9tdm

Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA

Method: ELECTRON MICROSCOPY

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Propionyl-CoA carboxylase beta chain × 2 （A0R616） Propionyl-CoA carboxylase beta chain × 4 （A0QTE7） Acetyl-/propionyl-coenzyme A carboxylase AccE5 × 2 （A0QTE6） ADENOSINE-5'-TRIPHOSPHATE × 2 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL × 5 propionyl Coenzyme A × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0QTE1_MYCS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A3a； PDBConstruct 1–598； UniProt 1–598 Author chain A3b； PDBConstruct 1–598； UniProt 1–598 Author chain A3c； PDBConstruct 1–598； UniProt 1–598 Author chain A3d； PDBConstruct 1–598； UniProt 1–598 Author chain A3e； PDBConstruct 1–598； UniProt 1–598 Author chain A3f； PDBConstruct 1–598； UniProt 1–598 Author chain A3g； PDBConstruct 1–598； UniProt 1–598 Author chain A3h； PDBConstruct 1–598； UniProt 1–598

Propionyl-CoA carboxylase beta chain

OrganismNot specified

UniProt A0R616

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit × 8 （A0QTE1） Propionyl-CoA carboxylase beta chain × 4 （A0QTE7） Acetyl-/propionyl-coenzyme A carboxylase AccE5 × 2 （A0QTE6） ADENOSINE-5'-TRIPHOSPHATE × 2 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL × 5 propionyl Coenzyme A × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R616_MYCS2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D4a； PDBConstruct 1–517； UniProt 1–517 Author chain D4b； PDBConstruct 1–517； UniProt 1–517

Propionyl-CoA carboxylase beta chain

OrganismNot specified

UniProt A0QTE7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit × 8 （A0QTE1） Propionyl-CoA carboxylase beta chain × 2 （A0R616） Acetyl-/propionyl-coenzyme A carboxylase AccE5 × 2 （A0QTE6） ADENOSINE-5'-TRIPHOSPHATE × 2 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL × 5 propionyl Coenzyme A × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0QTE7_MYCS2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D5a； PDBConstruct 1–542； UniProt 1–542 Author chain D5b； PDBConstruct 1–542； UniProt 1–542 Author chain D5c； PDBConstruct 1–542； UniProt 1–542 Author chain D5d； PDBConstruct 1–542； UniProt 1–542

Acetyl-/propionyl-coenzyme A carboxylase AccE5

OrganismNot specified

UniProt A0QTE6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit × 8 （A0QTE1） Propionyl-CoA carboxylase beta chain × 2 （A0R616） Propionyl-CoA carboxylase beta chain × 4 （A0QTE7） ADENOSINE-5'-TRIPHOSPHATE × 2 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL × 5 propionyl Coenzyme A × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0QTE6_MYCS2
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E5a； PDBConstruct 1–94； UniProt 1–94 Author chain E5b； PDBConstruct 1–94； UniProt 1–94

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9tdm
Deposition date deposition_date	2025-11-24
Structure title title	Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
Keywords keywords	Bio-dependent acyl-CoA carboxylase, long chain/short chain acyl-CoA carboxylase, TRANSFERASE; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9tdm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9tdm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9tdm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	76.44 Å
Rg (electron density)	76.40 Å
Total Rg	76.17 Å
Atom count	114486
Residues	7618
Excluded volume	1028400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9tdm__assembly_1__model_1`	16-meric （16）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
Molecular weight formula_weight	63215.2 kDa
EC 编号 ec_number	6.3.4.14
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A3a,A3b,A3c,A3d,A3e,A3f,A3g,A3h
Atom count atom_count	114486

MANHASSKISKVLVANRGEIAVRVIRAAKDAGLASVAVYAEPDADAPHVRLADEAFALGGQTSAESYLVFEKILDAAEKSGANAIHPGYGFLSENADFAQAVIDAGLIWIGPSPQSIRDLGDKVTARHIAARAKAPLVPGTPDPVKDADEVVAFAKEHGVPVAIKAAFGGGGRGMKVARTLEEIPELFESATREAIAAFGRGECFVERYLDKPRHVEAQVIADQHGNVVVAGTRDCSLQRRFQKLVEEAPAPFLTDAQRKEIHESAKRICKEAGYYGAGTVEYLVGQDGLISFLEVNTRLQVEHPVTEETSGIDLVRQQFKIANGEPLDITEDPTPRGHSFEFRINGEDAGRGFLPAPGPVTKFVAPTGPGVRMDSGVETGSVIGGQFDSMLAKLIVTGATREEALERSRRALAEFTVEGLATVIPFHRAVVSDPAFIGDGEKFDVHTRWIETEWNNTVEPFTGGDPIEEEDTVPRQTVVVEVGGRRLEVSLPGDLAIGGGGGAAAPGVVRKKPKPRKRGGGGAKAASGDAVTAPMQGTVVKVAVEEGQEVSAGDLVVVLEAMKMENPVTAHKDGTITGLAVEAGAAITQGTVIAEIK

