3prc

PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (QB-DEPLETED)

Method: X-RAY DIFFRACTION

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

PHOTOSYNTHETIC REACTION CENTER

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	PHOTOSYNTHETIC REACTION CENTER × 2 （P06009） PHOTOSYNTHETIC REACTION CENTER × 2 （P06010） PHOTOSYNTHETIC REACTION CENTER × 2 （P06008） PROTOPORPHYRIN IX CONTAINING FE × 8 BACTERIOCHLOROPHYLL B × 8 BACTERIOPHEOPHYTIN B × 4 LAURYL DIMETHYLAMINE-N-OXIDE × 14 FE (II) ION × 2 SULFATE ION × 8 MENAQUINONE-7 × 2 15-cis-1,2-dihydroneurosporene × 2 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PHOTOSYNTHETIC REACTION CENTER × 1 （P06009） PHOTOSYNTHETIC REACTION CENTER × 1 （P06010） PHOTOSYNTHETIC REACTION CENTER × 1 （P06008） PROTOPORPHYRIN IX CONTAINING FE × 4 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 LAURYL DIMETHYLAMINE-N-OXIDE × 7 FE (II) ION × 1 SULFATE ION × 4 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1 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

PHOTOSYNTHETIC REACTION CENTER

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 8	PHOTOSYNTHETIC REACTION CENTER × 2 （P07173） PHOTOSYNTHETIC REACTION CENTER × 2 （P06010） PHOTOSYNTHETIC REACTION CENTER × 2 （P06008） PROTOPORPHYRIN IX CONTAINING FE × 8 BACTERIOCHLOROPHYLL B × 8 BACTERIOPHEOPHYTIN B × 4 LAURYL DIMETHYLAMINE-N-OXIDE × 14 FE (II) ION × 2 SULFATE ION × 8 MENAQUINONE-7 × 2 15-cis-1,2-dihydroneurosporene × 2 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PHOTOSYNTHETIC REACTION CENTER × 1 （P07173） PHOTOSYNTHETIC REACTION CENTER × 1 （P06010） PHOTOSYNTHETIC REACTION CENTER × 1 （P06008） PROTOPORPHYRIN IX CONTAINING FE × 4 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 LAURYL DIMETHYLAMINE-N-OXIDE × 7 FE (II) ION × 1 SULFATE ION × 4 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1 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	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–273； UniProt 1–273

PHOTOSYNTHETIC REACTION CENTER

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 8	PHOTOSYNTHETIC REACTION CENTER × 2 （P07173） PHOTOSYNTHETIC REACTION CENTER × 2 （P06009） PHOTOSYNTHETIC REACTION CENTER × 2 （P06008） PROTOPORPHYRIN IX CONTAINING FE × 8 BACTERIOCHLOROPHYLL B × 8 BACTERIOPHEOPHYTIN B × 4 LAURYL DIMETHYLAMINE-N-OXIDE × 14 FE (II) ION × 2 SULFATE ION × 8 MENAQUINONE-7 × 2 15-cis-1,2-dihydroneurosporene × 2 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PHOTOSYNTHETIC REACTION CENTER × 1 （P07173） PHOTOSYNTHETIC REACTION CENTER × 1 （P06009） PHOTOSYNTHETIC REACTION CENTER × 1 （P06008） PROTOPORPHYRIN IX CONTAINING FE × 4 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 LAURYL DIMETHYLAMINE-N-OXIDE × 7 FE (II) ION × 1 SULFATE ION × 4 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1 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	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–323； UniProt 1–323

