7vnm

Rba sphaeroides PufY-KO RC-LH1 monomer

Method: ELECTRON MICROSCOPY

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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 30	Reaction center protein M chain × 1 （Q3J1A6） Reaction center protein H chain × 1 （Q3J170） Light-harvesting protein B-875 alpha chain × 13 （Q3J1A4） Light-harvesting protein B-875 beta chain × 13 （Q3J1A3） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 30 BACTERIOPHEOPHYTIN A × 2 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 7 UBIQUINONE-10 × 2 FE (II) ION × 1 SPHEROIDENE × 22 CARDIOLIPIN × 1	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	1
Chains and sequence ranges	Author chain L； PDBConstruct 1–282； UniProt 1–282

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 30	Reaction center protein L chain × 1 （Q3J1A5） Reaction center protein H chain × 1 （Q3J170） Light-harvesting protein B-875 alpha chain × 13 （Q3J1A4） Light-harvesting protein B-875 beta chain × 13 （Q3J1A3） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 30 BACTERIOPHEOPHYTIN A × 2 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 7 UBIQUINONE-10 × 2 FE (II) ION × 1 SPHEROIDENE × 22 CARDIOLIPIN × 1	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	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–308； UniProt 1–308

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 30	Reaction center protein L chain × 1 （Q3J1A5） Reaction center protein M chain × 1 （Q3J1A6） Light-harvesting protein B-875 alpha chain × 13 （Q3J1A4） Light-harvesting protein B-875 beta chain × 13 （Q3J1A3） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 30 BACTERIOPHEOPHYTIN A × 2 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 7 UBIQUINONE-10 × 2 FE (II) ION × 1 SPHEROIDENE × 22 CARDIOLIPIN × 1	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 1–260； UniProt 1–260

Light-harvesting protein B-875 alpha chain

OrganismNot specified

UniProt Q3J1A4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 30	Reaction center protein L chain × 1 （Q3J1A5） Reaction center protein M chain × 1 （Q3J1A6） Reaction center protein H chain × 1 （Q3J170） Light-harvesting protein B-875 beta chain × 13 （Q3J1A3） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 30 BACTERIOPHEOPHYTIN A × 2 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 7 UBIQUINONE-10 × 2 FE (II) ION × 1 SPHEROIDENE × 22 CARDIOLIPIN × 1	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	4
Chains and sequence ranges	Author chain 1； PDBConstruct 1–58； UniProt 1–58 Author chain 7； PDBConstruct 1–58； UniProt 1–58 Author chain 9； PDBConstruct 1–58； UniProt 1–58 Author chain A； PDBConstruct 1–58； UniProt 1–58 Author chain D； PDBConstruct 1–58； UniProt 1–58 Author chain F； PDBConstruct 1–58； UniProt 1–58 Author chain I； PDBConstruct 1–58； UniProt 1–58 Author chain K； PDBConstruct 1–58； UniProt 1–58 Author chain O； PDBConstruct 1–58； UniProt 1–58 Author chain Q； PDBConstruct 1–58； UniProt 1–58 Author chain S； PDBConstruct 1–58； UniProt 1–58 Author chain U； PDBConstruct 1–58； UniProt 1–58 Author chain W； PDBConstruct 1–58； UniProt 1–58

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 30	Reaction center protein L chain × 1 （Q3J1A5） Reaction center protein M chain × 1 （Q3J1A6） Reaction center protein H chain × 1 （Q3J170） Light-harvesting protein B-875 alpha chain × 13 （Q3J1A4） Intrinsic membrane protein PufX × 1 （P13402） BACTERIOCHLOROPHYLL A × 30 BACTERIOPHEOPHYTIN A × 2 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 7 UBIQUINONE-10 × 2 FE (II) ION × 1 SPHEROIDENE × 22 CARDIOLIPIN × 1	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	5
Chains and sequence ranges	Author chain 0； PDBConstruct 1–49； UniProt 1–49 Author chain 2； PDBConstruct 1–49； UniProt 1–49 Author chain 8； PDBConstruct 1–49； UniProt 1–49 Author chain B； PDBConstruct 1–49； UniProt 1–49 Author chain C； PDBConstruct 1–49； UniProt 1–49 Author chain E； PDBConstruct 1–49； UniProt 1–49 Author chain G； PDBConstruct 1–49； UniProt 1–49 Author chain J； PDBConstruct 1–49； UniProt 1–49 Author chain N； PDBConstruct 1–49； UniProt 1–49 Author chain P； PDBConstruct 1–49； UniProt 1–49 Author chain R； PDBConstruct 1–49； UniProt 1–49 Author chain T； PDBConstruct 1–49； UniProt 1–49 Author chain V； PDBConstruct 1–49； UniProt 1–49

