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- EMDB-42790: E. coli acetyl-CoA carboxylase, wide stacked local reconstruction... -

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Basic information

Entry
Database: EMDB / ID: EMD-42790
TitleE. coli acetyl-CoA carboxylase, wide stacked local reconstruction, 3.20 Angstrom
Map data
Sample
  • Complex: Escherichia coli acetyl-CoA carboxylase
    • Protein or peptide: Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
    • Protein or peptide: Biotin carboxyl carrier protein of acetyl-CoA carboxylase
    • Protein or peptide: Biotin carboxylase
    • Protein or peptide: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
  • Ligand: BIOTIN
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ACETYL COENZYME *A
Keywordscomplex / enzyme / biosynthesis of fatty acids / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


acetate CoA-transferase complex / acetyl-CoA carboxytransferase / carboxyl- or carbamoyltransferase activity / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / long-chain fatty acid biosynthetic process ...acetate CoA-transferase complex / acetyl-CoA carboxytransferase / carboxyl- or carbamoyltransferase activity / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / long-chain fatty acid biosynthetic process / fatty acid biosynthetic process / molecular adaptor activity / negative regulation of translation / mRNA binding / protein homodimerization activity / DNA binding / zinc ion binding / ATP binding / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / Acetyl-CoA biotin carboxyl carrier / Acetyl-coA carboxylase zinc finger domain / Acetyl-CoA carboxylase zinc finger domain / Acetyl-CoA carboxylase carboxyl transferase, beta subunit / : / Acetyl-CoA carboxylase, biotin carboxylase / : / Acetyl-coenzyme A carboxyltransferase, C-terminal ...Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / Acetyl-CoA biotin carboxyl carrier / Acetyl-coA carboxylase zinc finger domain / Acetyl-CoA carboxylase zinc finger domain / Acetyl-CoA carboxylase carboxyl transferase, beta subunit / : / Acetyl-CoA carboxylase, biotin carboxylase / : / 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-coenzyme A carboxylase carboxyl transferase subunit beta / Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha / Biotin carboxyl carrier protein of acetyl-CoA carboxylase / Biotin carboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXu X / Silva de Sousa A / Boram TJ / Jiang W / Lohman RJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140290 United States
CitationJournal: To Be Published
Title: E. coli acetyl-CoA carboxylase, wide stacked local reconstruction, 3.20 Angstrom
Authors: Xu X / Silva de Sousa A / Boram TJ / Jiang W / Lohman RJ
History
DepositionNov 11, 2023-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42790.png

Downloads & links

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Map

FileDownload / File: emd_42790.map.gz / Format: CCP4 / Size: 299.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 428 pix.
= 493.2 Å		1.15 Å/pix.
x 428 pix.
= 493.2 Å		1.15 Å/pix.
x 428 pix.
= 493.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15234 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-2.3368597 - 2.8179648
Average (Standard dev.)0.00075614115 (±0.040645555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions428428428
Spacing428428428
CellA=B=C: 493.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42790_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42790_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42790_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Escherichia coli acetyl-CoA carboxylase

EntireName: Escherichia coli acetyl-CoA carboxylase
Components
  • Complex: Escherichia coli acetyl-CoA carboxylase
    • Protein or peptide: Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
    • Protein or peptide: Biotin carboxyl carrier protein of acetyl-CoA carboxylase
    • Protein or peptide: Biotin carboxylase
    • Protein or peptide: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
  • Ligand: BIOTIN
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ACETYL COENZYME *A

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Supramolecule #1: Escherichia coli acetyl-CoA carboxylase

SupramoleculeName: Escherichia coli acetyl-CoA carboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha

MacromoleculeName: Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: acetyl-CoA carboxytransferase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 34.956098 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: NFLDFEQPIA ELEAKIDSLT AVSRQDEKLD INIDEEVHRL REKSVELTRK IFADLGAWQI AQLARHPQRP YTLDYVRLAF DEFDELAGD RAYADDKAIV GGIARLDGRP VMIIGHQKGR ETKEKIRRNF GMPAPEGYRK ALRLMQMAER FKMPIITFID T PGAYPGVG ...String:
NFLDFEQPIA ELEAKIDSLT AVSRQDEKLD INIDEEVHRL REKSVELTRK IFADLGAWQI AQLARHPQRP YTLDYVRLAF DEFDELAGD RAYADDKAIV GGIARLDGRP VMIIGHQKGR ETKEKIRRNF GMPAPEGYRK ALRLMQMAER FKMPIITFID T PGAYPGVG AEERGQSEAI ARNLREMSRL GVPVVCTVIG EGGSGGALAI GVGDKVNMLQ YSTYSVISPE GCASILWKSA DK APLAAEA MGIIAPRLKE LKLIDSIIPE PLGGAHRNPE AMAASLKAQL LADLADLDVL STEDLKNRRY QRLMSYGYA