PHOTOSYNTHETIC REACTION CENTER

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 8	PHOTOSYNTHETIC REACTION CENTER × 2 （P07173） PHOTOSYNTHETIC REACTION CENTER × 2 （P06009） PHOTOSYNTHETIC REACTION CENTER × 2 （P06010） PROTOPORPHYRIN IX CONTAINING FE × 8 BACTERIOCHLOROPHYLL B × 8 BACTERIOPHEOPHYTIN B × 4 LAURYL DIMETHYLAMINE-N-OXIDE × 14 FE (II) ION × 2 SULFATE ION × 8 MENAQUINONE-7 × 2 15-cis-1,2-dihydroneurosporene × 2 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	PHOTOSYNTHETIC REACTION CENTER × 1 （P07173） PHOTOSYNTHETIC REACTION CENTER × 1 （P06009） PHOTOSYNTHETIC REACTION CENTER × 1 （P06010） PROTOPORPHYRIN IX CONTAINING FE × 4 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 LAURYL DIMETHYLAMINE-N-OXIDE × 7 FE (II) ION × 1 SULFATE ION × 4 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1 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	4
Chains and sequence ranges	Author chain H； 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	3prc
Deposition date deposition_date	1997-07-29
Structure title title	PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (QB-DEPLETED)
Keywords keywords	PHOTOSYNTHETIC REACTION CENTER, SECONDARY QUINONE (QB)-DEPLETED; PHOTOSYNTHETIC REACTION CENTER
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.

3prc__assembly_1__model_1

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

Download this curve (.dat)

3prc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3prc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.28 Å
Rg (electron density)	52.71 Å
Total Rg	52.92 Å
Atom count	20258
Residues	2370
Excluded volume	367090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3prc__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3prc__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 (13)

Entity 1 Entity 1 polymer

Description description	PHOTOSYNTHETIC REACTION CENTER
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	10606

CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIKAAAK

Entity 2 Entity 2 polymer

Description description	PHOTOSYNTHETIC REACTION CENTER
Molecular weight formula_weight	30469.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS

Entity 3 Entity 3 polymer

Description description	PHOTOSYNTHETIC REACTION CENTER
Molecular weight formula_weight	35932.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK

Entity 4 Entity 4 polymer

Description description	PHOTOSYNTHETIC REACTION CENTER
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 5 Entity 5 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 non-polymer

Description description	LAURYL DIMETHYLAMINE-N-OXIDE
Molecular weight formula_weight	229.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 9 Entity 9 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 10 Entity 10 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	425

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3prcc_
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	d3prch1
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	d3prch2
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	d3prch3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3prcl_
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	d3prcm_
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	3prcC01
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	3prcC02
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	3prcH01
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	3prcH02
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	3prcL01
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	3prcL02
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	3prcM01
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	3prcM02
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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7. Citations (8)

;The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB. ;

Structure (1997)

PMID: 9351808 · DOI: 10.1016/S0969-2126(97)00285-2 PRIMARY

;Refined Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis in Complexes with the Herbicide Atrazine and Two Chiral Atrazine Derivatives Also Lead to a New Model of the Bound Carotenoid ;

J.Mol.Biol. (1999)

;Ubiquinone Reduction and Protonation in the Reaction Centre of Rhodopseudomonas Viridis: X-Ray Structures and Their Functional Implications ;

Biochim.Biophys.Acta (1998)

;Crystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre from Rhodopseudomonas Viridis ;

J.Mol.Biol. (1995)

The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis

Science (1989)

Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3 Angstroms Resolution

Nature (1985)

;X-Ray Structure Analysis of a Membrane Protein Complex. Electron Density Map at 3 A Resolution and a Model of the Chromophores of the Photosynthetic Reaction Center from Rhodopseudomonas Viridis ;

J.Mol.Biol. (1984)

Three-Dimensional Crystals of a Membrane Protein Complex. The Photosynthetic Reaction Centre from Rhodopseudomonas Viridis

J.Mol.Biol. (1982)

Unit-cell length a length_a	223.500 Å
Unit-cell length b length_b	223.500 Å
Unit-cell length c length_c	113.600 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1780
R_work r_work	0.1780
R_free r_free	0.2150

PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (QB-DEPLETED)

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

PHOTOSYNTHETIC REACTION CENTER

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHOTOSYNTHETIC REACTION CENTER

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHOTOSYNTHETIC REACTION CENTER

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHOTOSYNTHETIC REACTION CENTER

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

3prc__assembly_1__model_1

3prc__assembly_1__model_1 | I(q)

3prc__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 (13)

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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (8)