9k3q

Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex

Method: ELECTRON MICROSCOPY

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

Light-harvesting protein B-870 beta chain

Rhodospirillum rubrum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 35	Light-harvesting protein B-870 alpha chain × 16 （P02947） Photoreaction center protein H × 1 （Q7M149） Reaction center protein L chain × 1 （P10717） Reaction center protein M chain × 1 （Q2RQ26） Trans-Geranyl BACTERIOCHLOROPHYLL A × 37 SPIRILLOXANTHIN × 17 FE (III) ION × 1 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LHB_RHORU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 1–44； UniProt 10–53 Author chain 3； PDBConstruct 1–44； UniProt 10–53 Author chain 5； PDBConstruct 1–44； UniProt 10–53 Author chain 7； PDBConstruct 1–44； UniProt 10–53 Author chain 9； PDBConstruct 1–44； UniProt 10–53 Author chain I； PDBConstruct 1–44； UniProt 10–53 Author chain K； PDBConstruct 1–44； UniProt 10–53 Author chain O； PDBConstruct 1–44； UniProt 10–53 Author chain Q； PDBConstruct 1–44； UniProt 10–53 Author chain S； PDBConstruct 1–44； UniProt 10–53 Author chain U； PDBConstruct 1–44； UniProt 10–53 Author chain W； PDBConstruct 1–44； UniProt 10–53 Author chain Y； PDBConstruct 1–44； UniProt 10–53 Author chain d； PDBConstruct 1–44； UniProt 10–53 Author chain m； PDBConstruct 1–44； UniProt 10–53 Author chain n； PDBConstruct 1–44； UniProt 10–53

Light-harvesting protein B-870 alpha chain

Rhodospirillum rubrum

UniProt P02947

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 35	Light-harvesting protein B-870 beta chain × 16 （P0C190） Photoreaction center protein H × 1 （Q7M149） Reaction center protein L chain × 1 （P10717） Reaction center protein M chain × 1 （Q2RQ26） Trans-Geranyl BACTERIOCHLOROPHYLL A × 37 SPIRILLOXANTHIN × 17 FE (III) ION × 1 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LHA_RHORU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 2； PDBConstruct 1–45； UniProt 2–46 Author chain 4； PDBConstruct 1–45； UniProt 2–46 Author chain 6； PDBConstruct 1–45； UniProt 2–46 Author chain 8； PDBConstruct 1–45； UniProt 2–46 Author chain A； PDBConstruct 1–45； UniProt 2–46 Author chain D； PDBConstruct 1–45； UniProt 2–46 Author chain E； PDBConstruct 1–45； UniProt 2–46 Author chain F； PDBConstruct 1–45； UniProt 2–46 Author chain G； PDBConstruct 1–45； UniProt 2–46 Author chain J； PDBConstruct 1–45； UniProt 2–46 Author chain N； PDBConstruct 1–45； UniProt 2–46 Author chain R； PDBConstruct 1–45； UniProt 2–46 Author chain T； PDBConstruct 1–45； UniProt 2–46 Author chain V； PDBConstruct 1–45； UniProt 2–46 Author chain X； PDBConstruct 1–45； UniProt 2–46 Author chain Z； PDBConstruct 1–45； UniProt 2–46

Photoreaction center protein H

Rhodospirillum rubrum

UniProt Q7M149

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 35	Light-harvesting protein B-870 beta chain × 16 （P0C190） Light-harvesting protein B-870 alpha chain × 16 （P02947） Reaction center protein L chain × 1 （P10717） Reaction center protein M chain × 1 （Q2RQ26） Trans-Geranyl BACTERIOCHLOROPHYLL A × 37 SPIRILLOXANTHIN × 17 FE (III) ION × 1 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7M149_RHORU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–255； UniProt 2–256

Reaction center protein L chain

Rhodospirillum rubrum

UniProt P10717

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 35	Light-harvesting protein B-870 beta chain × 16 （P0C190） Light-harvesting protein B-870 alpha chain × 16 （P02947） Photoreaction center protein H × 1 （Q7M149） Reaction center protein M chain × 1 （Q2RQ26） Trans-Geranyl BACTERIOCHLOROPHYLL A × 37 SPIRILLOXANTHIN × 17 FE (III) ION × 1 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEL_RHORU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain L； PDBConstruct 1–274； UniProt 2–275

Reaction center protein M chain

Rhodospirillum rubrum

UniProt Q2RQ26

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 35	Light-harvesting protein B-870 beta chain × 16 （P0C190） Light-harvesting protein B-870 alpha chain × 16 （P02947） Photoreaction center protein H × 1 （Q7M149） Reaction center protein L chain × 1 （P10717） Trans-Geranyl BACTERIOCHLOROPHYLL A × 37 SPIRILLOXANTHIN × 17 FE (III) ION × 1 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2RQ26_RHORT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–259； UniProt 48–306

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	9k3q
Deposition date deposition_date	2024-10-19
Structure title title	Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Keywords keywords	reaction centre light-harvesting 1, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method method	ELECTRON MICROSCOPY

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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.

