4ac5

Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography

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） PROTOPORPHYRIN IX CONTAINING FE × 4 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 FE (II) ION × 1 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1	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） PROTOPORPHYRIN IX CONTAINING FE × 4 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 FE (II) ION × 1 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1	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） PROTOPORPHYRIN IX CONTAINING FE × 4 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 FE (II) ION × 1 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1	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） PROTOPORPHYRIN IX CONTAINING FE × 4 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 FE (II) ION × 1 MENAQUINONE-7 × 1 15-cis-1,2-dihydroneurosporene × 1	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	4ac5
Deposition date deposition_date	2011-12-14
Structure title title	Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography
Keywords keywords	;PHOTOSYNTHESIS, LIPIDIC-SPONGE PHASE, REACTION CENTER, ELECTRON TRANSPORT, CELL MEMBRANE, METAL- BINDING, TRANSMEMBRANE, FORMYLATION, CHROMOPHORE, LIPOPROTEIN ;; 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.

4ac5__assembly_1__model_1

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

Download this curve (.dat)

4ac5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ac5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.65 Å
Rg (electron density)	35.72 Å
Total Rg	36.37 Å
Atom count	9835
Residues	1170
Excluded volume	177540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ac5__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 (10)

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	9835

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	36091.4 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	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	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

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

Entity 10 Entity 10 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

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Unit-cell length a length_a	57.500 Å
Unit-cell length b length_b	84.600 Å
Unit-cell length c length_c	375.800 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	8.200 Å
Low-resolution limit resolution_low	46.100 Å
R factor r_factor	0.3524
R_work r_work	0.3507
R_free r_free	0.3840

Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography

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

REACTION CENTER PROTEIN H CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

REACTION CENTER PROTEIN L CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

REACTION CENTER PROTEIN M CHAIN

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

4ac5__assembly_1__model_1

4ac5__assembly_1__model_1 | I(q)

4ac5__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 (10)

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

7. Citations (1)

Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography

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

4ac5__assembly_1__model_1

4ac5__assembly_1__model_1 | I(q)

4ac5__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 (10)

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

7. Citations (1)