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 30	Reaction center protein L chain × 1 （Q3J1A5） Reaction center protein M chain × 1 （Q3J1A6） Reaction center protein H chain × 1 （Q3J170） Light-harvesting protein B-875 alpha chain × 13 （Q3J1A4） Light-harvesting protein B-875 beta chain × 13 （Q3J1A3） BACTERIOCHLOROPHYLL A × 30 BACTERIOPHEOPHYTIN A × 2 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 7 UBIQUINONE-10 × 2 FE (II) ION × 1 SPHEROIDENE × 22 CARDIOLIPIN × 1	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	6
Chains and sequence ranges	Author chain X； PDBConstruct 1–82； UniProt 1–82

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	7vnm
Deposition date deposition_date	2021-10-11
Structure title title	Rba sphaeroides PufY-KO RC-LH1 monomer
Keywords keywords	photosystem, Complex, Mutant, 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.

7vnm__assembly_1__model_1

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

Download this curve (.dat)

7vnm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7vnm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.20 Å
Rg (electron density)	42.61 Å
Total Rg	43.08 Å
Atom count	20588
Residues	2112
Excluded volume	386460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7vnm__assembly_1__model_1`	30-meric （30）	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 (13)

Entity 1 Entity 1 polymer

Description description	Reaction center protein L chain
Molecular weight formula_weight	31477.6 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	20588

MALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Entity 2 Entity 2 polymer

Description description	Reaction center protein M chain
Molecular weight formula_weight	34529.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MAEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGMAPLN

Entity 3 Entity 3 polymer

Description description	Reaction center protein H chain
Molecular weight formula_weight	28066.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKSVVAAMLAEYA

Entity 4 Entity 4 polymer

Description description	Light-harvesting protein B-875 alpha chain
Molecular weight formula_weight	6816.2 kDa
Source method src_method	nat
Copy count entity_count	13

Polymer Polymer

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

MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVAVAE

Entity 5 Entity 5 polymer

Description description	Light-harvesting protein B-875 beta chain
Molecular weight formula_weight	5592.4 kDa
Source method src_method	nat
Copy count entity_count	13

Polymer Polymer

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

MADKSDLGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF

Entity 6 Entity 6 polymer

Description description	Intrinsic membrane protein PufX
Molecular weight formula_weight	9061.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MADKTIFNDHLNTNPKTNLRLWVAFQMMKGAGWAGGVFFGTLLLIGFFRVVGRMLPIQENQAPAPNITGALETGIELIKHLV

Entity 7 Entity 7 non-polymer

Description description	BACTERIOCHLOROPHYLL A
Molecular weight formula_weight	911.5 kDa
Source method src_method	syn
Copy count entity_count	30

Entity 8 Entity 8 non-polymer

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

Entity 9 Entity 9 non-polymer

Description description	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	790.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 non-polymer

Description description	FE (II) 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	SPHEROIDENE
Molecular weight formula_weight	568.9 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 13 Entity 13 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id	7vnmA01
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	7vnmD01
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	7vnmF01
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	7vnmH01
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	7vnmI01
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	7vnmK01
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	7vnmO01
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	7vnmQ01
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	7vnmS01
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	7vnmU01
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	7vnmW01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

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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	2.86 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	56391

Rba sphaeroides PufY-KO RC-LH1 monomer

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

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

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

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

7vnm__assembly_1__model_1

7vnm__assembly_1__model_1 | I(q)

7vnm__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 (13)

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

6. Fold Classification (SCOP + CATH) 11 domains