9wqv

Cryo-EM structure of LH1-RC from Rhodovulum sulfidophilum

Method: ELECTRON MICROSCOPY

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

Antenna pigment protein beta 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 37	Antenna pigment protein alpha chain × 16 （Q9WXE0） Photosynthetic reaction center cytochrome c subunit × 1 （Q9WXE3） photosynthetic reaction center subunit H × 1 Reaction center protein L chain × 1 （Q9WXE1） Reaction center protein M chain × 1 （Q9WXE2） NADH:ubiquinone oxidoreductase 41 kd complex i subunit × 1 BACTERIOCHLOROPHYLL A × 36 UNKNOWN LIGAND × 13 SPHEROIDENE × 16 ;(4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-2-ol ; × 14 DODECYL-BETA-D-MALTOSIDE × 10 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 13 HEME C × 3 MAGNESIUM ION × 4 FE (III) ION × 2 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 4 water × 27	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WXD9_RHOSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 0； PDBConstruct 1–48； UniProt 1–48 Author chain 2； PDBConstruct 1–48； UniProt 1–48 Author chain 4； PDBConstruct 1–48； UniProt 1–48 Author chain 6； PDBConstruct 1–48； UniProt 1–48 Author chain 8； PDBConstruct 1–48； UniProt 1–48 Author chain B； PDBConstruct 1–48； UniProt 1–48 Author chain E； PDBConstruct 1–48； UniProt 1–48 Author chain G； PDBConstruct 1–48； UniProt 1–48 Author chain J； PDBConstruct 1–48； UniProt 1–48 Author chain N； PDBConstruct 1–48； UniProt 1–48 Author chain P； PDBConstruct 1–48； UniProt 1–48 Author chain R； PDBConstruct 1–48； UniProt 1–48 Author chain T； PDBConstruct 1–48； UniProt 1–48 Author chain V； PDBConstruct 1–48； UniProt 1–48 Author chain X； PDBConstruct 1–48； UniProt 1–48 Author chain Z； PDBConstruct 1–48； UniProt 1–48

Antenna pigment protein alpha chain

OrganismNot specified

UniProt Q9WXE0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 37	Antenna pigment protein beta chain × 16 （Q9WXD9） Photosynthetic reaction center cytochrome c subunit × 1 （Q9WXE3） photosynthetic reaction center subunit H × 1 Reaction center protein L chain × 1 （Q9WXE1） Reaction center protein M chain × 1 （Q9WXE2） NADH:ubiquinone oxidoreductase 41 kd complex i subunit × 1 BACTERIOCHLOROPHYLL A × 36 UNKNOWN LIGAND × 13 SPHEROIDENE × 16 ;(4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-2-ol ; × 14 DODECYL-BETA-D-MALTOSIDE × 10 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 13 HEME C × 3 MAGNESIUM ION × 4 FE (III) ION × 2 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 4 water × 27	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WXE0_RHOSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 1； PDBConstruct 1–54； UniProt 1–54 Author chain 3； PDBConstruct 1–54； UniProt 1–54 Author chain 5； PDBConstruct 1–54； UniProt 1–54 Author chain 7； PDBConstruct 1–54； UniProt 1–54 Author chain 9； PDBConstruct 1–54； UniProt 1–54 Author chain A； PDBConstruct 1–54； UniProt 1–54 Author chain D； PDBConstruct 1–54； UniProt 1–54 Author chain F； PDBConstruct 1–54； UniProt 1–54 Author chain I； PDBConstruct 1–54； UniProt 1–54 Author chain K； PDBConstruct 1–54； UniProt 1–54 Author chain O； PDBConstruct 1–54； UniProt 1–54 Author chain Q； PDBConstruct 1–54； UniProt 1–54 Author chain S； PDBConstruct 1–54； UniProt 1–54 Author chain U； PDBConstruct 1–54； UniProt 1–54 Author chain W； PDBConstruct 1–54； UniProt 1–54 Author chain Y； PDBConstruct 1–54； UniProt 1–54

