5y5s

Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution

Method: X-RAY DIFFRACTION

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

Photosynthetic reaction center cytochrome c subunit

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 36	Photosynthetic reaction center L subunit × 1 （D2Z0P3） Photosynthetic reaction center M subunit × 1 （A8ASG6） Photosynthetic reaction center H subunit × 1 （D2Z0P9） LH1 alpha polypeptide × 16 （D2Z0P2） LH1 beta polypeptide × 16 （D2Z0P1） HEME C × 4 MAGNESIUM ION × 1 GLYCEROL × 2 SULFATE ION × 3 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 10 BACTERIOCHLOROPHYLL A × 36 BACTERIOPHEOPHYTIN A × 2 Ubiquinone-8 × 5 UNKNOWN LIGAND × 16 FE (III) ION × 1 MENAQUINONE 8 × 1 SPIRILLOXANTHIN × 17 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 13 LAURYL DIMETHYLAMINE-N-OXIDE × 5 CARDIOLIPIN × 9 DODECYL-BETA-D-MALTOSIDE × 2 CALCIUM ION × 16 water × 36	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYCR_THETI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–404； UniProt 1–404

Photosynthetic reaction center L subunit

OrganismNot specified

UniProt D2Z0P3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 36	Photosynthetic reaction center cytochrome c subunit × 1 （D2Z0P5） Photosynthetic reaction center M subunit × 1 （A8ASG6） Photosynthetic reaction center H subunit × 1 （D2Z0P9） LH1 alpha polypeptide × 16 （D2Z0P2） LH1 beta polypeptide × 16 （D2Z0P1） HEME C × 4 MAGNESIUM ION × 1 GLYCEROL × 2 SULFATE ION × 3 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 10 BACTERIOCHLOROPHYLL A × 36 BACTERIOPHEOPHYTIN A × 2 Ubiquinone-8 × 5 UNKNOWN LIGAND × 16 FE (III) ION × 1 MENAQUINONE 8 × 1 SPIRILLOXANTHIN × 17 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 13 LAURYL DIMETHYLAMINE-N-OXIDE × 5 CARDIOLIPIN × 9 DODECYL-BETA-D-MALTOSIDE × 2 CALCIUM ION × 16 water × 36	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D2Z0P3_THETI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–281； UniProt 1–281

Photosynthetic reaction center M subunit

OrganismNot specified

UniProt A8ASG6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 36	Photosynthetic reaction center cytochrome c subunit × 1 （D2Z0P5） Photosynthetic reaction center L subunit × 1 （D2Z0P3） Photosynthetic reaction center H subunit × 1 （D2Z0P9） LH1 alpha polypeptide × 16 （D2Z0P2） LH1 beta polypeptide × 16 （D2Z0P1） HEME C × 4 MAGNESIUM ION × 1 GLYCEROL × 2 SULFATE ION × 3 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 10 BACTERIOCHLOROPHYLL A × 36 BACTERIOPHEOPHYTIN A × 2 Ubiquinone-8 × 5 UNKNOWN LIGAND × 16 FE (III) ION × 1 MENAQUINONE 8 × 1 SPIRILLOXANTHIN × 17 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 13 LAURYL DIMETHYLAMINE-N-OXIDE × 5 CARDIOLIPIN × 9 DODECYL-BETA-D-MALTOSIDE × 2 CALCIUM ION × 16 water × 36	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8ASG6_THETI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–325； UniProt 1–325

Photosynthetic reaction center H subunit

OrganismNot specified

UniProt D2Z0P9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 36	Photosynthetic reaction center cytochrome c subunit × 1 （D2Z0P5） Photosynthetic reaction center L subunit × 1 （D2Z0P3） Photosynthetic reaction center M subunit × 1 （A8ASG6） LH1 alpha polypeptide × 16 （D2Z0P2） LH1 beta polypeptide × 16 （D2Z0P1） HEME C × 4 MAGNESIUM ION × 1 GLYCEROL × 2 SULFATE ION × 3 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 10 BACTERIOCHLOROPHYLL A × 36 BACTERIOPHEOPHYTIN A × 2 Ubiquinone-8 × 5 UNKNOWN LIGAND × 16 FE (III) ION × 1 MENAQUINONE 8 × 1 SPIRILLOXANTHIN × 17 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 13 LAURYL DIMETHYLAMINE-N-OXIDE × 5 CARDIOLIPIN × 9 DODECYL-BETA-D-MALTOSIDE × 2 CALCIUM ION × 16 water × 36	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D2Z0P9_THETI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–259； UniProt 1–259