9k3q__assembly_1__model_1

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

Download this curve (.dat)

9k3q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9k3q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.37 Å
Rg (electron density)	43.49 Å
Total Rg	43.85 Å
Atom count	21510
Residues	2212
Excluded volume	388250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9k3q__assembly_1__model_1`	35-meric （35）	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	Light-harvesting protein B-870 beta chain
Molecular weight formula_weight	5037.8 kDa
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,3,5,7,9,I,K,O,Q,S,U,W,Y,d,m,n
Atom count atom_count	21510

ITEGEAKEFHKIFTSSILVFFGVAAFAHLLVWIWRPWVPGPNGY

Source Source

Source organism organism	Rhodospirillum rubrum
NCBI taxonomy ID ncbi_taxonomy_id	1085
Host organism host_organism	Rhodospirillum rubrum

Entity 2 Entity 2 polymer

Description description	Light-harvesting protein B-870 alpha chain
Molecular weight formula_weight	5308.2 kDa
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2,4,6,8,A,D,E,F,G,J,N,R,T,V,X,Z

WRIWQLFDPRQALVGLATFLFVLALLIHFILLSTERFNWLEGAST

Source Source

Source organism organism	Rhodospirillum rubrum
NCBI taxonomy ID ncbi_taxonomy_id	1085
Host organism host_organism	Rhodospirillum rubrum

Entity 3 Entity 3 polymer

Description description	Photoreaction center protein H
Molecular weight formula_weight	27745.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

NKGDITGYMDVAQVVLYAFWIFFAGLIIYLRREDRREGYPLEDAISGKINSLQGLGSVFSIARPKIFKLKTGATYAAPNFKRDAVAIKATRTAPTAGAPFEPTGNPMTDAVGPAAYALRDELPDLTLGGQPAIVPLRVAPTFSVAAEDTDPRGLPVVDRKGAVAGKVTDLWIDRASIAIRYLEVELAATPGRKVLLPFAATRINAKTKSKTVTVQSILARHFANVPTIAKTDSITRREEDKVMAYYSSGYLYSDR

Source Source

Source organism organism	Rhodospirillum rubrum
NCBI taxonomy ID ncbi_taxonomy_id	1085
Host organism host_organism	Rhodospirillum rubrum

Entity 4 Entity 4 polymer

Description description	Reaction center protein L chain
Molecular weight formula_weight	30472.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ALLSFERKYRVRGGTLIGGDLFDFWVGPFYVGFFGVTTLLFTVLGTALIVWGAALGPSWTFWQISINPPDVSYGLAMAPMAKGGLWQIITFSAIGAFVSWALREVEICRKLGIGYHIPFAFGFAILAYVSLVVIRPVMMGAWGYGFPYGFMTHLDWVSNTGYQYANFHYNPAHMLGITLFFTTCLALALHGSLILSAANPGKGEVVKGPEHENTYFQDTIGYSVGTLGIHRVGLILALSAVVWSIICMILSGPIYTGSWPDWWLWWQKLPFWNH

Source Source

Source organism organism	Rhodospirillum rubrum
NCBI taxonomy ID ncbi_taxonomy_id	1085
Host organism host_organism	Rhodospirillum rubrum

Entity 5 Entity 5 polymer

Description description	Reaction center protein M chain
Molecular weight formula_weight	29131.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

GPIYLGTTGVLSLVFGFFAIEIIGFNLLASVNWSPMEFGRQFFWLGLEPPAAEYGLGFAPLAEGGWWQIAGFFLTTSILLWWVRMYRRARALKMGTHTAWAFASAIFLFLSLGFIRPLLMGNFSESVPFGIFPHLEWTNSFSLNYGNFFYNPFHMLSIAFLYGSALLFAMHGATILAVSRLGGDREVEQITDRGTAAERAALFWRWTMGFNATMESIHRWAWWFAVLCTFTGAIGILLTGTVVDNWFEWGVKHGLAPAP

Source Source

Source organism organism	Rhodospirillum rubrum
NCBI taxonomy ID ncbi_taxonomy_id	1085
Host organism host_organism	Rhodospirillum rubrum

Entity 6 Entity 6 non-polymer

Description description	Trans-Geranyl BACTERIOCHLOROPHYLL A
Molecular weight formula_weight	901.4 kDa
Source method src_method	syn
Copy count entity_count	37

Entity 7 Entity 7 non-polymer

Description description	SPIRILLOXANTHIN
Molecular weight formula_weight	596.9 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 8 Entity 8 non-polymer

Description description	FE (III) 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	BACTERIOPHEOPHYTIN A
Molecular weight formula_weight	889.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	UBIQUINONE-10
Molecular weight formula_weight	863.3 kDa
Source method src_method	syn
Copy count entity_count	3

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.02 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	97584

Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex

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

Light-harvesting protein B-870 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

Light-harvesting protein B-870 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

Photoreaction center protein H

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

9k3q__assembly_1__model_1

9k3q__assembly_1__model_1 | I(q)

9k3q__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

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)