9vdx

Serial synchrotron crystallography structure of a photosynthetic reaction center using a goniometer-compatible chip-based platform

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 SULFATE ION × 15 LAURYL DIMETHYLAMINE-N-OXIDE × 7 HEPTANE-1,2,3-TRIOL × 3 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 FE (II) ION × 1 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_BLAVI
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 SULFATE ION × 15 LAURYL DIMETHYLAMINE-N-OXIDE × 7 HEPTANE-1,2,3-TRIOL × 3 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 FE (II) ION × 1 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_BLAVI
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 SULFATE ION × 15 LAURYL DIMETHYLAMINE-N-OXIDE × 7 HEPTANE-1,2,3-TRIOL × 3 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 FE (II) ION × 1 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_BLAVI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain L； PDBConstruct 1–273； UniProt 2–274

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 SULFATE ION × 15 LAURYL DIMETHYLAMINE-N-OXIDE × 7 HEPTANE-1,2,3-TRIOL × 3 BACTERIOCHLOROPHYLL B × 4 BACTERIOPHEOPHYTIN B × 2 FE (II) ION × 1 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_BLAVI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain M； PDBConstruct 1–323； UniProt 2–324

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	9vdx
Deposition date deposition_date	2025-06-09
Structure title title	Serial synchrotron crystallography structure of a photosynthetic reaction center using a goniometer-compatible chip-based platform
Keywords keywords	Bioenergetics, photosynthesis, serial crystallography, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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.

9vdx__assembly_1__model_1

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

Download this curve (.dat)

9vdx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vdx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.00 Å
Rg (electron density)	35.94 Å
Total Rg	36.58 Å
Atom count	10255
Residues	1185
Excluded volume	185880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vdx__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 (15)

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	10352

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	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 4 Entity 4 polymer

Description description	Reaction center protein M chain
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 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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	15

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	HEPTANE-1,2,3-TRIOL
Molecular weight formula_weight	148.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 non-polymer

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

Entity 12 Entity 12 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 13 Entity 13 non-polymer

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

Entity 14 Entity 14 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 15 Entity 15 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	96

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Unit-cell length a length_a	223.800 Å
Unit-cell length b length_b	223.800 Å
Unit-cell length c length_c	113.500 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	2.800 Å
Low-resolution limit resolution_low	36.800 Å
R factor r_factor	—
R_work r_work	0.2150
R_free r_free	0.2530

Serial synchrotron crystallography structure of a photosynthetic reaction center using a goniometer-compatible chip-based platform

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

9vdx__assembly_1__model_1

9vdx__assembly_1__model_1 | I(q)

9vdx__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 (15)

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

Entity 15 Entity 15 water

7. Citations (1)