8vqj

CryoEM structure of DPOR under turnover

Method: ELECTRON MICROSCOPY

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

Light-independent protochlorophyllide reductase subunit N

Cereibacter sphaeroides

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Light-independent protochlorophyllide reductase subunit B × 2 （B9KK25） Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein × 2 （Q9RFD6） IRON/SULFUR CLUSTER × 3 Protochlorophyllide × 2 COPPER (II) ION × 2 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCHN_CERSK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–428； UniProt 1–428 Author chain C； PDBConstruct 1–428； UniProt 1–428

Light-independent protochlorophyllide reductase subunit B

Cereibacter sphaeroides

UniProt B9KK25

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Light-independent protochlorophyllide reductase subunit N × 2 （B9KK24） Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein × 2 （Q9RFD6） IRON/SULFUR CLUSTER × 3 Protochlorophyllide × 2 COPPER (II) ION × 2 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCHB_CERSK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–536； UniProt 1–536 Author chain D； PDBConstruct 1–536； UniProt 1–536

Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein

Cereibacter sphaeroides

UniProt Q9RFD6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Light-independent protochlorophyllide reductase subunit N × 2 （B9KK24） Light-independent protochlorophyllide reductase subunit B × 2 （B9KK25） IRON/SULFUR CLUSTER × 3 Protochlorophyllide × 2 COPPER (II) ION × 2 MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCHL_RHOS4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 22–318； UniProt 1–297 Author chain F； PDBConstruct 22–318； UniProt 1–297

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	8vqj
Deposition date deposition_date	2024-01-18
Structure title title	CryoEM structure of DPOR under turnover
Keywords keywords	Plant Protein, Electron Transfer Enzymes, Photosynthesis, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

8vqj__assembly_1__model_1

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

Download this curve (.dat)

8vqj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8vqj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.84 Å
Rg (electron density)	45.60 Å
Total Rg	45.69 Å
Atom count	17048
Residues	2230
Excluded volume	303210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8vqj__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 (7)

Entity 1 Entity 1 polymer

Description description	Light-independent protochlorophyllide reductase subunit N
Molecular weight formula_weight	46188.8 kDa
EC 编号 ec_number	1.3.7.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	17048

MSLDLPPPPARGCRSTEVLKERGQREVFCGLTGIIWLHRKMQDAFFLVVGSRTCAHLLQSAAGVMIFAEPRFGTAVLEEKDLAGLADANAELDREVDRLLARRPDIRQLFLVGSCPSEVIKLDLHRAAERLSAHHGPAVRVYNFSGSGIETTFTQGEDACLASIVPTLPATEARELLLVGALPDVVEDQAVSLLTQLGIGPVRCLPAHHAAEAPGVGPNTVFALVQPFLGDTHGALTRRGARHIAAPFPFGEEGTTLWLKAIADEFGVSAETFEAVTAAPRARARKAVAAASEGLRGKSVFFLPDSQLEPSLARFLTRECGMSAVEVGTPFLHRGILGPDLDLLAEGPVLSEGQDVERQLDRVRAARPDLTVCGLGLANPLEAEGFTTKWAIELVFTPVHFYEQAGDLAGLFSRPVRRRAILRREAAE

Source Source

Source organism organism	Cereibacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Light-independent protochlorophyllide reductase subunit B
Molecular weight formula_weight	58374.3 kDa
EC 编号 ec_number	1.3.7.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKLTLWTYEGPPHVGAMRVATGMTGMHYVLHAPQGDTYADLLFTMIERRGKRPPVSYTTFQARDLGSDTAELFQSACRDAYERFQPQAIMVGSSCTAELIQDDTGGLADALSLPVPVVHLELPSYQRKENFGADESFLQICRKLARPMERTEKVSCNLLGPTALGFRHRDDILEVTRLLEGMGIAVNAVAPMGASPADIARLGAAHFNVLLYPETGESAARWAEKTLKQPYTKTVPIGVGATRDFVAEVAALAGVAPVADDSRLRQPWWSASVDSTYLTGKRVFLFGDATHVIAAARVARDEMGFEVVGMGCYNREFARPMRAAAKGYGLEALVTDDYLEVEEAIQALAPELILGTQMERHIAKRLGIPCAVISAPVHVQDFPARYSPQMGFEGANVLFDTWIHPLTMGLEEHLLTMFREDFEFHDEAGPSHHGGKAVPASAPRADEAAEALPATGAETAEGGSIPPEAVPPAAAAAAEAPAGEIVWLTDAERELKKIPFFVRGKARRNTEKFAAEKGLTRISIETLYEAKAHYAR

Source Source

Source organism organism	Cereibacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
Molecular weight formula_weight	34850.3 kDa
EC 编号 ec_number	1.3.7.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGSSHHHHHHSQDPENLYFQSMSPKDLTIPTGADGEGSVQVHLDEADKITGAKVFAVYGKGGIGKSTTSSNLSAAFSILGKRVLQIGCDPKHDSTFTLTGSLVPTVIDVLKDVDFHPEELRPEDFVFEGFNGVMCVEAGGPPAGTGCGGYVVGQTVKLLKQHHLLDDTDVVIFDVLGDVVCGGFAAPLQHADQAVVVTANDFDSIYAMNRIIAAVQAKSKNYKVRLAGCVANRSRATDEVDRFCKETNFRRLAHMPDLDAIRRSRLKKKTLFEMDEDQDVLAARAEYIRLAESLWRGLDPIDPHSLPDREIFELLGFD

Source Source

Source organism organism	Cereibacter sphaeroides
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	Protochlorophyllide
Molecular weight formula_weight	613.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

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

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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	3.820 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.82 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	18965

CryoEM structure of DPOR under turnover

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

Light-independent protochlorophyllide reductase subunit N

State in the Current Structure

Other States of the Same Protein in the Database

Light-independent protochlorophyllide reductase subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein

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

8vqj__assembly_1__model_1

8vqj__assembly_1__model_1 | I(q)

8vqj__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)

CryoEM structure of DPOR under turnover

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

Light-independent protochlorophyllide reductase subunit N

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Light-independent protochlorophyllide reductase subunit 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

Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein

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

8vqj__assembly_1__model_1

8vqj__assembly_1__model_1 | I(q)

8vqj__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)