1l9j

X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals

Method: X-RAY DIFFRACTION

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

REACTION CENTER PROTEIN L CHAIN

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 M CHAIN × 1 （P02953） REACTION CENTER PROTEIN H CHAIN × 1 （P11846） cytochrome c-2 × 1 （P00095） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 FE (II) ION × 1 CHLORIDE ION × 1 UBIQUINONE-10 × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	REACTION CENTER PROTEIN M CHAIN × 1 （P02953） REACTION CENTER PROTEIN H CHAIN × 1 （P11846） cytochrome c-2 × 1 （P00095） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 FE (II) ION × 1 CHLORIDE ION × 1 UBIQUINONE-10 × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEL_RHOSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 1–281； UniProt 1–281 Author chain R； PDBConstruct 1–281； UniProt 1–281

REACTION CENTER PROTEIN M CHAIN

OrganismNot specified

UniProt P02953

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 （P02954） REACTION CENTER PROTEIN H CHAIN × 1 （P11846） cytochrome c-2 × 1 （P00095） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 FE (II) ION × 1 CHLORIDE ION × 1 UBIQUINONE-10 × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	REACTION CENTER PROTEIN L CHAIN × 1 （P02954） REACTION CENTER PROTEIN H CHAIN × 1 （P11846） cytochrome c-2 × 1 （P00095） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 FE (II) ION × 1 CHLORIDE ION × 1 UBIQUINONE-10 × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEM_RHOSH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–307； UniProt 1–307 Author chain S； PDBConstruct 1–307； UniProt 1–307

REACTION CENTER PROTEIN H CHAIN

OrganismNot specified

UniProt P11846

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 （P02954） REACTION CENTER PROTEIN M CHAIN × 1 （P02953） cytochrome c-2 × 1 （P00095） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 FE (II) ION × 1 CHLORIDE ION × 1 UBIQUINONE-10 × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	REACTION CENTER PROTEIN L CHAIN × 1 （P02954） REACTION CENTER PROTEIN M CHAIN × 1 （P02953） cytochrome c-2 × 1 （P00095） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 FE (II) ION × 1 CHLORIDE ION × 1 UBIQUINONE-10 × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEH_RHOSH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–260； UniProt 1–260 Author chain T； PDBConstruct 1–260； UniProt 1–260

cytochrome c-2

OrganismNot specified

UniProt P00095

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 （P02954） REACTION CENTER PROTEIN M CHAIN × 1 （P02953） REACTION CENTER PROTEIN H CHAIN × 1 （P11846） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 FE (II) ION × 1 CHLORIDE ION × 1 UBIQUINONE-10 × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	REACTION CENTER PROTEIN L CHAIN × 1 （P02954） REACTION CENTER PROTEIN M CHAIN × 1 （P02953） REACTION CENTER PROTEIN H CHAIN × 1 （P11846） BACTERIOCHLOROPHYLL A × 4 BACTERIOPHEOPHYTIN A × 2 FE (II) ION × 1 CHLORIDE ION × 1 UBIQUINONE-10 × 1 LAURYL DIMETHYLAMINE-N-OXIDE × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYC2_RHOSH
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–124； UniProt 22–145 Author chain D； PDBConstruct 1–124； UniProt 22–145

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	1l9j
Deposition date deposition_date	2002-03-24
Structure title title	X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals
Keywords keywords	;bacterial photosynthesis, electron transfer proteins, protein-protein interactions, membrane proteins, protein complexes, 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.

1l9j__assembly_1__model_1

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

Download this curve (.dat)

1l9j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1l9j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.61 Å
Rg (electron density)	31.15 Å
Total Rg	31.97 Å
Atom count	7684
Residues	918
Excluded volume	139400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1l9j__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1l9j__assembly_2__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 (12)

Entity 1 Entity 1 polymer

Description description	REACTION CENTER PROTEIN L CHAIN
Molecular weight formula_weight	31346.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,R
Atom count atom_count	15497

ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Entity 2 Entity 2 polymer

Description description	REACTION CENTER PROTEIN M CHAIN
Molecular weight formula_weight	34398.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,S

AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGMAPLN

Entity 3 Entity 3 polymer

Description description	REACTION CENTER PROTEIN H CHAIN
Molecular weight formula_weight	28066.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,T

MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKSVVAAMLAEYA

Entity 4 Entity 4 polymer

Description description	cytochrome c-2
Molecular weight formula_weight	13488.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

QEGDPEAGAKAFNQCQTCHVIVDDSGTTIAGRNAKTGPNLYGVVGRTAGTQADFKGYGEGMKEAGAKGLAWDEEHFVQYVQDPTKFLKEYTGDAKAKGKMTFKLKKEADAHNIWAYLQQVAVRP

Entity 5 Entity 5 non-polymer

Description description	BACTERIOCHLOROPHYLL A
Molecular weight formula_weight	911.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	BACTERIOPHEOPHYTIN A
Molecular weight formula_weight	889.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	UBIQUINONE-10
Molecular weight formula_weight	863.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	LAURYL DIMETHYLAMINE-N-OXIDE
Molecular weight formula_weight	229.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	129

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1l9jc_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d1l9jd_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d1l9jh1
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	d1l9jh2
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	d1l9jl_
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	d1l9jm_
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	d1l9jr_
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	d1l9js_
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	d1l9jt1
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	d1l9jt2
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

CATH v4.4 (14 domains)

Domain ID domain_id	1l9jC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1l9jD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1l9jH01
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	1l9jH02
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	1l9jL01
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	1l9jL02
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	1l9jM01
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	1l9jM02
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	1l9jR01
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	1l9jR02
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	1l9jS01
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	1l9jS02
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	1l9jT01
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	1l9jT02
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	77.930 Å
Unit-cell length b length_b	80.312 Å
Unit-cell length c length_c	246.575 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	49.320 Å
R factor r_factor	0.2630
R_work r_work	0.2480
R_free r_free	0.2870

X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals

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

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

cytochrome c-2

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

1l9j__assembly_1__model_1

1l9j__assembly_1__model_1 | I(q)

1l9j__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 (12)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (10 domains)

CATH v4.4 (14 domains)

7. Citations (1)