2wjm

Lipidic sponge phase crystal structure of the photosynthetic reaction centre from Blastochloris viridis (low dose)

Method: X-RAY DIFFRACTION

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

PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C 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 4	REACTION CENTER PROTEIN H CHAIN × 1 （P06008） REACTION CENTER PROTEIN L CHAIN × 1 （P06009） REACTION CENTER PROTEIN M CHAIN × 1 （P06010） HEME C × 4 DIACYL GLYCEROL × 1 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate × 3 FE (II) ION × 1 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1 PHOSPHATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYCR_RHOVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–336； UniProt 21–356

REACTION CENTER PROTEIN H CHAIN

OrganismNot specified

UniProt P06008

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT × 1 （P07173） REACTION CENTER PROTEIN L CHAIN × 1 （P06009） REACTION CENTER PROTEIN M CHAIN × 1 （P06010） HEME C × 4 DIACYL GLYCEROL × 1 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate × 3 FE (II) ION × 1 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1 PHOSPHATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEH_RHOVI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–258； UniProt 1–258

REACTION CENTER PROTEIN L CHAIN

OrganismNot specified

UniProt P06009

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT × 1 （P07173） REACTION CENTER PROTEIN H CHAIN × 1 （P06008） REACTION CENTER PROTEIN M CHAIN × 1 （P06010） HEME C × 4 DIACYL GLYCEROL × 1 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate × 3 FE (II) ION × 1 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1 PHOSPHATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEL_RHOVI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain L； PDBConstruct 1–274； UniProt 1–274

REACTION CENTER PROTEIN M CHAIN

OrganismNot specified

UniProt P06010

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT × 1 （P07173） REACTION CENTER PROTEIN H CHAIN × 1 （P06008） REACTION CENTER PROTEIN L CHAIN × 1 （P06009） HEME C × 4 DIACYL GLYCEROL × 1 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate × 3 FE (II) ION × 1 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1 PHOSPHATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEM_RHOVI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain M； PDBConstruct 1–324； UniProt 1–324

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	2wjm
Deposition date deposition_date	2009-05-27
Structure title title	Lipidic sponge phase crystal structure of the photosynthetic reaction centre from Blastochloris viridis (low dose)
Keywords keywords	;REACTION CENTRE, PHOTOSYNTHESIS, MEMBRANE PROTEIN, LIPIDS, MONOOLEIN, POSTTRANSLATIONAL MODIFICATION, THIOETHER BOND, UBIQUINONE, LIPIDIC SPONGE PHASE ;; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

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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.

2wjm__assembly_1__model_1

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

Download this curve (.dat)

2wjm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wjm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.55 Å
Rg (electron density)	35.52 Å
Total Rg	36.15 Å
Atom count	9951
Residues	1170
Excluded volume	180210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wjm__assembly_1__model_1`	tetrameric （4）	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 (14)

Entity 1 Entity 1 polymer

Description description	PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
Molecular weight formula_weight	37450.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	10671

CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIKAAAK

Entity 2 Entity 2 polymer

Description description	REACTION CENTER PROTEIN H CHAIN
Molecular weight formula_weight	28557.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVYELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL

Entity 3 Entity 3 polymer

Description description	REACTION CENTER PROTEIN L CHAIN
Molecular weight formula_weight	30600.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS

Entity 4 Entity 4 polymer

Description description	REACTION CENTER PROTEIN M CHAIN
Molecular weight formula_weight	36063.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK

Entity 5 Entity 5 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	DIACYL GLYCEROL
Molecular weight formula_weight	625.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	BACTERIOCHLOROPHYLL B
Molecular weight formula_weight	909.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	BACTERIOPHEOPHYTIN B
Molecular weight formula_weight	887.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	MENAQUINONE-7
Molecular weight formula_weight	649.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	15-cis-1,2-dihydroneurosporene
Molecular weight formula_weight	540.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 14 Entity 14 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	711

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2wjmc_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.2 — Photosynthetic reaction centre (cytochrome subunit)

Domain ID domain_id	d2wjmh1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.10 — Photosystem II reaction centre subunit H, transmembrane region
Family Family family	f.23.10.1 — Photosystem II reaction centre subunit H, transmembrane region

Domain ID domain_id	d2wjmh2
Class class	b — All beta proteins
Fold Fold fold	b.41 — PRC-barrel domain
Superfamily Superfamily superfamily	b.41.1 — PRC-barrel domain
Family Family family	b.41.1.1 — Photosynthetic reaction centre, H-chain, cytoplasmic domain

Domain ID domain_id	d2wjml_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamily	f.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family family	f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits

Domain ID domain_id	d2wjmm_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamily	f.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family family	f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits

CATH v4.4 (8 domains)

Domain ID domain_id	2wjmC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	468 — Photosynthetic Reaction Center, subunit C; domain 2
Homologous superfamily homologous superfamily	10 — Photosynthetic Reaction Center, subunit C, domain 2

Domain ID domain_id	2wjmC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	468 — Photosynthetic Reaction Center, subunit C; domain 2
Homologous superfamily homologous superfamily	10 — Photosynthetic Reaction Center, subunit C, domain 2

Domain ID domain_id	2wjmH01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	540 — Photosynthetic Reaction Center; Chain H, domain 1
Homologous superfamily homologous superfamily	10 — Photosynthetic reaction centre, H subunit, N-terminal domain

Domain ID domain_id	2wjmH02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	50 — Photosynthetic Reaction Center; Chain H, domain 2
Homologous superfamily homologous superfamily	10 — Photosynthetic Reaction Center, subunit H, domain 2

Domain ID domain_id	2wjmL01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

Domain ID domain_id	2wjmL02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

Domain ID domain_id	2wjmM01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

Domain ID domain_id	2wjmM02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

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Unit-cell length a length_a	84.450 Å
Unit-cell length b length_b	138.498 Å
Unit-cell length c length_c	177.770 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	176.780 Å
R factor r_factor	0.1745
R_work r_work	0.1731
R_free r_free	0.2012

Lipidic sponge phase crystal structure of the photosynthetic reaction centre from Blastochloris viridis (low dose)

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

PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C 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

REACTION CENTER PROTEIN H 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

REACTION CENTER PROTEIN L 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

REACTION CENTER PROTEIN M 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2wjm__assembly_1__model_1

2wjm__assembly_1__model_1 | I(q)

2wjm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (14)

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

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

CATH v4.4 (8 domains)

7. Citations (1)