV ELIYEGVKYV LKVTRQSPNS YVVIMNGSCV EVDVHRLSDG GLLLSYDG S SYTTYMKEEV DRYRITIGNK TCVFEKENDP SVMRSPSAGK LIQYIVEDGG HVFAGQCYAE IEVMKMVMTL TAVESGCIH YVKRPGAALD PGCVLAKMQL DNPSKVQQAE LHTGSLPRIQ STALRGEKLH RVFHYVLDNL VNVMNGYCLP DPFFSSKVKD WVERLMKTL RDPSLPLLEL QDIMTSVSGR IPPNVEKSIK KEMAQYASNI TSVLCQFPSQ QIANILDSHA ATLNRKSERE V FFMNTQSI VQLVQRYRSG IRGHMKAVVM DLLRQYLRVE TQFQNGHYDK CVFALREENK SDMNTVLNYI FSHAQVTKKN LL VTMLIDQ LCGRDPTLTD ELLNILTELT QLSKTTNAKV ALRARQVLIA SHLPSYELRH NQVESIFLSA IDMYGHQFCI ENL QKLILS ETSIFDVLPN FFYHSNQVVR MAALEVYVRR AYIAYELNSV QHRQLKDNTC VVEFQFMLPT SHPNRGNIPT LNRM SFSSN LNHYGMTHVA SVSDVLLDNS FTPPCQRMGG MVSFRTFEDF VRIFDEVMGC FSDSPPQ(SEP)PT FPEAGHTSLY D EDKVPRDE PIHILNVAIK TDCDIEDDRL AAMFREFTQQ NKATLVDHGI RRLTFLVAQK DFRKQVNYEV DRRFHREFPK FF TFRARDK FEEDRIYRHL EPALAFQLEL NRMRNFDLTA IPCANHKMHL YLGAAKVEVG TEVTDYRFFV RAIIRHSDLV TKE ASFEYL QNEGERLLLE AMDELEVAFN NTNVRTDCNH IFLNFVPTVI MDPSKIEESV RSMVMRYGSR LWKLRVLQAE LKIN IRLTP TGKAIPIRLF LTNESGYYLD ISLYKEVTDS RTAQIMFQAY GDKQGPLHGM LINTPYVTKD LLQSKRFQAQ SLGTT YIYD IPEMFRQSLI KLWESMSTQA FLPSPPLPSD MLTYTELVLD DQGQLVHMNR LPGGNEIGMV AWKMTFKSPE YPEGRD IIV IGNDITYRIG SFGPQEDLLF LRASELARAE GIPRIYVSAN SGARIGLAEE IRHMFHVAWV DPEDPYKGYR YLYLTPQ DY KRVSALNSVH CEHVEDEGES RYKITDIIGK EEGIGPENLR GSGMIAGESS LAYNEIITIS LVTCRAIGIG AYLVRLGQ R TIQVENSHLI LTGAGALNKV LGREVYTSNN QLGGIQIMHN NGVTHCTVCD DFEGVFTVLH WLSYMPKSVH SSVPLLNSK DPIDRIIEFV PTKTPYDPRW MLAGRPHPTQ KGQWLSGFFD YGSFSEIMQP WAQTVVVGRA RLGGIPVGVV AVETRTVELS IPADPANLD SEAKIIQQAG QVWFPDSAFK TYQAIKDFNR EGLPLMVFAN WRGFSGGMKD MYDQVLKFGA YIVDGLRECC Q PVLVYIPP QAELRGGSWV VIDSSINPRH MEMYADRESR GSVLEPEGTV EIKFRRKDLV KTMRRVDPVY IHLAERLGTP EL STAERKE LENKLKEREE FLIPIYHQVA VQFADLHDTP GRMQEKGVIS DILDWKTSRT FFYWRLRRLL LEDLVKKKIH NAN PELTDG QIQAMLRRWF VEVEGTVKAY VWDNNKDLAE WLEKQLTEED GVHSVIEENI KCISRDYVLK QIRSLVQANP EVAM DSIIH MTQHISPTQR AEVIRILSTM DSPST

UniProtKB: Acetyl-CoA carboxylase 1

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Macromolecule #2: Breast cancer type 1 susceptibility protein

MacromoleculeName: Breast cancer type 1 susceptibility protein / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.664869 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKHHHHHHPM TSLYKKAGLE NLYFQGVNKR MSMVVSGLTP EEFMLVYKFA RKHHITLTNL ITEETTHVVM KTDAEFVCER TLKYFLGIA GGKWVVSYFW VTQSIKERKM LNEHDFEVRG DVVNGRNHQG PKRARESQDR KIFRGLEICC YGPFTNMPTD Q LEWMVQLC ...String:
MKHHHHHHPM TSLYKKAGLE NLYFQGVNKR MSMVVSGLTP EEFMLVYKFA RKHHITLTNL ITEETTHVVM KTDAEFVCER TLKYFLGIA GGKWVVSYFW VTQSIKERKM LNEHDFEVRG DVVNGRNHQG PKRARESQDR KIFRGLEICC YGPFTNMPTD Q LEWMVQLC GASVVKELSS FTLGTGVHPI VVVQPDAWTE DNGFHAIGQM CEAPVVTREW VLDSVALYQC QELDTYLIPQ IP

UniProtKB: Breast cancer type 1 susceptibility protein

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 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
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

Startup modelType of model: OTHER
Details: Initial model was generated form 2D class averages using e2initialmodel.py in EMAN2. PDB IDs: 2yl2; 5i87; 4asi; 4y18
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.01) / Number images used: 48483
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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