LH1 alpha polypeptide

OrganismNot specified

UniProt D2Z0P2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 36	Photosynthetic reaction center cytochrome c subunit × 1 （D2Z0P5） Photosynthetic reaction center L subunit × 1 （D2Z0P3） Photosynthetic reaction center M subunit × 1 （A8ASG6） Photosynthetic reaction center H subunit × 1 （D2Z0P9） LH1 beta polypeptide × 16 （D2Z0P1） HEME C × 4 MAGNESIUM ION × 1 GLYCEROL × 2 SULFATE ION × 3 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 10 BACTERIOCHLOROPHYLL A × 36 BACTERIOPHEOPHYTIN A × 2 Ubiquinone-8 × 5 UNKNOWN LIGAND × 16 FE (III) ION × 1 MENAQUINONE 8 × 1 SPIRILLOXANTHIN × 17 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 13 LAURYL DIMETHYLAMINE-N-OXIDE × 5 CARDIOLIPIN × 9 DODECYL-BETA-D-MALTOSIDE × 2 CALCIUM ION × 16 water × 36	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D2Z0P2_THETI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain 1； PDBConstruct 1–61； UniProt 1–61 Author chain 3； PDBConstruct 1–61； UniProt 1–61 Author chain 5； PDBConstruct 1–61； UniProt 1–61 Author chain 7； PDBConstruct 1–61； UniProt 1–61 Author chain 9； PDBConstruct 1–61； UniProt 1–61 Author chain A； PDBConstruct 1–61； UniProt 1–61 Author chain D； PDBConstruct 1–61； UniProt 1–61 Author chain F； PDBConstruct 1–61； UniProt 1–61 Author chain I； PDBConstruct 1–61； UniProt 1–61 Author chain K； PDBConstruct 1–61； UniProt 1–61 Author chain O； PDBConstruct 1–61； UniProt 1–61 Author chain Q； PDBConstruct 1–61； UniProt 1–61 Author chain S； PDBConstruct 1–61； UniProt 1–61 Author chain U； PDBConstruct 1–61； UniProt 1–61 Author chain W； PDBConstruct 1–61； UniProt 1–61 Author chain Y； PDBConstruct 1–61； UniProt 1–61

LH1 beta polypeptide

OrganismNot specified

UniProt D2Z0P1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 36	Photosynthetic reaction center cytochrome c subunit × 1 （D2Z0P5） Photosynthetic reaction center L subunit × 1 （D2Z0P3） Photosynthetic reaction center M subunit × 1 （A8ASG6） Photosynthetic reaction center H subunit × 1 （D2Z0P9） LH1 alpha polypeptide × 16 （D2Z0P2） HEME C × 4 MAGNESIUM ION × 1 GLYCEROL × 2 SULFATE ION × 3 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 10 BACTERIOCHLOROPHYLL A × 36 BACTERIOPHEOPHYTIN A × 2 Ubiquinone-8 × 5 UNKNOWN LIGAND × 16 FE (III) ION × 1 MENAQUINONE 8 × 1 SPIRILLOXANTHIN × 17 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 13 LAURYL DIMETHYLAMINE-N-OXIDE × 5 CARDIOLIPIN × 9 DODECYL-BETA-D-MALTOSIDE × 2 CALCIUM ION × 16 water × 36	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D2Z0P1_THETI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain 0； PDBConstruct 1–47； UniProt 1–47 Author chain 2； PDBConstruct 1–47； UniProt 1–47 Author chain 4； PDBConstruct 1–47； UniProt 1–47 Author chain 6； PDBConstruct 1–47； UniProt 1–47 Author chain 8； PDBConstruct 1–47； UniProt 1–47 Author chain B； PDBConstruct 1–47； UniProt 1–47 Author chain E； PDBConstruct 1–47； UniProt 1–47 Author chain G； PDBConstruct 1–47； UniProt 1–47 Author chain J； PDBConstruct 1–47； UniProt 1–47 Author chain N； PDBConstruct 1–47； UniProt 1–47 Author chain P； PDBConstruct 1–47； UniProt 1–47 Author chain R； PDBConstruct 1–47； UniProt 1–47 Author chain T； PDBConstruct 1–47； UniProt 1–47 Author chain V； PDBConstruct 1–47； UniProt 1–47 Author chain X； PDBConstruct 1–47； UniProt 1–47 Author chain Z； PDBConstruct 1–47； UniProt 1–47

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	5y5s
Deposition date deposition_date	2017-08-09
Structure title title	Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution
Keywords keywords	LH1-RC, photosynthesis, purple bacteria; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

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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.

