7pil

Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A

Method: ELECTRON MICROSCOPY

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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 33	Light-harvesting protein B-875 beta chain × 14 （Q3J1A3） Reaction center protein H chain × 1 （Q3J170） Reaction center protein L chain × 1 （Q3J1A5） Reaction center protein M chain × 1 （Q3J1A6） RC-Y × 1 （U5NME9） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 32 SPHEROIDENE × 26 DODECYL-BETA-D-MALTOSIDE × 4 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 UBIQUINONE-1 × 1 ;(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 ; × 1 FE (III) ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LHA1_RHOS4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AA； PDBConstruct 1–55； UniProt 1–55 Author chain AB； PDBConstruct 1–55； UniProt 1–55 Author chain AC； PDBConstruct 1–55； UniProt 1–55 Author chain AD； PDBConstruct 1–55； UniProt 1–55 Author chain AE； PDBConstruct 1–55； UniProt 1–55 Author chain AF； PDBConstruct 1–55； UniProt 1–55 Author chain AG； PDBConstruct 1–55； UniProt 1–55 Author chain AH； PDBConstruct 1–55； UniProt 1–55 Author chain AI； PDBConstruct 1–55； UniProt 1–55 Author chain AJ； PDBConstruct 1–55； UniProt 1–55 Author chain AK； PDBConstruct 1–55； UniProt 1–55 Author chain AL； PDBConstruct 1–55； UniProt 1–55 Author chain AM； PDBConstruct 1–55； UniProt 1–55 Author chain AN； PDBConstruct 1–55； UniProt 1–55

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 33	Light-harvesting protein B-875 alpha chain × 14 （Q3J1A4） Reaction center protein H chain × 1 （Q3J170） Reaction center protein L chain × 1 （Q3J1A5） Reaction center protein M chain × 1 （Q3J1A6） RC-Y × 1 （U5NME9） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 32 SPHEROIDENE × 26 DODECYL-BETA-D-MALTOSIDE × 4 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 UBIQUINONE-1 × 1 ;(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 ; × 1 FE (III) ION × 1 water × 3	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	2
Chains and sequence ranges	Author chain BA； PDBConstruct 1–43； UniProt 7–49 Author chain BB； PDBConstruct 1–43； UniProt 7–49 Author chain BC； PDBConstruct 1–43； UniProt 7–49 Author chain BD； PDBConstruct 1–43； UniProt 7–49 Author chain BE； PDBConstruct 1–43； UniProt 7–49 Author chain BF； PDBConstruct 1–43； UniProt 7–49 Author chain BG； PDBConstruct 1–43； UniProt 7–49 Author chain BH； PDBConstruct 1–43； UniProt 7–49 Author chain BI； PDBConstruct 1–43； UniProt 7–49 Author chain BJ； PDBConstruct 1–43； UniProt 7–49 Author chain BK； PDBConstruct 1–43； UniProt 7–49 Author chain BL； PDBConstruct 1–43； UniProt 7–49 Author chain BM； PDBConstruct 1–43； UniProt 7–49 Author chain BN； PDBConstruct 1–43； UniProt 7–49

Reaction center protein H chain

OrganismNot specified

UniProt Q3J170

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Light-harvesting protein B-875 alpha chain × 14 （Q3J1A4） Light-harvesting protein B-875 beta chain × 14 （Q3J1A3） Reaction center protein L chain × 1 （Q3J1A5） Reaction center protein M chain × 1 （Q3J1A6） RC-Y × 1 （U5NME9） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 32 SPHEROIDENE × 26 DODECYL-BETA-D-MALTOSIDE × 4 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 UBIQUINONE-1 × 1 ;(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 ; × 1 FE (III) ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEH_RHOS4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–246； UniProt 1–246

Reaction center protein L chain

OrganismNot specified

UniProt Q3J1A5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Light-harvesting protein B-875 alpha chain × 14 （Q3J1A4） Light-harvesting protein B-875 beta chain × 14 （Q3J1A3） Reaction center protein H chain × 1 （Q3J170） Reaction center protein M chain × 1 （Q3J1A6） RC-Y × 1 （U5NME9） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 32 SPHEROIDENE × 26 DODECYL-BETA-D-MALTOSIDE × 4 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 UBIQUINONE-1 × 1 ;(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 ; × 1 FE (III) ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCEL_RHOS4
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain L； PDBConstruct 1–281； UniProt 2–282