Entity 2 Entity 2 polymer

Description description	Propionyl-CoA carboxylase beta chain
Molecular weight formula_weight	56234.1 kDa
EC 编号 ec_number	6.4.1.3
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D4a,D4b

MTNKTTAELLAELREKLELAKEPGGEKAVAKREKKGIPSARARINALLDPGSFIEIGALAKTPGDPNALYGDGVVTGRGTIDGRPVGVFSHDQTVFQGSVGEMFGRKVARLMEWVAMVGCPIIGINDSAGARIQDAVTSLAWYAELGRRHEMLRGLVPEISLIFGKCAGGAVYSPIQTDLLVAVRDQGYMFITGPDVIKDVTGEDVTFDELGGADEQAKRGNIHKVVNSEAEAYQYVRDYLSFLPSNHFDNPPIVNPGMEPEITPHDLELDSIVPDADNMAYDMHEILLRIFDDGDVFEIAEQRGPAMITAFARVDGHPVGVIANQPMVLSGAIDNEASDKAASFIRFCDSYNLPLVFVVDTPGAMPGVAEEKGGIIKRGGRFFNAIVEADVPKVTVIIRKAYGGGYAVMGSKQLSADLNFAWPTARIAVIGAEGAAQLLVKRFPDPNAPEVQKIRDDFIEGYNLNMATPWIAAERGYIDAVIQPHETRLLLRKSLRLLRDKQNGPKVQRKHGLLPL

Entity 3 Entity 3 polymer

Description description	Propionyl-CoA carboxylase beta chain
Molecular weight formula_weight	58488.1 kDa
EC 编号 ec_number	6.4.1.3
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D5a,D5b,D5c,D5d

MTSVTEPSAEHQVDIHTTAGKLADLKRRTEETLHPVGEAAVDKVHAKGKLTARERILALLDEGSFVELDALAKHRSTNFGLEKNRPLGDGVITGYGTIDGRDVCIFSQDATVFGGSLGEVYGEKIVKVQELAIKTGRPLIGINDGAGARIQEGVVSLGLYSRIFHNNIKASGVIPQISLIMGAAAGGHVYSPALTDFVVMVDQTSQMFITGPDVIKTVTGEDVTMEELGGAHTHMAKSGTAHYVASGEQDAFDYVRDLLSYLPPNNYADPPLYPVAIPEGSIEETLTDEDLELDTLIPDSPNQPYDMHEVITRILDDDEFLEVQAGYAGNIVVGFGRVEGRPVGIVANQPTQFAGCLDINASEKAARFIRTCDCFNIPIVLLVDVPGFLPGTDQEYNGIIRRGAKLLYAYGEATVAKVTVITRKSYGGAYCVMGSKDMGADVVVAWPTAQIAVMGASGAVGFVYRQQLKEAAKNGEDVDALRLELQQTYEDTLVNPYIAAERGYVDAVIPPSHTRGYVANALRLLERKIVQMPPKKHGNIPL

Entity 4 Entity 4 polymer

Description description	Acetyl-/propionyl-coenzyme A carboxylase AccE5
Molecular weight formula_weight	10357.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E5a,E5b

MSGANDSTTVSGEVQADVTDEAKADHEAHIKVLRGEPTPEEMAALMAVLASAGGGPAEPVKKERNMWGHPVDKLRYSVFSWQRVTLLERTHMRR

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
Molecular weight formula_weight	228.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	propionyl Coenzyme A
Molecular weight formula_weight	823.6 kDa
Source method src_method	syn
Copy count entity_count	4

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	380.800 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	52469

Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA

1. Protein Identity and Related Structures Protein Identity & Related Structures

Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit

State in the Current Structure

Other States of the Same Protein in the Database

Propionyl-CoA carboxylase beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Propionyl-CoA carboxylase beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Acetyl-/propionyl-coenzyme A carboxylase AccE5

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9tdm__assembly_1__model_1

9tdm__assembly_1__model_1 | I(q)

9tdm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)

Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA

1. Protein Identity and Related Structures Protein Identity & Related Structures

Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Propionyl-CoA carboxylase beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Propionyl-CoA carboxylase beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Acetyl-/propionyl-coenzyme A carboxylase AccE5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9tdm__assembly_1__model_1

9tdm__assembly_1__model_1 | I(q)

9tdm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)