4v9g

RC-LH1-PufX dimer complex from Rhodobacter sphaeroides

Method: X-RAY DIFFRACTION

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

Light-harvesting protein B-875 alpha 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 64	Intrinsic membrane protein PufX × 2 （P13402） Light-harvesting protein B-875 beta chain × 28 （Q3J1A3） Reaction center protein H chain × 2 （P0C0Y7） Reaction center protein L chain × 2 （P0C0Y8） Reaction center protein M chain × 2 （P0C0Y9） BACTERIOCHLOROPHYLL A × 64 BACTERIOPHEOPHYTIN A × 4 UBIQUINONE-10 × 3 PHOSPHATE ION × 2 FE (II) ION × 2 SPHEROIDENE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LHA1_RHOSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A1； PDBConstruct 1–58； UniProt 1–58 Author chain A2； PDBConstruct 1–58； UniProt 1–58 Author chain A3； PDBConstruct 1–58； UniProt 1–58 Author chain A5； PDBConstruct 1–58； UniProt 1–58 Author chain A7； PDBConstruct 1–58； UniProt 1–58 Author chain AD； PDBConstruct 1–58； UniProt 1–58 Author chain AF； PDBConstruct 1–58； UniProt 1–58 Author chain AJ； PDBConstruct 1–58； UniProt 1–58 Author chain AN； PDBConstruct 1–58； UniProt 1–58 Author chain AP； PDBConstruct 1–58； UniProt 1–58 Author chain AT； PDBConstruct 1–58； UniProt 1–58 Author chain AV； PDBConstruct 1–58； UniProt 1–58 Author chain AX； PDBConstruct 1–58； UniProt 1–58 Author chain AZ； PDBConstruct 1–58； UniProt 1–58 Author chain B1； PDBConstruct 1–58； UniProt 1–58 Author chain B2； PDBConstruct 1–58； UniProt 1–58 Author chain B3； PDBConstruct 1–58； UniProt 1–58 Author chain B5； PDBConstruct 1–58； UniProt 1–58 Author chain B7； PDBConstruct 1–58； UniProt 1–58 Author chain BD； PDBConstruct 1–58； UniProt 1–58 Author chain BF； PDBConstruct 1–58； UniProt 1–58 Author chain BJ； PDBConstruct 1–58； UniProt 1–58 Author chain BN； PDBConstruct 1–58； UniProt 1–58 Author chain BP； PDBConstruct 1–58； UniProt 1–58 Author chain BT； PDBConstruct 1–58； UniProt 1–58 Author chain BV； PDBConstruct 1–58； UniProt 1–58 Author chain BX； PDBConstruct 1–58； UniProt 1–58 Author chain BZ； PDBConstruct 1–58； UniProt 1–58

Intrinsic membrane protein PufX

OrganismNot specified

UniProt P13402

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 64	Light-harvesting protein B-875 alpha chain × 28 （P0C0X9） Light-harvesting protein B-875 beta chain × 28 （Q3J1A3） Reaction center protein H chain × 2 （P0C0Y7） Reaction center protein L chain × 2 （P0C0Y8） Reaction center protein M chain × 2 （P0C0Y9） BACTERIOCHLOROPHYLL A × 64 BACTERIOPHEOPHYTIN A × 4 UBIQUINONE-10 × 3 PHOSPHATE ION × 2 FE (II) ION × 2 SPHEROIDENE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PUFX_RHOS4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain AB； PDBConstruct 1–82； UniProt 1–82 Author chain BB； PDBConstruct 1–82； UniProt 1–82

