7eqd

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLUM RUBRUM

Method: ELECTRON MICROSCOPY

▼

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

Reaction center protein L 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 35	Reaction center protein M chain × 1 （Q2RQ26） Photoreaction center protein H × 1 （Q7M149） Light-harvesting protein B-870 alpha chain × 16 （P02947） Light-harvesting protein B-870 beta chain × 16 （Q2RQ23） Trans-Geranyl BACTERIOCHLOROPHYLL A × 36 Trans-Geranyl BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 DODECYL-BETA-D-MALTOSIDE × 23 FE (III) ION × 1 ;2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione ; × 1 SPIRILLOXANTHIN × 17 CARDIOLIPIN × 5 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 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	1
Chains and sequence ranges	Author chain L； PDBConstruct 1–275； UniProt 2–276

Reaction center protein M chain

OrganismNot specified

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	Reaction center protein L chain × 1 （P10717） Photoreaction center protein H × 1 （Q7M149） Light-harvesting protein B-870 alpha chain × 16 （P02947） Light-harvesting protein B-870 beta chain × 16 （Q2RQ23） Trans-Geranyl BACTERIOCHLOROPHYLL A × 36 Trans-Geranyl BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 DODECYL-BETA-D-MALTOSIDE × 23 FE (III) ION × 1 ;2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione ; × 1 SPIRILLOXANTHIN × 17 CARDIOLIPIN × 5 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 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	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–305； UniProt 2–306

Photoreaction center protein H

OrganismNot specified

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	Reaction center protein L chain × 1 （P10717） Reaction center protein M chain × 1 （Q2RQ26） Light-harvesting protein B-870 alpha chain × 16 （P02947） Light-harvesting protein B-870 beta chain × 16 （Q2RQ23） Trans-Geranyl BACTERIOCHLOROPHYLL A × 36 Trans-Geranyl BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 DODECYL-BETA-D-MALTOSIDE × 23 FE (III) ION × 1 ;2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione ; × 1 SPIRILLOXANTHIN × 17 CARDIOLIPIN × 5 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 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 1–256； UniProt 2–257

Light-harvesting protein B-870 alpha chain

OrganismNot specified

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	Reaction center protein L chain × 1 （P10717） Reaction center protein M chain × 1 （Q2RQ26） Photoreaction center protein H × 1 （Q7M149） Light-harvesting protein B-870 beta chain × 16 （Q2RQ23） Trans-Geranyl BACTERIOCHLOROPHYLL A × 36 Trans-Geranyl BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 DODECYL-BETA-D-MALTOSIDE × 23 FE (III) ION × 1 ;2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione ; × 1 SPIRILLOXANTHIN × 17 CARDIOLIPIN × 5 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 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	4
Chains and sequence ranges	Author chain 1； PDBConstruct 1–62； UniProt 1–62 Author chain 3； PDBConstruct 1–62； UniProt 1–62 Author chain 5； PDBConstruct 1–62； UniProt 1–62 Author chain 7； PDBConstruct 1–62； UniProt 1–62 Author chain 9； PDBConstruct 1–62； UniProt 1–62 Author chain A； PDBConstruct 1–62； UniProt 1–62 Author chain D； PDBConstruct 1–62； UniProt 1–62 Author chain F； PDBConstruct 1–62； UniProt 1–62 Author chain I； PDBConstruct 1–62； UniProt 1–62 Author chain K； PDBConstruct 1–62； UniProt 1–62 Author chain O； PDBConstruct 1–62； UniProt 1–62 Author chain Q； PDBConstruct 1–62； UniProt 1–62 Author chain S； PDBConstruct 1–62； UniProt 1–62 Author chain U； PDBConstruct 1–62； UniProt 1–62 Author chain W； PDBConstruct 1–62； UniProt 1–62 Author chain Y； PDBConstruct 1–62； UniProt 1–62

Light-harvesting protein B-870 beta chain

OrganismNot specified

UniProt Q2RQ23

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 35	Reaction center protein L chain × 1 （P10717） Reaction center protein M chain × 1 （Q2RQ26） Photoreaction center protein H × 1 （Q7M149） Light-harvesting protein B-870 alpha chain × 16 （P02947） Trans-Geranyl BACTERIOCHLOROPHYLL A × 36 Trans-Geranyl BACTERIOPHEOPHYTIN A × 2 UBIQUINONE-10 × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 DODECYL-BETA-D-MALTOSIDE × 23 FE (III) ION × 1 ;2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione ; × 1 SPIRILLOXANTHIN × 17 CARDIOLIPIN × 5 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LHB_RHORT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain 0； PDBConstruct 1–55； UniProt 2–56 Author chain 2； PDBConstruct 1–55； UniProt 2–56 Author chain 4； PDBConstruct 1–55； UniProt 2–56 Author chain 6； PDBConstruct 1–55； UniProt 2–56 Author chain 8； PDBConstruct 1–55； UniProt 2–56 Author chain B； PDBConstruct 1–55； UniProt 2–56 Author chain E； PDBConstruct 1–55； UniProt 2–56 Author chain G； PDBConstruct 1–55； UniProt 2–56 Author chain J； PDBConstruct 1–55； UniProt 2–56 Author chain N； PDBConstruct 1–55； UniProt 2–56 Author chain P； PDBConstruct 1–55； UniProt 2–56 Author chain R； PDBConstruct 1–55； UniProt 2–56 Author chain T； PDBConstruct 1–55； UniProt 2–56 Author chain V； PDBConstruct 1–55； UniProt 2–56 Author chain X； PDBConstruct 1–55； UniProt 2–56 Author chain Z； PDBConstruct 1–55； UniProt 2–56

