5m7l

Blastochloris viridis photosynthetic reaction center synchrotron structure

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 L chain × 1 （P06009） Reaction center protein M chain × 1 （P06010） Reaction center protein H chain × 1 （P06008） HEME C × 4 DIACYL GLYCEROL × 1 BACTERIOCHLOROPHYLL A × 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 (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE × 1 PHOSPHATE ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYCR_BLAVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–356； UniProt 1–356

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 M chain × 1 （P06010） Reaction center protein H chain × 1 （P06008） HEME C × 4 DIACYL GLYCEROL × 1 BACTERIOCHLOROPHYLL A × 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 (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE × 1 PHOSPHATE ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEL_BLAVI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； 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 L chain × 1 （P06009） Reaction center protein H chain × 1 （P06008） HEME C × 4 DIACYL GLYCEROL × 1 BACTERIOCHLOROPHYLL A × 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 (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE × 1 PHOSPHATE ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEM_BLAVI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–324； UniProt 1–324

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 A × 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 (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE × 1 PHOSPHATE ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEH_BLAVI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 2–258； UniProt 2–258

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	5m7l
Deposition date deposition_date	2016-10-28
Structure title title	Blastochloris viridis photosynthetic reaction center synchrotron structure
Keywords keywords	Photosynthetic, Reaction Center, photosynthesis; 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.

5m7l__assembly_1__model_1

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

Download this curve (.dat)

5m7l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5m7l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.62 Å
Rg (electron density)	35.51 Å
Total Rg	36.09 Å
Atom count	9881
Residues	1170
Excluded volume	179080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5m7l__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	39419.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9890

MKQLIVNSVATVALASLVAGCFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIKAAAK

Entity 2 Entity 2 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	B

MALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS

Entity 3 Entity 3 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	C

MADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK

Entity 4 Entity 4 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	D

MYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVYELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL

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 A
Molecular weight formula_weight	911.5 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	(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE
Molecular weight formula_weight	722.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 14 Entity 14 non-polymer

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

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5m7lA01
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	5m7lA02
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	5m7lB01
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	5m7lB02
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	5m7lC01
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	5m7lC02
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	5m7lD01
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	5m7lD02
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

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Unit-cell length a length_a	57.600 Å
Unit-cell length b length_b	82.900 Å
Unit-cell length c length_c	382.100 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	50.502 Å
R factor r_factor	0.2442
R_work r_work	0.2423
R_free r_free	0.2800

Blastochloris viridis photosynthetic reaction center synchrotron structure

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 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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5m7l__assembly_1__model_1

5m7l__assembly_1__model_1 | I(q)

5m7l__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 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)