Light-harvesting protein B-875 beta chain

OrganismNot specified

UniProt Q3J1A3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 64	Light-harvesting protein B-875 alpha chain × 28 （P0C0X9） Intrinsic membrane protein PufX × 2 （P13402） Reaction center protein H chain × 2 （P0C0Y7） Reaction center protein L chain × 2 （P0C0Y8） Reaction center protein M chain × 2 （P0C0Y9） BACTERIOCHLOROPHYLL A × 64 BACTERIOPHEOPHYTIN A × 4 UBIQUINONE-10 × 3 PHOSPHATE ION × 2 FE (II) ION × 2 SPHEROIDENE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LHB1_RHOS4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A4； PDBConstruct 1–49； UniProt 1–49 Author chain A6； PDBConstruct 1–49； UniProt 1–49 Author chain A8； PDBConstruct 1–49； UniProt 1–49 Author chain A9； PDBConstruct 1–49； UniProt 1–49 Author chain AE； PDBConstruct 1–49； UniProt 1–49 Author chain AG； PDBConstruct 1–49； UniProt 1–49 Author chain AI； PDBConstruct 1–49； UniProt 1–49 Author chain AK； PDBConstruct 1–49； UniProt 1–49 Author chain AO； PDBConstruct 1–49； UniProt 1–49 Author chain AQ； PDBConstruct 1–49； UniProt 1–49 Author chain AS； PDBConstruct 1–49； UniProt 1–49 Author chain AU； PDBConstruct 1–49； UniProt 1–49 Author chain AW； PDBConstruct 1–49； UniProt 1–49 Author chain AY； PDBConstruct 1–49； UniProt 1–49 Author chain B4； PDBConstruct 1–49； UniProt 1–49 Author chain B6； PDBConstruct 1–49； UniProt 1–49 Author chain B8； PDBConstruct 1–49； UniProt 1–49 Author chain B9； PDBConstruct 1–49； UniProt 1–49 Author chain BE； PDBConstruct 1–49； UniProt 1–49 Author chain BG； PDBConstruct 1–49； UniProt 1–49 Author chain BI； PDBConstruct 1–49； UniProt 1–49 Author chain BK； PDBConstruct 1–49； UniProt 1–49 Author chain BO； PDBConstruct 1–49； UniProt 1–49 Author chain BQ； PDBConstruct 1–49； UniProt 1–49 Author chain BS； PDBConstruct 1–49； UniProt 1–49 Author chain BU； PDBConstruct 1–49； UniProt 1–49 Author chain BW； PDBConstruct 1–49； UniProt 1–49 Author chain BY； PDBConstruct 1–49； UniProt 1–49

Reaction center protein H chain

OrganismNot specified

UniProt P0C0Y7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 64	Light-harvesting protein B-875 alpha chain × 28 （P0C0X9） Intrinsic membrane protein PufX × 2 （P13402） Light-harvesting protein B-875 beta chain × 28 （Q3J1A3） Reaction center protein L chain × 2 （P0C0Y8） Reaction center protein M chain × 2 （P0C0Y9） BACTERIOCHLOROPHYLL A × 64 BACTERIOPHEOPHYTIN A × 4 UBIQUINONE-10 × 3 PHOSPHATE ION × 2 FE (II) ION × 2 SPHEROIDENE × 1	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	4
Chains and sequence ranges	Author chain AH； PDBConstruct 1–260； UniProt 1–260 Author chain BH； PDBConstruct 1–260； UniProt 1–260

Reaction center protein L chain

OrganismNot specified

UniProt P0C0Y8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 64	Light-harvesting protein B-875 alpha chain × 28 （P0C0X9） Intrinsic membrane protein PufX × 2 （P13402） Light-harvesting protein B-875 beta chain × 28 （Q3J1A3） Reaction center protein H chain × 2 （P0C0Y7） Reaction center protein M chain × 2 （P0C0Y9） BACTERIOCHLOROPHYLL A × 64 BACTERIOPHEOPHYTIN A × 4 UBIQUINONE-10 × 3 PHOSPHATE ION × 2 FE (II) ION × 2 SPHEROIDENE × 1	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	5
Chains and sequence ranges	Author chain AL； PDBConstruct 1–282； UniProt 1–282 Author chain BL； PDBConstruct 1–282； UniProt 1–282

