[English] 日本語
Yorodumi- EMDB-38434: Core region of the human acetyl-CoA carboxylase 1 filament in com... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38434 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Core region of the human acetyl-CoA carboxylase 1 filament in complex with acetyl-CoA (ACC1-inact) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Biotin-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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.57 Å | |||||||||
Authors | Zhou FY / Zhang YY / Zhou Q / Hu Q | |||||||||
Funding support | 1 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_38434.map.gz | 118.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-38434-v30.xml emd-38434.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_38434.png | 30.7 KB | ||
Filedesc metadata | emd-38434.cif.gz | 6.5 KB | ||
Others | emd_38434_half_map_1.map.gz emd_38434_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38434 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38434 | HTTPS FTP |
-Validation report
Summary document | emd_38434_validation.pdf.gz | 850.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_38434_full_validation.pdf.gz | 850 KB | Display | |
Data in XML | emd_38434_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_38434_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38434 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38434 | HTTPS FTP |
-Related structure data
Related structure data | 8xl1MC 8xkzC 8xl0C 8xl2C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_38434.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0773 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_38434_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_38434_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Core region of the human acetyl-CoA carboxylase 1 filament in com...
Entire | Name: Core region of the human acetyl-CoA carboxylase 1 filament in complex with acetyl-CoA (ACC1-inact) |
---|---|
Components |
|
-Supramolecule #1: Core region of the human acetyl-CoA carboxylase 1 filament in com...
Supramolecule | Name: Core region of the human acetyl-CoA carboxylase 1 filament in complex with acetyl-CoA (ACC1-inact) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Acetyl-CoA carboxylase 1
Macromolecule | Name: 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 weight | Theoretical: 265.869375 KDa |
Sequence | String: 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 |
-Macromolecule #2: ACETYL COENZYME *A
Macromolecule | Name: ACETYL COENZYME *A / type: ligand / ID: 2 / Number of copies: 2 / Formula: ACO |
---|---|
Molecular weight | Theoretical: 809.571 Da |
Chemical component information | ChemComp-ACO: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172311 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |