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- EMDB-38433: Citrate-induced filament of human acetyl-coenzyme A carboxylase 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-38433
TitleCitrate-induced filament of human acetyl-coenzyme A carboxylase 1 (ACC1-citrate)
Map data
Sample
  • Complex: Citrate-induced filament of human acetyl-coenzyme A carboxylase 1 (ACC1-citrate)
    • Protein or peptide: Acetyl-CoA carboxylase 1
  • Ligand: BIOTIN
KeywordsBiotin-dependent carboxylase / LIGASE
Function / homology
Function and homology information


fatty-acyl-CoA biosynthetic process / acetyl-CoA carboxylase / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / protein metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA carboxylase activity ...fatty-acyl-CoA biosynthetic process / acetyl-CoA carboxylase / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / protein metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA carboxylase activity / tissue homeostasis / Carnitine shuttle / lipid homeostasis / Activation of gene expression by SREBF (SREBP) / fibrillar center / fatty acid biosynthetic process / cellular response to prostaglandin E stimulus / 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 / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / 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: 4.14 Å
AuthorsZhou FY / Zhang YY / Zhou Q / Hu Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2024
Title: Filament structures unveil the dynamic organization of human acetyl-CoA carboxylase.
Authors: Fayang Zhou / Yuanyuan Zhang / Yuyao Zhu / Qiang Zhou / Yigong Shi / Qi Hu /
Abstract: Human acetyl-coenzyme A (CoA) carboxylases (ACCs) catalyze the carboxylation of acetyl-CoA, which is the rate-limiting step in fatty acid synthesis. The molecular mechanism underlying the dynamic ...Human acetyl-coenzyme A (CoA) carboxylases (ACCs) catalyze the carboxylation of acetyl-CoA, which is the rate-limiting step in fatty acid synthesis. The molecular mechanism underlying the dynamic organization of ACCs is largely unknown. Here, we determined the cryo-electron microscopy (EM) structure of human ACC1 in its inactive state, which forms a unique filament structure and is in complex with acetyl-CoA. We also determined the cryo-EM structure of human ACC1 activated by dephosphorylation and citrate treatment, at a resolution of 2.55 Å. Notably, the covalently linked biotin binds to a site that is distant from the acetyl-CoA binding site when acetyl-CoA is absent, suggesting a potential coordination between biotin binding and acetyl-CoA binding. These findings provide insights into the structural dynamics and regulatory mechanisms of human ACCs.
History
DepositionDec 25, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38433.png

Downloads & links

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Map

FileDownload / File: emd_38433.map.gz / Format: CCP4 / Size: 443.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 488 pix.
= 525.722 Å		1.08 Å/pix.
x 488 pix.
= 525.722 Å		1.08 Å/pix.
x 488 pix.
= 525.722 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.6691074 - 1.7191802
Average (Standard dev.)0.001038832 (±0.047452424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions488488488
Spacing488488488
CellA=B=C: 525.72235 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38433_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_38433_half_map_2.map
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Sample components

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Entire : Citrate-induced filament of human acetyl-coenzyme A carboxylase 1...

EntireName: Citrate-induced filament of human acetyl-coenzyme A carboxylase 1 (ACC1-citrate)
Components
  • Complex: Citrate-induced filament of human acetyl-coenzyme A carboxylase 1 (ACC1-citrate)
    • Protein or peptide: Acetyl-CoA carboxylase 1
  • Ligand: BIOTIN

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Supramolecule #1: Citrate-induced filament of human acetyl-coenzyme A carboxylase 1...

SupramoleculeName: Citrate-induced filament of human acetyl-coenzyme A carboxylase 1 (ACC1-citrate)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 6 / Enantiomer: LEVO / EC number: acetyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 265.869375 KDa
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 FSDSPPQSPT FPEAGHTSLY DEDKV PRDE PIHILNVAIK TDCDIEDDRL AAMFREFTQQ NKATLVDHGI RRLTFLVAQK DFRKQVNYEV DRRFHREFPK FFTFRA RDK FEEDRIYRHL EPALAFQLEL NRMRNFDLTA IPCANHKMHL YLGAAKVEVG TEVTDYRFFV RAIIRHSDLV TKEASFE YL QNEGERLLLE AMDELEVAFN NTNVRTDCNH IFLNFVPTVI MDPSKIEESV RSMVMRYGSR LWKLRVLQAE LKINIRLT P TGKAIPIRLF LTNESGYYLD ISLYKEVTDS RTAQIMFQAY GDKQGPLHGM LINTPYVTKD LLQSKRFQAQ SLGTTYIYD IPEMFRQSLI KLWESMSTQA FLPSPPLPSD MLTYTELVLD DQGQLVHMNR LPGGNEIGMV AWKMTFKSPE YPEGRDIIVI GNDITYRIG SFGPQEDLLF LRASELARAE GIPRIYVSAN SGARIGLAEE IRHMFHVAWV DPEDPYKGYR YLYLTPQDYK R VSALNSVH CEHVEDEGES RYKITDIIGK EEGIGPENLR GSGMIAGESS LAYNEIITIS LVTCRAIGIG AYLVRLGQRT IQ VENSHLI LTGAGALNKV LGREVYTSNN QLGGIQIMHN NGVTHCTVCD DFEGVFTVLH WLSYMPKSVH SSVPLLNSKD PID RIIEFV PTKTPYDPRW MLAGRPHPTQ KGQWLSGFFD YGSFSEIMQP WAQTVVVGRA RLGGIPVGVV AVETRTVELS IPAD PANLD SEAKIIQQAG QVWFPDSAFK TYQAIKDFNR EGLPLMVFAN WRGFSGGMKD MYDQVLKFGA YIVDGLRECC QPVLV YIPP QAELRGGSWV VIDSSINPRH MEMYADRESR GSVLEPEGTV EIKFRRKDLV KTMRRVDPVY IHLAERLGTP ELSTAE RKE LENKLKEREE FLIPIYHQVA VQFADLHDTP GRMQEKGVIS DILDWKTSRT FFYWRLRRLL LEDLVKKKIH NANPELT DG QIQAMLRRWF VEVEGTVKAY VWDNNKDLAE WLEKQLTEED GVHSVIEENI KCISRDYVLK QIRSLVQANP EVAMDSII H MTQHISPTQR AEVIRILSTM DSPST

UniProtKB: Acetyl-CoA carboxylase 1

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Macromolecule #2: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 2 / Number of copies: 5 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6g2d

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36041
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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