Photosynthetic reaction center cytochrome c subunit

OrganismNot specified

UniProt Q9WXE3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 37	Antenna pigment protein beta chain × 16 （Q9WXD9） Antenna pigment protein alpha chain × 16 （Q9WXE0） photosynthetic reaction center subunit H × 1 Reaction center protein L chain × 1 （Q9WXE1） Reaction center protein M chain × 1 （Q9WXE2） NADH:ubiquinone oxidoreductase 41 kd complex i subunit × 1 BACTERIOCHLOROPHYLL A × 36 UNKNOWN LIGAND × 13 SPHEROIDENE × 16 ;(4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-2-ol ; × 14 DODECYL-BETA-D-MALTOSIDE × 10 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 13 HEME C × 3 MAGNESIUM ION × 4 FE (III) ION × 2 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 4 water × 27	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WXE3_RHOSU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–356； UniProt 1–356

Reaction center protein L chain

OrganismNot specified

UniProt Q9WXE1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 37	Antenna pigment protein beta chain × 16 （Q9WXD9） Antenna pigment protein alpha chain × 16 （Q9WXE0） Photosynthetic reaction center cytochrome c subunit × 1 （Q9WXE3） photosynthetic reaction center subunit H × 1 Reaction center protein M chain × 1 （Q9WXE2） NADH:ubiquinone oxidoreductase 41 kd complex i subunit × 1 BACTERIOCHLOROPHYLL A × 36 UNKNOWN LIGAND × 13 SPHEROIDENE × 16 ;(4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-2-ol ; × 14 DODECYL-BETA-D-MALTOSIDE × 10 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 13 HEME C × 3 MAGNESIUM ION × 4 FE (III) ION × 2 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 4 water × 27	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WXE1_RHOSU
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain L； PDBConstruct 1–284； UniProt 1–284

Reaction center protein M chain

OrganismNot specified

UniProt Q9WXE2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 37	Antenna pigment protein beta chain × 16 （Q9WXD9） Antenna pigment protein alpha chain × 16 （Q9WXE0） Photosynthetic reaction center cytochrome c subunit × 1 （Q9WXE3） photosynthetic reaction center subunit H × 1 Reaction center protein L chain × 1 （Q9WXE1） NADH:ubiquinone oxidoreductase 41 kd complex i subunit × 1 BACTERIOCHLOROPHYLL A × 36 UNKNOWN LIGAND × 13 SPHEROIDENE × 16 ;(4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-2-ol ; × 14 DODECYL-BETA-D-MALTOSIDE × 10 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 13 HEME C × 3 MAGNESIUM ION × 4 FE (III) ION × 2 BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 4 water × 27	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WXE2_RHOSU
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain M； PDBConstruct 1–321； UniProt 1–321

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	9wqv
Deposition date deposition_date	2025-09-11
Structure title title	Cryo-EM structure of LH1-RC from Rhodovulum sulfidophilum
Keywords keywords	light harvesting complex 1, Rhodovulum sulfidophilum, 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.

9wqv__assembly_1__model_1

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

Download this curve (.dat)

9wqv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9wqv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.19 Å
Rg (electron density)	45.34 Å
Total Rg	45.54 Å
Atom count	28036
Residues	2852
Excluded volume	519870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9wqv__assembly_1__model_1`	37-meric （37）	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	Antenna pigment protein beta chain
Molecular weight formula_weight	5427.2 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	0,2,4,6,8,B,E,G,J,N,P,R,T,V,X,Z
Atom count atom_count	28553

MAESDVSFTGLTDEQAQEIHAVYMSGLWLFSAVAVLAHLAVYIWRPWL

Entity 2 Entity 2 polymer

Description description	Antenna pigment protein alpha chain
Molecular weight formula_weight	6238.5 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,3,5,7,9,A,D,F,I,K,O,Q,S,U,W,Y

MAKFYKIWMIFDPRRVLVAQGVFLFLLAVMIHLVLLSTDYFNWLTIAAEKAAGA

Entity 3 Entity 3 polymer

Description description	Photosynthetic reaction center cytochrome c subunit
Molecular weight formula_weight	39176.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MMLKFPKWFFKWSEENPTDLMGPGILVGTVGGAVAVAAIIVAFGNPNATIDHQTGPRGIGMAVSKFVKDNPQFDVYEAEYQVFDRVEAPEGTPTAAEAYGDSVVAFGDMDQANFDQLTKAMSAWVGMDVVLYDDGEVDETTLAITKNCIEATQYLNDSWDTHNLATEGKGVNCYTCHRGQPTPPGSWMKSGNVNSAMEGWSGVQNRLLVGRKYTDSQYTSLPVDALEKLLLDGDSIKVTDTESRVDQQKGDPTWQDAERTFSLMNHQANSLNVGCVYCHNTRAFYDPTQVTPQWSVTTLAQQMSIDINQTFYEPRSEILGHESAKVDCMTCHMGVISPLNGHDMVAEWPELAAPAE

