7pqd

Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 A: the structural basis for dimerisation

Method: ELECTRON MICROSCOPY

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

Reaction center protein M 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 70	LH1-alpha × 28 LH1-beta × 28 RC-H × 2 RC-L × 2 PufZ × 4 PufY × 2 PufX × 2 BACTERIOCHLOROPHYLL A × 64 3,4-DIHYDROSPHEROIDENE × 54 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 ;(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate ; × 4 UBIQUINONE-1 × 2 UBIQUINONE-10 × 4 BACTERIOPHEOPHYTIN A × 4 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 DODECYL-BETA-D-MALTOSIDE × 2 FE (III) ION × 2 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEM_RHOS4
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–307； UniProt 2–308 Author chain m； PDBConstruct 1–307； UniProt 2–308

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	7pqd
Deposition date deposition_date	2021-09-17
Structure title title	Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 A: the structural basis for dimerisation
Keywords keywords	light harvesting complex, photosynthesis, Cryo-EM, purple bacteria, RC-LH1, RC-LH1-PufXYZ, dimer, dimeric core complex; 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.

7pqd__assembly_1__model_1

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

Download this curve (.dat)

7pqd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7pqd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	65.69 Å
Rg (electron density)	66.47 Å
Total Rg	66.45 Å
Atom count	45808
Residues	4672
Excluded volume	862530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7pqd__assembly_1__model_1`	70-meric （70）	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 (19)

Entity 1 Entity 1 polymer

Description description	LH1-alpha
Molecular weight formula_weight	6844.2 kDa
Source method src_method	nat
Copy count entity_count	28

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AK,AL,AM,AN,aa,ab,ac,ad,ae,af,ag,ah,ai,aj,ak,al,am,an
Atom count atom_count	45952

MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVAVAE

Entity 2 Entity 2 polymer

Description description	LH1-beta
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	BA,BB,BC,BD,BE,BF,BG,BH,BI,BJ,BK,BL,BM,BN,ba,bb,bc,bd,be,bf,bg,bh,bi,bj,bk,bl,bm,bn

MADKSDLGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF

Entity 3 Entity 3 polymer

Description description	RC-H
Molecular weight formula_weight	26544.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,h

MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAP

Entity 4 Entity 4 polymer

Description description	RC-L
Molecular weight formula_weight	31346.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,l

ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Entity 5 Entity 5 polymer

Description description	Reaction center protein M chain
Molecular weight formula_weight	34398.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,m

AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGMAPLN

Entity 6 Entity 6 polymer

Description description	PufZ
Molecular weight formula_weight	3517.3 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	UA,UB,ua,ub

MAYMFGIIVFLAMLAVCWFGFMAAERQAGRL

Entity 7 Entity 7 polymer

Description description	PufY
Molecular weight formula_weight	5126.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	UU,uu

EVSEFAFRLMMAAVIFVGVGIMFAFAGGHWFVGLVVGGLVAAFFAATPN

Entity 8 Entity 8 polymer

Description description	PufX
Molecular weight formula_weight	6024.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,x

PKTNLRLWVAFQMMKGAGWAGGVFFGTLLLIGFFRVVGRMLPIQENQAPAPNITG

Entity 9 Entity 9 non-polymer

Description description	BACTERIOCHLOROPHYLL A
Molecular weight formula_weight	911.5 kDa
Source method src_method	syn
Copy count entity_count	64

Entity 10 Entity 10 non-polymer

Description description	3,4-DIHYDROSPHEROIDENE
Molecular weight formula_weight	570.9 kDa
Source method src_method	syn
Copy count entity_count	54

Entity 11 Entity 11 non-polymer

Description description	1,2-Distearoyl-sn-glycerophosphoethanolamine
Molecular weight formula_weight	748.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 12 Entity 12 non-polymer

Description description	;(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate ;
Molecular weight formula_weight	1241.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 13 Entity 13 non-polymer

Description description	UBIQUINONE-1
Molecular weight formula_weight	250.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 14 Entity 14 non-polymer

Description description	UBIQUINONE-10
Molecular weight formula_weight	863.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 15 Entity 15 non-polymer

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

Entity 16 Entity 16 non-polymer

Description description	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
Molecular weight formula_weight	795.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 17 Entity 17 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 18 Entity 18 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 19 Entity 19 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	144

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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	triclinic

Resolution resolution	2.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	58945

Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 A: the structural basis for dimerisation

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

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

7pqd__assembly_1__model_1

7pqd__assembly_1__model_1 | I(q)

7pqd__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 (19)

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 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer 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 non-polymer

Entity 16 Entity 16 non-polymer

Entity 17 Entity 17 non-polymer

Entity 18 Entity 18 non-polymer

Entity 19 Entity 19 water

7. Citations (2)