Reaction center protein M chain

OrganismNot specified

UniProt P0C0Y9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 64	Light-harvesting protein B-875 alpha chain × 28 （P0C0X9） Intrinsic membrane protein PufX × 2 （P13402） Light-harvesting protein B-875 beta chain × 28 （Q3J1A3） Reaction center protein H chain × 2 （P0C0Y7） Reaction center protein L chain × 2 （P0C0Y8） BACTERIOCHLOROPHYLL A × 64 BACTERIOPHEOPHYTIN A × 4 UBIQUINONE-10 × 3 PHOSPHATE ION × 2 FE (II) ION × 2 SPHEROIDENE × 1	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	6
Chains and sequence ranges	Author chain AM； PDBConstruct 1–308； UniProt 1–308 Author chain BM； PDBConstruct 1–308； UniProt 1–308

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	4v9g
Deposition date deposition_date	2013-02-21
Structure title title	RC-LH1-PufX dimer complex from Rhodobacter sphaeroides
Keywords keywords	;photosynthesis, antenna complex LH1, Reaction Centre, chromophores, Photosynthetic Complexes, Photosynthetic Light Capture and electron transfer, Photosynthetic Chromophores, membrane spherical vesicles, PufX, quinol, quinone ;; 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.

4v9g__assembly_1__model_1

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

Download this curve (.dat)

4v9g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4v9g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	65.53 Å
Rg (electron density)	65.60 Å
Total Rg	65.49 Å
Atom count	38094
Residues	4302
Excluded volume	693770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4v9g__assembly_1__model_1`	64-meric （64）	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	Light-harvesting protein B-875 alpha chain
Molecular weight formula_weight	6816.2 kDa
Source method src_method	nat
Copy count entity_count	28

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A5,AT,AV,AX,A3,A7,AD,AF,A1,AJ,A2,AN,AP,AZ,B5,BT,BV,BX,B3,B7,BD,BF,B1,BJ,B2,BN,BP,BZ
Atom count atom_count	38108

MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVAVAE

Entity 2 Entity 2 polymer

Description description	Intrinsic membrane protein PufX
Molecular weight formula_weight	9061.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AB,BB

MADKTIFNDHLNTNPKTNLRLWVAFQMMKGAGWAGGVFFGTLLLIGFFRVVGRMLPIQENQAPAPNITGALETGIELIKHLV

Entity 3 Entity 3 polymer

Description description	Light-harvesting protein B-875 beta chain
Molecular weight formula_weight	5592.4 kDa
Source method src_method	nat
Copy count entity_count	28

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AS,A9,AO,AQ,A6,AU,AW,AY,A4,A8,AE,AG,AI,AK,BS,B9,BO,BQ,B6,BU,BW,BY,B4,B8,BE,BG,BI,BK

MADKSDLGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF

Entity 4 Entity 4 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	AH,BH

MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKSVVAAMLAEYA

Entity 5 Entity 5 polymer

Description description	Reaction center protein L chain
Molecular weight formula_weight	31477.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AL,BL

MALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Entity 6 Entity 6 polymer

Description description	Reaction center protein M chain
Molecular weight formula_weight	34529.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AM,BM

MAEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGMAPLN

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	64

Entity 8 Entity 8 non-polymer

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

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	3

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 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 12 Entity 12 non-polymer

Description description	SPHEROIDENE
Molecular weight formula_weight	568.9 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	78.077 Å
Unit-cell length b length_b	415.075 Å
Unit-cell length c length_c	129.818 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	56

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

Resolution resolution	7.780 Å
Low-resolution limit resolution_low	20.390 Å
R factor r_factor	0.2294
R_work r_work	0.2279
R_free r_free	0.2577

RC-LH1-PufX dimer complex from Rhodobacter sphaeroides

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

Light-harvesting protein B-875 alpha 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

Intrinsic membrane protein PufX

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Light-harvesting protein B-875 beta 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

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

4v9g__assembly_1__model_1

4v9g__assembly_1__model_1 | I(q)

4v9g__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 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer 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

7. Citations (1)