5y5s__assembly_1__model_1

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

Download this curve (.dat)

5y5s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5y5s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.76 Å
Rg (electron density)	43.82 Å
Total Rg	44.24 Å
Atom count	26968
Residues	2726
Excluded volume	504120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5y5s__assembly_1__model_1`	36-meric （36）	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 (25)

Entity 1 Entity 1 polymer

Description description	Photosynthetic reaction center cytochrome c subunit
Molecular weight formula_weight	43177.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	27981

MSPAQQLTLPAVIVVASVMLLGCEGPPPGTEQIGYRGVGMENYYNKRQRALSIQANQPVESLPAADSTGPKASEVYQNVQVLKDLSVGEFTRTMVAVTTWVSPKEGCNYCHVPGNWASDDIYTKVVSRRMFELVRAANSDWKAHVAETGVTCYTCHRGNPVPKYAWVTDPGPKYPSGLKPTGQNYGSKTVAYASLPFDPLTPFLDQANEIRITGNAALAGSNPASLKQAEWTFGLMMNISDSLGVGCTFCHNTRAFNDWTQSTPKRTTAWYAIRHVRDINQNYIWPLNDVLPASRKGPYGDPLRVSCMTCHQAVNKPLYGAQMAKDYPGLYKTAVTQEALAGSAPASEAAPAAATEAAPEAPAQEVPAAEAVPAAAEPGAAEAAGSVEPAPVEEVAPAPAAQRL

Entity 2 Entity 2 polymer

Description description	Photosynthetic reaction center L subunit
Molecular weight formula_weight	31520.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MAMLSFEKKYRVRGGTLIGGDLFDFWVGPFYVGFFGVVGFCFTLLGVLLIVWGATIGPTGPTSDLQTYNLWRISIAPPDLSYGLRMAPLTEGGLWQIITICAAGAFISWALREVEICRKLGIGFHVPFAFSFAIGAYLVLVFVRPLLMGAWGHGFPYGILSHLDWVSNVGYQFLHFHYNPAHMLAISFFFTNCLALSMHGSLILSVTNPQKGEPVKTSEHENTFFRDIVGYSIGALAIHRLGLFLALSAAFWSAVCILISGPFWTRGWPEWWNWWLELPLW

Entity 3 Entity 3 polymer

Description description	Photosynthetic reaction center M subunit
Molecular weight formula_weight	36605.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MPEYQNIFTAVQVRAPAYPGVPLPKGNLPRIGRPIFSYWLGKIGDAQIGPIYLGLTGTLSIFFGLVAISIIGFNMLASVHWDVFQFLKHFFWLGLEPPPPQYGLRIPPLSEGGWWLMAGLFLTLSILLWWVRTYKRAEALGMSQHLSWAFAAAIFFYLVLGFIRPVMMGSWAKAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILSVSRFGGDREIDQITHRGTAAERAALFWRWTMGFNVTMESIHRWAWWCAVLTVITAGIGILLSGTVVDNWYLWAVKHGMAPAYPEVVTAVNPYETAAEVMQ

Entity 4 Entity 4 polymer

Description description	Photosynthetic reaction center H subunit
Molecular weight formula_weight	28213.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSAGITHYIDAAQITIWAFWLFFFGLIIYLRREDKREGYPLDSDRTERSGGRVKVVGFPDLPDPKTFVLPHNGGTVVAPRVEAPVAVNATPFSPAPGSPLVPNGDPMLSGFGPAASPDRPKHCDLTFEGLPKIVPMRVAKEFSIAEGDPDPRGMTVVGLDGEVAGTVSDVWVDRSEPQIRYLEVEVAANKKKVLLPIGFSRFDKKARKVKVDAIKAAHFANVPTLSNPDQVTLYEEDKVCAYYAGGKLYATAERAGPLL

Entity 5 Entity 5 polymer

Description description	LH1 alpha polypeptide
Molecular weight formula_weight	7034.4 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

MFTMNANLYKIWLILDPRRVLVSIVAFQIVLGLLIHMIVLSTDLNWLDDNIPVSYQALGKK

Entity 6 Entity 6 polymer

Description description	LH1 beta polypeptide
Molecular weight formula_weight	5534.5 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

MAEQKSLTGLTDDEAKEFHAIFMQSMYAWFGLVVIAHLLAWLYRPWL

Entity 7 Entity 7 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 11 Entity 11 non-polymer