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7eqd
Deposition date deposition_date	2021-05-01
Structure title title	STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLUM RUBRUM
Keywords keywords	LH1-RC COMPLEX, PHOTOSYNTHESIS, PURPLE BACTERIA; PHOTOSYNTHESIS
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

7eqd__assembly_1__model_1

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

Download this curve (.dat)

7eqd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7eqd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.34 Å
Rg (electron density)	43.56 Å
Total Rg	43.97 Å
Atom count	23122
Residues	2286
Excluded volume	418910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7eqd__assembly_1__model_1`	35-meric （35）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (15)

Entity 1 Entity 1 polymer

Description description	Reaction center protein L chain
Molecular weight formula_weight	30529.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	23122

ALLSFERKYRVRGGTLIGGDLFDFWVGPFYVGFFGVTTLLFTVLGTALIVWGAALGPSWTFWQISINPPDVSYGLAMAPMAKGGLWQIITFSAIGAFVSWALREVEICRKLGIGYHIPFAFGFAILAYVSLVVIRPVMMGAWGYGFPYGFMTHLDWVSNTGYQYANFHYNPAHMLGITLFFTTCLALALHGSLILSAANPGKGEVVKGPEHENTYFQDTIGYSVGTLGIHRVGLILALSAVVWSIICMILSGPIYTGSWPDWWLWWQKLPFWNHG

Entity 2 Entity 2 polymer

Description description	Reaction center protein M chain
Molecular weight formula_weight	34103.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

SEYQNILTGVQVRTAPHSAPIAKGIFPRLGKPGFSYWLGKIGDAQIGPIYLGTTGVLSLVFGFFAIEIIGFNLLASVNWSPMEFGRQFFWLGLEPPAAEYGLGFAPLAEGGWWQIAGFFLTTSILLWWVRMYRRARALKMGTHTAWAFASAIFLFLSLGFIRPLLMGNFSESVPFGIFPHLEWTNSFSLNYGNFFYNPFHMLSIAFLYGSALLFAMHGATILAVSRLGGDREVEQITDRGTAAERAALFWRWTMGFNATMESIHRWAWWFAVLCTFTGAIGILLTGTVVDNWFEWGVKHGLAPAP

Entity 3 Entity 3 polymer

Description description	Photoreaction center protein H
Molecular weight formula_weight	27845.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

NKGDITGYMDVAQVVLYAFWIFFAGLIIYLRREDRREGYPLEDAISGKINSLQGLGSVFSIARPKIFKLKTGATYAAPNFKRDAVAIKATRTAPTAGAPFEPTGNPMTDAVGPAAYALRDELPDLTLGGQPAIVPLRVAPTFSVAAEDTDPRGLPVVDRKGAVAGKVTDLWIDRASIAIRYLEVELAATPGRKVLLPFAATRINAKTKSKTVTVQSILARHFANVPTIAKTDSITRREEDKVMAYYSSGYLYSDRV

Entity 4 Entity 4 polymer

Description description	Light-harvesting protein B-870 alpha chain
Molecular weight formula_weight	7140.4 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

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

MWRIWQLFDPRQALVGLATFLFVLALLIHFILLSTERFNWLEGASTKPVQTSMVMPSSDLAV

Entity 5 Entity 5 polymer

Description description	Light-harvesting protein B-870 beta chain
Molecular weight formula_weight	6155.0 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

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

AEVKQESLSGITEGEAKEFHKIFTSSILVFFGVAAFAHLLVWIWRPWVPGPNGYS

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	36

Entity 7 Entity 7 non-polymer

Description description	Trans-Geranyl BACTERIOPHEOPHYTIN A
Molecular weight formula_weight	879.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

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

Entity 9 Entity 9 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	2

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	23

Entity 11 Entity 11 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 12 Entity 12 non-polymer

Description description	;2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione ;
Molecular weight formula_weight	844.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

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

Entity 14 Entity 14 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 15 Entity 15 non-polymer

Description description	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	692.0 kDa
Source method src_method	syn
Copy count entity_count	3

▶

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	2.76 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	145033

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLUM RUBRUM

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

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

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7eqd__assembly_1__model_1

7eqd__assembly_1__model_1 | I(q)

7eqd__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 (15)

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 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

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

7. Citations (1)