UniProtKB: Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha

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Macromolecule #2: Biotin carboxyl carrier protein of acetyl-CoA carboxylase

MacromoleculeName: Biotin carboxyl carrier protein of acetyl-CoA carboxylase
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.370667 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GHIVRSPMVG TFYRTPSPDA KAFIEVGQKV NVGDTLCIVE AMKMMNQIEA DKSGTVKAIL VESGQPVEFD EPLVVIE

UniProtKB: Biotin carboxyl carrier protein of acetyl-CoA carboxylase

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Macromolecule #3: Biotin carboxylase

MacromoleculeName: Biotin carboxylase / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: biotin carboxylase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 49.00023 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLDKIVIANR GEIALRILRA CKELGIKTVA VHSSADRDLK HVLLADETVC IGPAPSVKSY LNIPAIISAA EITGAVAIHP GYGFLSENA NFAEQVERSG FIFIGPKAET IRLMGDKVSA IAAMKKAGVP CVPGSDGPLG DDMDKNRAIA KRIGYPVIIK A SGGGGGRG ...String:
MLDKIVIANR GEIALRILRA CKELGIKTVA VHSSADRDLK HVLLADETVC IGPAPSVKSY LNIPAIISAA EITGAVAIHP GYGFLSENA NFAEQVERSG FIFIGPKAET IRLMGDKVSA IAAMKKAGVP CVPGSDGPLG DDMDKNRAIA KRIGYPVIIK A SGGGGGRG MRVVRGDAEL AQSISMTRAE AKAAFSNDMV YMEKYLENPR HVEIQVLADG QGNAIYLAER DCSMQRRHQK VV EEAPAPG ITPELRRYIG ERCAKACVDI GYRGAGTFEF LFENGEFYFI EMNTRIQVEH PVTEMITGVD LIKEQLRIAA GQP LSIKQE EVHVRGHAVE CRINAEDPNT FLPSPGKITR FHAPGGFGVR WESHIYAGYT VPPYYDSMIG KLICYGENRD VAIA RMKNA LQELIIDGIK TNVDLQIRIM NDENFQHGGT NIHYLEKKLG L

UniProtKB: Biotin carboxylase

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Macromolecule #4: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta

MacromoleculeName: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO / EC number: acetyl-CoA carboxytransferase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 31.23457 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SWIERIKSNI TPTRKASIPE GVWTKCDSCG QVLYRAELER NLEVCPKCDH HMRMTARNRL HSLLDEGSLV ELGSELEPKD VLKFRDSKK YKDRLASAQK ETGEKDALVV MKGTLYGMPV VAAAFEFAFM GGSMGSVVGA RFVRAVEQAL EDNCPLICFS A SGGARMQE ...String:
SWIERIKSNI TPTRKASIPE GVWTKCDSCG QVLYRAELER NLEVCPKCDH HMRMTARNRL HSLLDEGSLV ELGSELEPKD VLKFRDSKK YKDRLASAQK ETGEKDALVV MKGTLYGMPV VAAAFEFAFM GGSMGSVVGA RFVRAVEQAL EDNCPLICFS A SGGARMQE ALMSLMQMAK TSAALAKMQE RGLPYISVLT DPTMGGVSAS FAMLGDLNIA EPKALIGFAG PRVIEQTVRE KL PPGFQRS EFLIEKGAID MIVRRPEMRL KLASILAKLM NLPAPNP

UniProtKB: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta

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Macromolecule #5: BIOTIN

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

ChemComp-BTN:
BIOTIN

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 9 / Number of copies: 2 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMHEPES

Details: 2.5 mg/ml ACC complex in 50 mM HEPES pH 7.5, 100 mM bicarbonate, 7.5 mM ATP, 20 mM MgCl2 and 1 mM acetyl-CoA
GridModel: Quantifoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.01 sec. / Average electron dose: 54.44 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 84.24 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.56 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 809111
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2f9y


Details: 2F9Y, 1BDO, 3RV4
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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