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- EMDB-38432: Core region of the citrate-induced human acetyl-CoA carboxylase 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-38432
TitleCore region of the citrate-induced human acetyl-CoA carboxylase 1 filament (ACC1-citrate)
Map data
Sample
  • Complex: Core region of the citrate-induced human acetyl-CoA carboxylase 1 filament (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: 2.55 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-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38432.png

Downloads & links

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Map

FileDownload / File: emd_38432.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 344.736 Å		1.08 Å/pix.
x 320 pix.
= 344.736 Å		1.08 Å/pix.
x 320 pix.
= 344.736 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1038359 - 1.9873847
Average (Standard dev.)0.0046327966 (±0.07690513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 344.736 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38432_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram (log scale)

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Half map: #1

Fileemd_38432_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Core region of the citrate-induced human acetyl-CoA carboxylase 1...

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

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Supramolecule #1: Core region of the citrate-induced human acetyl-CoA carboxylase 1...

SupramoleculeName: Core region of the citrate-induced human acetyl-CoA carboxylase 1 filament (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: 2 / Enantiomer: LEVO / EC number: acetyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 254.443312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RDFTVASPAE FVTRFGGNKV IEKVLIANNG IAAVKCMRSI RRWSYEMFRN ERAIRFVVMV TPEDLKANAE YIKMADHYVP VPGGPNNNN YANVELILDI AKRIPVQAVW AGWGHASENP KLPELLLKNG IAFMGPPSQA MWALGDKIAS SIVAQTAGIP T LPWSGSGL ...String:
RDFTVASPAE FVTRFGGNKV IEKVLIANNG IAAVKCMRSI RRWSYEMFRN ERAIRFVVMV TPEDLKANAE YIKMADHYVP VPGGPNNNN YANVELILDI AKRIPVQAVW AGWGHASENP KLPELLLKNG IAFMGPPSQA MWALGDKIAS SIVAQTAGIP T LPWSGSGL RVDWQENDFS KRILNVPQEL YEKGYVKDVD DGLQAAEEVG YPVMIKASEG GGGKGIRKVN NADDFPNLFR QV QAEVPGS PIFVMRLAKQ SRHLEVQILA DQYGNAISLF GRDCSVQRRH QKIIEEAPAT IATPAVFEHM EQCAVKLAKM VGY VSAGTV EYLYSQDGSF YFLELNPRLQ VEHPCTEMVA DVNLPAAQLQ IAMGIPLYRI KDIRMMYGVS PWGDSPIDFE DSAH VPCPR GHVIAARITS ENPDEGFKPS SGTVQELNFR SNKNVWGYFS VAAAGGLHEF ADSQFGHCFS WGENREEAIS NMVVA LKEL SIRGDFRTTV EYLIKLLETE SFQMNRIDTG WLDRLIAEKV QAERPDTMLG VVCGALHVAD VSLRNSVSNF LHSLER GQV LPAHTLLNTV DVELIYEGVK YVLKVTRQSP NSYVVIMNGS CVEVDVHRLS DGGLLLSYDG SSYTTYMKEE VDRYRIT IG NKTCVFEKEN DPSVMRSPSA GKLIQYIVED GGHVFAGQCY AEIEVMKMVM TLTAVESGCI HYVKRPGAAL DPGCVLAK M QLDNPSKVQQ AELHTGSLPR IQSTALRGEK LHRVFHYVLD NLVNVMNGYC LPDPFFSSKV KDWVERLMKT LRDPSLPLL ELQDIMTSVS GRIPPNVEKS IKKEMAQYAS NITSVLCQFP SQQIANILDS HAATLNRKSE REVFFMNTQS IVQLVQRYRS GIRGHMKAV VMDLLRQYLR VETQFQNGHY DKCVFALREE NKSDMNTVLN YIFSHAQVTK KNLLVTMLID QLCGRDPTLT D ELLNILTE LTQLSKTTNA KVALRARQVL IASHLPSYEL RHNQVESIFL SAIDMYGHQF CIENLQKLIL SETSIFDVLP NF FYHSNQV VRMAALEVYV RRAYIAYELN SVQHRQLKDN TCVVEFQFML PTSHPNRGNI PTLNRMSFSS NLNHYGMTHV ASV SDVLLD NSFTPPCQRM GGMVSFRTFE DFVRIFDEVM GCFSDSPPQS PTFPEAGHTS LYDEDKVPRD EPIHILNVAI KTDC DIEDD RLAAMFREFT QQNKATLVDH GIRRLTFLVA QKDFRKQVNY EVDRRFHREF PKFFTFRARD KFEEDRIYRH LEPAL AFQL ELNRMRNFDL TAIPCANHKM HLYLGAAKVE VGTEVTDYRF FVRAIIRHSD LVTKEASFEY LQNEGERLLL EAMDEL EVA FNNTNVRTDC NHIFLNFVPT VIMDPSKIEE SVRSMVMRYG SRLWKLRVLQ AELKINIRLT PTGKAIPIRL FLTNESG YY LDISLYKEVT DSRTAQIMFQ AYGDKQGPLH GMLINTPYVT KDLLQSKRFQ AQSLGTTYIY DIPEMFRQSL IKLWESMS T QAFLPSPPLP SDMLTYTELV LDDQGQLVHM NRLPGGNEIG MVAWKMTFKS PEYPEGRDII VIGNDITYRI GSFGPQEDL LFLRASELAR AEGIPRIYVS ANSGARIGLA EEIRHMFHVA WVDPEDPYKG YRYLYLTPQD YKRVSALNSV HCEHVEDEGE SRYKITDII GKEEGIGPEN LRGSGMIAGE SSLAYNEIIT ISLVTCRAIG IGAYLVRLGQ RTIQVENSHL ILTGAGALNK V LGREVYTS NNQLGGIQIM HNNGVTHCTV CDDFEGVFTV LHWLSYMPKS VHSSVPLLNS KDPIDRIIEF VPTKTPYDPR WM LAGRPHP TQKGQWLSGF FDYGSFSEIM QPWAQTVVVG RARLGGIPVG VVAVETRTVE LSIPADPANL DSEAKIIQQA GQV WFPDSA FKTYQAIKDF NREGLPLMVF ANWRGFSGGM KDMYDQVLKF GAYIVDGLRE CCQPVLVYIP PQAELRGGSW VVID SSINP RHMEMYADRE SRGSVLEPEG TVEIKFRRKD LVKTMRRVDP VYIHLAERLG TPELSTAERK ELENKLKERE EFLIP IYHQ VAVQFADLHD TPGRMQEKGV ISDILDWKTS RTFFYWRLRR LLLEDLVKKK IHNANPELTD GQIQAMLRRW FVEVEG TVK AYVWDNNKDL AEWLEKQLTE EDGVHSVIEE NIKCISRDYV LKQIRSLVQA NPEVAMDSII HMTQHISPTQ RAEVIRI

UniProtKB: Acetyl-CoA carboxylase 1

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Macromolecule #2: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 2 / Number of copies: 2 / 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 statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
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: Talos Arctica / 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: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 224904
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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