Description description	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Molecular weight formula_weight	723.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 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	10

Entity 13 Entity 13 non-polymer

Description description	BACTERIOCHLOROPHYLL A
Molecular weight formula_weight	911.5 kDa
Source method src_method	syn
Copy count entity_count	36

Entity 14 Entity 14 non-polymer

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

Entity 15 Entity 15 non-polymer

Description description	Ubiquinone-8
Molecular weight formula_weight	727.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 16 Entity 16 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	16

Entity 17 Entity 17 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 18 Entity 18 non-polymer

Description description	MENAQUINONE 8
Molecular weight formula_weight	717.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 19 Entity 19 non-polymer

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

Entity 20 Entity 20 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	13

Entity 21 Entity 21 non-polymer

Description description	LAURYL DIMETHYLAMINE-N-OXIDE
Molecular weight formula_weight	229.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 22 Entity 22 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 23 Entity 23 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 24 Entity 24 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 25 Entity 25 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	954

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6. Fold Classification (SCOP + CATH) 75 domains

SCOP 2.08 (36 domains)

Domain ID domain_id	d5y5s0_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5s1_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5s2_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5s3_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5s4_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5s5_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5s6_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5s7_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5s8_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5s9_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sa_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sc_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.2 — Photosynthetic reaction centre (cytochrome subunit)

Domain ID domain_id	d5y5sd_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5se_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sf_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sg_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sh1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.10 — Photosystem II reaction centre subunit H, transmembrane region
Family Family family	f.23.10.0 — automated matches

Domain ID domain_id	d5y5sh2
Class class	b — All beta proteins
Fold Fold fold	b.41 — PRC-barrel domain
Superfamily Superfamily superfamily	b.41.1 — PRC-barrel domain
Family Family family	b.41.1.1 — Photosynthetic reaction centre, H-chain, cytoplasmic domain

Domain ID domain_id	d5y5si_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sj_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sk_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sm_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.26 — Bacterial photosystem II reaction centre, L and M subunits
Superfamily Superfamily superfamily	f.26.1 — Bacterial photosystem II reaction centre, L and M subunits
Family Family family	f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits

Domain ID domain_id	d5y5sn_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5so_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sp_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sq_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sr_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5ss_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5st_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5su_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sv_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sw_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sx_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sy_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

Domain ID domain_id	d5y5sz_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.0 — automated matches

CATH v4.4 (39 domains)

Domain ID domain_id	5y5s000
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5s100
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5s200
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5s300
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5s400
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5s500
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5s600
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5s700
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5s800
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5s900
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5sC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	468 — Photosynthetic Reaction Center, subunit C; domain 2
Homologous superfamily homologous superfamily	10 — Photosynthetic Reaction Center, subunit C, domain 2

Domain ID domain_id	5y5sC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	468 — Photosynthetic Reaction Center, subunit C; domain 2
Homologous superfamily homologous superfamily	10 — Photosynthetic Reaction Center, subunit C, domain 2

Domain ID domain_id	5y5sD00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sF00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5sH01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	540 — Photosynthetic Reaction Center; Chain H, domain 1
Homologous superfamily homologous superfamily	10 — Photosynthetic reaction centre, H subunit, N-terminal domain

Domain ID domain_id	5y5sH02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	50 — Photosynthetic Reaction Center; Chain H, domain 2
Homologous superfamily homologous superfamily	10 — Photosynthetic Reaction Center, subunit H, domain 2

Domain ID domain_id	5y5sI00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5sK00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sL01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

Domain ID domain_id	5y5sL02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

Domain ID domain_id	5y5sM01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

Domain ID domain_id	5y5sM02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
Homologous superfamily homologous superfamily	10 — Photosystem II protein D1-like

Domain ID domain_id	5y5sN00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5sO00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sP00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5sQ00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sR00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5sS00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sT00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5sU00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sV00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5sW00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sX00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	5y5sY00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	5y5sZ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

▶

Unit-cell length a length_a	145.280 Å
Unit-cell length b length_b	143.810 Å
Unit-cell length c length_c	210.280 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	64

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	46.919 Å
R factor r_factor	0.1831
R_work r_work	0.1814
R_free r_free	0.2152

Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution

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

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

Photosynthetic reaction center L 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

Photosynthetic reaction center M 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

Photosynthetic reaction center H 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

LH1 alpha polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

LH1 beta polypeptide

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

5y5s__assembly_1__model_1

5y5s__assembly_1__model_1 | I(q)

5y5s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (25)

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 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