7f04

Cytochrome c-type biogenesis protein CcmABCD from E. coli in complex with Heme and ATP.

Method: ELECTRON MICROSCOPY

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

Cytochrome c biogenesis ATP-binding export protein CcmA

Escherichia coli BL21(DE3)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Heme exporter protein B × 2 （P0ABL8） Heme exporter protein C × 1 （P0ABM1） Heme exporter protein D × 1 （P0ABM5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCMA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–207； UniProt 1–207 Author chain E； PDBConstruct 1–207； UniProt 1–207

Heme exporter protein B

Escherichia coli BL21(DE3)

UniProt P0ABL8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Cytochrome c biogenesis ATP-binding export protein CcmA × 2 （P33931） Heme exporter protein C × 1 （P0ABM1） Heme exporter protein D × 1 （P0ABM5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCMB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–220； UniProt 1–220 Author chain F； PDBConstruct 1–220； UniProt 1–220

Heme exporter protein C

Escherichia coli BL21(DE3)

UniProt P0ABM1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Cytochrome c biogenesis ATP-binding export protein CcmA × 2 （P33931） Heme exporter protein B × 2 （P0ABL8） Heme exporter protein D × 1 （P0ABM5） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCMC_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–245； UniProt 1–245

Heme exporter protein D

Escherichia coli BL21(DE3)

UniProt P0ABM5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Cytochrome c biogenesis ATP-binding export protein CcmA × 2 （P33931） Heme exporter protein B × 2 （P0ABL8） Heme exporter protein C × 1 （P0ABM1） MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCMD_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–69； UniProt 1–69

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7f04
Deposition date deposition_date	2021-06-03
Structure title title	Cytochrome c-type biogenesis protein CcmABCD from E. coli in complex with Heme and ATP.
Keywords keywords	ATP-binding exporter, Heme transmembrane transporter, Cytochrome c biogenesis protein., MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

7f04__assembly_1__model_1

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

Download this curve (.dat)

7f04__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7f04__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.73 Å
Rg (electron density)	31.81 Å
Total Rg	32.41 Å
Atom count	8930
Residues	1130
Excluded volume	162350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7f04__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Cytochrome c biogenesis ATP-binding export protein CcmA
Molecular weight formula_weight	23080.2 kDa
EC 编号 ec_number	7.6.2.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	8934

MGMLEARELLCERDERTLFSGLSFTLNAGEWVQITGSNGAGKTTLLRLLTGLSRPDAGEVLWQGQPLHQVRDSYHQNLLWIGHQPGIKTRLTALENLHFYHRDGDTAQCLEALAQAGLAGFEDIPVNQLSAGQQRRVALARLWLTRATLWILDEPFTAIDVNGVDRLTQRMAQHTEQGGIVILTTHQPLNVAESKIRRISLTQTRAA

Source Source

Source organism organism	Escherichia coli BL21(DE3)
NCBI taxonomy ID ncbi_taxonomy_id	469008
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Heme exporter protein B
Molecular weight formula_weight	23632.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MMFWRIFRLELRVAFRHSAEIANPLWFFLIVITLFPLSIGPEPQLLARIAPGIIWVAALLSSLLALERLFRDDLQDGSLEQLMLLPLPLPAVVLAKVMAHWMVTGLPLLILSPLVAMLLGMDVYGWQVMALTLLLGTPTLGFLGAPGVALTVGLKRGGVLLSILVLPLTIPLLIFATAAMDAASMHLPVDGYLAILGALLAGTATLSPFATAAALRISIQ

Source Source

Source organism organism	Escherichia coli BL21(DE3)
NCBI taxonomy ID ncbi_taxonomy_id	469008
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Heme exporter protein C
Molecular weight formula_weight	27911.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MWKTLHQLAIPPRLYQICGWFIPWLAIASVVVLTVGWIWGFGFAPADYQQGNSYRIIYLHVPAAIWSMGIYASMAVAAFIGLVWQMKMANLAVAAMAPIGAVFTFIALVTGSAWGKPMWGTWWVWDARLTSELVLLFLYVGVIALWHAFDDRRLAGRAAGILVLIGVVNLPIIHYSVEWWNTLHQGSTRMQQSIDPAMRSPLRWSIFGFLLLSATLTLMRMRNLILLMEKRRPWVSELILKRGRK

Source Source

Source organism organism	Escherichia coli BL21(DE3)
NCBI taxonomy ID ncbi_taxonomy_id	469008
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Heme exporter protein D
Molecular weight formula_weight	7753.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MTPAFASWNEFFAMGGYAFFVWLAVVMTVIPLVVLVVHSVMQHRAILRGVAQQRAREARLRAAQQQEAA

Source Source

Source organism organism	Escherichia coli BL21(DE3)
NCBI taxonomy ID ncbi_taxonomy_id	469008
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	1,2-Distearoyl-sn-glycerophosphoethanolamine
Molecular weight formula_weight	748.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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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	2.86 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	270825

Cytochrome c-type biogenesis protein CcmABCD from E. coli in complex with Heme and ATP.

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

Cytochrome c biogenesis ATP-binding export protein CcmA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Heme exporter protein B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Heme exporter protein C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Heme exporter protein D

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

7f04__assembly_1__model_1

7f04__assembly_1__model_1 | I(q)

7f04__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)