[English] 日本語
Yorodumi
- PDB-30hu: cryo-EM structure of AccA3-AccE5 complex in the presence of Arach... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 30hu
Titlecryo-EM structure of AccA3-AccE5 complex in the presence of Arachidyl-CoA
Components
  • Acetyl-/propionyl-coenzyme A carboxylase AccE5
  • Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
KeywordsTRANSFERASE / Bio-dependent acyl-CoA carboxylase / AccA3-AccE5 complex
Function / homology
Function and homology information


biotin carboxylase / propionyl-CoA carboxylase activity / biotin carboxylase activity / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit / : / 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-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit / : / 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. / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-BTI / Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit / Acetyl-/propionyl-coenzyme A carboxylase AccE5
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMullapudi, E. / Thai, H.M. / de Carvalho, L.P.S. / Wilmanns, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cryo-EM structure of AccA3-AccE5 complex in the presence of Arachidyl-CoA
Authors: Mullapudi, E. / Thai, H.M. / de Carvalho, L.P.S. / Wilmanns, M.
History
DepositionApr 27, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A3a: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3b: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3c: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3d: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
E5a: Acetyl-/propionyl-coenzyme A carboxylase AccE5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,9547
Polymers263,2185
Non-polymers7352
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit


Mass: 63215.176 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTE1, biotin carboxylase
#2: Protein Acetyl-/propionyl-coenzyme A carboxylase AccE5