Entity 4 Entity 4 polymer

Description description	photosynthetic reaction center subunit H
Molecular weight formula_weight	28762.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MVNAFFGNFDIASLAIWSFWLFFAGLIFYLQRMNMHEGYPLEDEVGNAAPNQGMFPLPAAKTFKLPHGQGEKTVPDMQTDPRNADLALQKVTKSNGYPLEPTGDPMVDGVGPAAWCARKDEPELDGRGHPKIQPLSVLKTFKVSAGRDPRGMPVIAGDGEAVGTIVDMWVDEPEQLVRYLELELDEAHGGGRRLLPMQLAKIGWFKPEVSVHSIYGKHFAAVPTIKSAKQITKLEEDKVCAYYAGGKLYADPAERLEPQF

Entity 5 Entity 5 polymer

Description description	Reaction center protein L chain
Molecular weight formula_weight	31674.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MALLSFERKYRVRGGTLIGGDLFDFWVGPFFVGFFGVTTIFFATLGTAMIFWGAALQGTFNPLKIHIAPPDLSYGLSIAPLAEGGLWQFITLCAIGAFVSWALREVEICRKLGIGYHIPIAFGMAIFAYLTLEVFRPMLMGAWGHAFPYGIFTHLDWVSNTGYHYLHFHYNPFHMLGVSLFFATCLALALHGGLILSACNPEKGEEAKTPDHEDSFFRDLIGYSIGTLGIHRAGWLLAINAVFFSAVCIIISGPLWTEGWPEWWTWWSNLPIWPEAIPAVQGSM

Entity 6 Entity 6 polymer

Description description	Reaction center protein M chain
Molecular weight formula_weight	36508.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MAEYQNIFTQVQVQGPSDWGMDNENNMMEERAGMGHFSILGWLGNAQLGPIYLGYTGVVSLIAGCFAFLIIGLNMLAQVDWSLVQLLRQGFWLALEPPSPEYGLRIPPLKEGGWYMVASFFLLISVWAWWARTYMLAVEHKMGKHIAWAFLSAIWLFMVLGFFRPILMGSWSEMVPYGIFPHLDWTTAFSIRYGNLYYNPFHALSIAFLYGSALLFAMHGGTILAVTRFGGDRELEQIYDRGTASERAALFWRWTMGFNATMEGIHRWAWWFAVLTPLTGGIGILLTGTVVDNWYIWAQEHNFVTEYTQPYGVDAYVGQGG

Entity 7 Entity 7 polymer

Description description	NADH:ubiquinone oxidoreductase 41 kd complex i subunit
Molecular weight formula_weight	24079.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a

MNISRTEARFKFAIFWWLVAALCGLTVATIGYGVGLWALGAFVGGFGTFVVAGVVLTWAFCHTDAEFSAMVAKKREAMAAMKPYRDANAAIVVPNRPKPGGPKVAPTVPRSTPKAAAAPAARVAPKADAAETSSPKPEAAPTAAQEKVGNGPAALSAPRAGGADDLKKIKGVGPKLEKQVNDLGIYHYDQIASWTAADVAWMDENLEGFKGRVSRDDWVAQARALAKEG

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	36

Entity 9 Entity 9 non-polymer

Description description	UNKNOWN LIGAND
Molecular weight formula_weight	254.5 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 10 Entity 10 non-polymer

Description description	SPHEROIDENE
Molecular weight formula_weight	568.9 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 11 Entity 11 non-polymer

Description description	;(4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-2-ol ;
Molecular weight formula_weight	554.9 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 12 Entity 12 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 13 Entity 13 non-polymer

Description description	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
Molecular weight formula_weight	749.0 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 14 Entity 14 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 15 Entity 15 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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	2

Entity 17 Entity 17 non-polymer

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

Entity 18 Entity 18 non-polymer

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

Entity 19 Entity 19 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	502

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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	1.81 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	108964

Cryo-EM structure of LH1-RC from Rhodovulum sulfidophilum

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

Antenna pigment protein 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

Antenna pigment protein 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

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 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

9wqv__assembly_1__model_1

9wqv__assembly_1__model_1 | I(q)

9wqv__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 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 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 (1)