Reaction center protein M chain

OrganismNot specified

UniProt Q3J1A6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Light-harvesting protein B-875 alpha chain × 14 （Q3J1A4） Light-harvesting protein B-875 beta chain × 14 （Q3J1A3） Reaction center protein H chain × 1 （Q3J170） Reaction center protein L chain × 1 （Q3J1A5） RC-Y × 1 （U5NME9） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 32 SPHEROIDENE × 26 DODECYL-BETA-D-MALTOSIDE × 4 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 UBIQUINONE-1 × 1 ;(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 ; × 1 FE (III) ION × 1 water × 3	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

RC-Y

OrganismNot specified

UniProt U5NME9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 33	Light-harvesting protein B-875 alpha chain × 14 （Q3J1A4） Light-harvesting protein B-875 beta chain × 14 （Q3J1A3） Reaction center protein H chain × 1 （Q3J170） Reaction center protein L chain × 1 （Q3J1A5） Reaction center protein M chain × 1 （Q3J1A6） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 32 SPHEROIDENE × 26 DODECYL-BETA-D-MALTOSIDE × 4 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 UBIQUINONE-1 × 1 ;(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 ; × 1 FE (III) ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	U5NME9_RHOS4
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain UU； PDBConstruct 1–49； UniProt 3–51

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 33	Light-harvesting protein B-875 alpha chain × 14 （Q3J1A4） Light-harvesting protein B-875 beta chain × 14 （Q3J1A3） Reaction center protein H chain × 1 （Q3J170） Reaction center protein L chain × 1 （Q3J1A5） Reaction center protein M chain × 1 （Q3J1A6） RC-Y × 1 （U5NME9） BACTERIOCHLOROPHYLL A × 32 SPHEROIDENE × 26 DODECYL-BETA-D-MALTOSIDE × 4 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 UBIQUINONE-1 × 1 ;(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 ; × 1 FE (III) ION × 1 water × 3	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	7
Chains and sequence ranges	Author chain X； PDBConstruct 1–55； UniProt 15–69

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	7pil
Deposition date deposition_date	2021-08-20
Structure title title	Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A
Keywords keywords	Photosynthetic bacteria, light harvesting complex, Cryo-EM, RC-LH1, RC-LH1-PufX, RC-LH1-PufX-Y, 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.

7pil__assembly_1__model_1

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

Download this curve (.dat)

7pil__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7pil__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.31 Å
Rg (electron density)	43.87 Å
Total Rg	44.34 Å
Atom count	22476
Residues	2291
Excluded volume	423170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7pil__assembly_1__model_1`	33-meric （33）	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 (17)

Entity 1 Entity 1 polymer

Description description	Light-harvesting protein B-875 alpha chain
Molecular weight formula_weight	6516.8 kDa
Source method src_method	nat
Copy count entity_count	14

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
Atom count atom_count	22480

MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVA

Entity 2 Entity 2 polymer

Description description	Light-harvesting protein B-875 beta chain
Molecular weight formula_weight	4943.7 kDa
Source method src_method	nat
Copy count entity_count	14

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

LGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF

Entity 3 Entity 3 polymer

Description description	Reaction center protein H chain
Molecular weight formula_weight	26544.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAP

Entity 4 Entity 4 polymer

Description description	Reaction center protein L chain
Molecular weight formula_weight	31346.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGMAPLN

Entity 6 Entity 6 polymer

Description description	RC-Y
Molecular weight formula_weight	5126.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	UU

EVSEFAFRLMMAAVIFVGVGIMFAFAGGHWFVGLVVGGLVAAFFAATPN

Entity 7 Entity 7 polymer

Description description	Intrinsic membrane protein PufX
Molecular weight formula_weight	5980.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

PKTNLRLWVAFQMMKGAGWAGGVFFGTLLLIGFFRVVGLMLPIQENQAPAPNITG

Entity 8 Entity 8 non-polymer

Description description	BACTERIOCHLOROPHYLL A
Molecular weight formula_weight	911.5 kDa
Source method src_method	syn
Copy count entity_count	32

Entity 9 Entity 9 non-polymer

Description description	SPHEROIDENE
Molecular weight formula_weight	568.9 kDa
Source method src_method	syn
Copy count entity_count	26

Entity 10 Entity 10 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	4

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	BACTERIOPHEOPHYTIN A
Molecular weight formula_weight	889.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 13 Entity 13 non-polymer

Description description	UBIQUINONE-10
Molecular weight formula_weight	863.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 14 Entity 14 non-polymer

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

Entity 15 Entity 15 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	1

Entity 16 Entity 16 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 17 Entity 17 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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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	2.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	250613

Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A

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

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

RC-Y

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7pil__assembly_1__model_1

7pil__assembly_1__model_1 | I(q)

7pil__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 (17)

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