Mass: 10357.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTE6
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Acyl-CoA carboxylase AccA3-AccE5 in complex with Arachdyl-CoA
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris-HCl1
2150 mMSodium chlorideNaCl1
32 mMDTTDTT1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2250 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44.4 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPUimage acquisition
4cryoSPARC4.4.1CTF correction
7UCSF ChimeraX1.10.1model fitting
9cryoSPARC4.4.1initial Euler assignment
10cryoSPARC4.4.1final Euler assignment
11cryoSPARC4.4.1classification
12cryoSPARC3D reconstruction
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1279569
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76111 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementResolution: 3.5→375.2 Å / Num. reflection obs: 2580199 / Average fsc work: 0.7479
Displacement parametersBiso mean: 183.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0101158040.0119
ELECTRON MICROSCOPYs_angle_nonh_deg1.713214481.8236
ELECTRON MICROSCOPYs_dihedral_angle_1_deg8.163820355
ELECTRON MICROSCOPYs_dihedral_angle_2_deg3.75155075
ELECTRON MICROSCOPYs_dihedral_angle_3_deg10.6328390610
ELECTRON MICROSCOPYs_dihedral_angle_6_deg16.149890910
ELECTRON MICROSCOPYs_chiral_restr0.081424150.1295
ELECTRON MICROSCOPYs_planes0.0061225250.02
ELECTRON MICROSCOPYs_nbd0.208203690.2
ELECTRON MICROSCOPYs_nbtor0.2204265780.2
ELECTRON MICROSCOPYs_hbond_nbd0.07394220.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
3.5-3.523ELECTRON MICROSCOPY498870.3412
3.523-3.556ELECTRON MICROSCOPY702970.3768
3.556-3.59ELECTRON MICROSCOPY702690.4067
3.59-3.625ELECTRON MICROSCOPY669430.4221
3.625-3.66ELECTRON MICROSCOPY668610.4344
3.661-3.696ELECTRON MICROSCOPY654970.4504
3.697-3.733ELECTRON MICROSCOPY640950.4647
3.733-3.771ELECTRON MICROSCOPY629050.4851
3.771-3.809ELECTRON MICROSCOPY610450.5159
3.809-3.848ELECTRON MICROSCOPY611490.5571
3.848-3.888ELECTRON MICROSCOPY593830.6039
3.888-3.929ELECTRON MICROSCOPY579450.6419
3.929-3.97ELECTRON MICROSCOPY561610.678
3.97-4.012ELECTRON MICROSCOPY553630.7082
4.013-4.056ELECTRON MICROSCOPY542730.738
4.056-4.1ELECTRON MICROSCOPY531730.7578
4.101-4.145ELECTRON MICROSCOPY518850.7759
4.146-4.192ELECTRON MICROSCOPY512950.7955
4.192-4.239ELECTRON MICROSCOPY498450.814
4.24-4.288ELECTRON MICROSCOPY486370.8288
4.288-4.337ELECTRON MICROSCOPY472390.8409
4.338-4.388ELECTRON MICROSCOPY465690.8518
4.388-4.44ELECTRON MICROSCOPY457690.8593
4.44-4.493ELECTRON MICROSCOPY440670.8639
4.494-4.547ELECTRON MICROSCOPY432730.8674
4.548-4.603ELECTRON MICROSCOPY423330.872
4.604-4.661ELECTRON MICROSCOPY415930.878
4.661-4.719ELECTRON MICROSCOPY400150.8853
4.72-4.779ELECTRON MICROSCOPY391890.8923
4.78-4.841ELECTRON MICROSCOPY378610.897
4.841-4.904ELECTRON MICROSCOPY374550.9034
4.905-4.969ELECTRON MICROSCOPY363730.9078
4.97-5.035ELECTRON MICROSCOPY350130.91
5.036-5.104ELECTRON MICROSCOPY348490.9125
5.105-5.175ELECTRON MICROSCOPY333430.9151
5.175-5.247ELECTRON MICROSCOPY328650.9162
5.248-5.322ELECTRON MICROSCOPY312850.9138
5.322-5.398ELECTRON MICROSCOPY306030.9099
5.399-5.477ELECTRON MICROSCOPY303130.9047
5.478-5.558ELECTRON MICROSCOPY287410.8986
5.559-5.641ELECTRON MICROSCOPY284550.8942
5.642-5.728ELECTRON MICROSCOPY271570.8911
5.728-5.817ELECTRON MICROSCOPY270450.8877
5.817-5.908ELECTRON MICROSCOPY257770.8847
5.91-6.003ELECTRON MICROSCOPY244350.8783
6.003-6.099ELECTRON MICROSCOPY242770.8714
6.101-6.201ELECTRON MICROSCOPY233170.8661
6.202-6.305ELECTRON MICROSCOPY228510.8621
6.306-6.412ELECTRON MICROSCOPY217450.8604
6.414-6.524ELECTRON MICROSCOPY210330.8628
6.525-6.64ELECTRON MICROSCOPY207130.8676
6.641-6.76ELECTRON MICROSCOPY196470.8672
6.761-6.884ELECTRON MICROSCOPY188410.8667
6.885-7.011ELECTRON MICROSCOPY182170.8706
7.013-7.146ELECTRON MICROSCOPY177270.878
7.147-7.284ELECTRON MICROSCOPY171250.8817
7.287-7.427ELECTRON MICROSCOPY161250.882
7.43-7.579ELECTRON MICROSCOPY158710.8924
7.58-7.735ELECTRON MICROSCOPY152250.9043
7.736-7.898ELECTRON MICROSCOPY145330.9087
7.899-8.067ELECTRON MICROSCOPY137530.9079
8.069-8.243ELECTRON MICROSCOPY130590.9091
8.247-8.43ELECTRON MICROSCOPY129730.9103
8.434-8.624ELECTRON MICROSCOPY120210.9113
8.626-8.824ELECTRON MICROSCOPY117310.919
8.829-9.039ELECTRON MICROSCOPY109810.93
9.042-9.262ELECTRON MICROSCOPY107250.9378
9.265-9.496ELECTRON MICROSCOPY101170.9428
9.499-9.743ELECTRON MICROSCOPY93750.9494
9.746-9.999ELECTRON MICROSCOPY91330.9512
10.006-10.277ELECTRON MICROSCOPY85770.9492
10.28-10.566ELECTRON MICROSCOPY82270.946
10.57-10.867ELECTRON MICROSCOPY75970.9452
10.877-11.196ELECTRON MICROSCOPY73770.949
11.201-11.541ELECTRON MICROSCOPY69010.9561
11.546-11.907ELECTRON MICROSCOPY63030.9598
11.913-12.297ELECTRON MICROSCOPY60730.9594
12.303-12.706ELECTRON MICROSCOPY56130.957
12.72-13.159ELECTRON MICROSCOPY52750.9573
13.167-13.637ELECTRON MICROSCOPY49810.961
13.646-14.141ELECTRON MICROSCOPY45330.9576
14.161-14.705ELECTRON MICROSCOPY43030.9453
14.717-15.305ELECTRON MICROSCOPY40170.9342
15.317-15.955ELECTRON MICROSCOPY35650.9283
15.97-16.663ELECTRON MICROSCOPY33010.9317
16.68-17.418ELECTRON MICROSCOPY29910.9456
17.456-18.286ELECTRON MICROSCOPY28570.9607
18.308-19.222ELECTRON MICROSCOPY25170.9681
19.273-20.229ELECTRON MICROSCOPY21790.9648
20.288-21.414ELECTRON MICROSCOPY20850.9428
21.449-22.708ELECTRON MICROSCOPY18610.895
22.75-24.169ELECTRON MICROSCOPY16690.9139
24.321-25.83ELECTRON MICROSCOPY13110.9536
25.891-27.66ELECTRON MICROSCOPY12490.9662
27.812-29.944ELECTRON MICROSCOPY10890.978
30.137-32.534ELECTRON MICROSCOPY9070.9848
32.657-35.296ELECTRON MICROSCOPY7290.9844
35.774-39.332ELECTRON MICROSCOPY6250.9784
39.55-43.914ELECTRON MICROSCOPY5710.9708
44.218-49.696ELECTRON MICROSCOPY3810.9749
50.138-57.217ELECTRON MICROSCOPY3010.9761
57.895-66.327ELECTRON MICROSCOPY2250.9749
68.502-81.875ELECTRON MICROSCOPY1750.9757
83.897-104.062ELECTRON MICROSCOPY1050.9663
108.311-132.653ELECTRON MICROSCOPY490.9673
153.175-375.2ELECTRON MICROSCOPY400.8483

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more