6ZXA | pdb_00006zxa

LH2 complex from Marichromatium purpuratum

PDB DOI: https://doi.org/10.2210/pdb6ZXA/pdb
EM Map EMD-11516: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Marichromatium purpuratum 984
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2020-07-29 Released: 2021-02-24
Deposition Author(s): Gardiner, A.T., Naydenova, K., Castro-Hartmann, P., Nguyen-Phan, T.C., Russo, C.J., Sader, K., Hunter, C.N., Cogdell, R.J., Qian, P.
Funding Organization(s): Department of Energy (DOE, United States), Medical Research Council (MRC, United Kingdom), Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.38 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The 2.4 angstrom cryo-EM structure of a heptameric light-harvesting 2 complex reveals two carotenoid energy transfer pathways.

Gardiner, A.T., Naydenova, K., Castro-Hartmann, P., Nguyen-Phan, T.C., Russo, C.J., Sader, K., Hunter, C.N., Cogdell, R.J., Qian, P.

(2021) Sci Adv 7

PubMed: 33579696 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abe4650
Primary Citation Related Structures:
6ZXA

PubMed Abstract:
We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from Marichromatium ( Mch. ) purpuratum determined by cryogenic electron microscopy. The structure contains a heptameric ring that is unique among all known LH2 structures, explaining the unusual spectroscopic properties of this bacterial antenna complex. We identify two sets of distinct carotenoids in the structure and describe a network of energy transfer pathways from the carotenoids to bacteriochlorophyll a molecules. The geometry imposed by the heptameric ring controls the resonant coupling of the long-wavelength energy absorption band. Together, these details reveal key aspects of the assembly and oligomeric form of purple bacterial LH2 complexes that were previously inaccessible by any technique.

Organizational Affiliation

Institute of Molecular, Cell and Systems Biology, Glasgow University, Glasgow G12 8QQ, UK.

Macromolecule Content

Total Structure Weight: 122.23 kDa
Atom Count: 8,442
Modeled Residue Count: 791
Deposited Residue Count: 826
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LHC domain-containing protein	A, C, E, G, I A, C, E, G, I, K, M	70	Marichromatium purpuratum 984	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for W0E6A1 (Marichromatium purpuratum 984) Explore W0E6A1 Go to UniProtKB: W0E6A1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W0E6A1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B:800-850 subunit beta	B, D, F, H, J B, D, F, H, J, L, N	48	Marichromatium purpuratum 984	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for W0E5B0 (Marichromatium purpuratum 984) Explore W0E5B0 Go to UniProtKB: W0E5B0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W0E5B0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL (Subject of Investigation/LOI) Query on BCL Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain WA [auth N] SDF format, chain W [auth D] SDF format, chain VA [auth N] SDF format, chain V [auth D] SDF format, chain U [auth C] SDF format, chain SA [auth M] SDF format, chain R [auth B] SDF format, chain QA [auth L] SDF format, chain Q [auth B] SDF format, chain PA [auth L] SDF format, chain O [auth A] SDF format, chain NA [auth K] SDF format, chain MA [auth J] SDF format, chain LA [auth J] SDF format, chain IA [auth I] SDF format, chain HA [auth H] SDF format, chain GA [auth H] SDF format, chain DA [auth G] SDF format, chain CA [auth F] SDF format, chain BA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain WA [auth N] MOL2 format, chain W [auth D] MOL2 format, chain VA [auth N] MOL2 format, chain V [auth D] MOL2 format, chain U [auth C] MOL2 format, chain SA [auth M] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth L] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth L] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth K] MOL2 format, chain MA [auth J] MOL2 format, chain LA [auth J] MOL2 format, chain IA [auth I] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain WA [auth N] mmCIF format, chain W [auth D] mmCIF format, chain VA [auth N] mmCIF format, chain V [auth D] mmCIF format, chain U [auth C] mmCIF format, chain SA [auth M] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth L] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth L] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth K] mmCIF format, chain MA [auth J] mmCIF format, chain LA [auth J] mmCIF format, chain IA [auth I] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F]	BA [auth F] CA [auth F] DA [auth G] GA [auth H] HA [auth H] BA [auth F], CA [auth F], DA [auth G], GA [auth H], HA [auth H], IA [auth I], LA [auth J], MA [auth J], NA [auth K], O [auth A], PA [auth L], Q [auth B], QA [auth L], R [auth B], SA [auth M], U [auth C], V [auth D], VA [auth N], W [auth D], WA [auth N], Y [auth E]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain IA [auth I] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain O [auth A] Focus chain PA [auth L] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain R [auth B] Focus chain SA [auth M] Focus chain U [auth C] Focus chain V [auth D] Focus chain VA [auth N] Focus chain W [auth D] Focus chain WA [auth N] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain IA [auth I] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain O [auth A] Focus chain PA [auth L] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain R [auth B] Focus chain SA [auth M] Focus chain U [auth C] Focus chain V [auth D] Focus chain VA [auth N] Focus chain W [auth D] Focus chain WA [auth N] Focus chain Y [auth E]
QS2 (Subject of Investigation/LOI) Query on QS2 Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain TA [auth M] SDF format, chain S [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth K] SDF format, chain JA [auth I] SDF format, chain EA [auth G] MOL2 format, chain Z [auth E] MOL2 format, chain TA [auth M] MOL2 format, chain S [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth K] MOL2 format, chain JA [auth I] MOL2 format, chain EA [auth G] mmCIF format, chain Z [auth E] mmCIF format, chain TA [auth M] mmCIF format, chain S [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth K] mmCIF format, chain JA [auth I] mmCIF format, chain EA [auth G]	EA [auth G] JA [auth I] OA [auth K] P [auth A] S [auth B] EA [auth G], JA [auth I], OA [auth K], P [auth A], S [auth B], TA [auth M], Z [auth E]	9-cis-okenone C₄₁ H₅₄ O₂ FSQZIFSGNDUYRQ-KKGQYTAFSA-N		Interactions Focus chain EA [auth G] Focus chain JA [auth I] Focus chain OA [auth K] Focus chain P [auth A] Focus chain S [auth B] Focus chain TA [auth M] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth G] Focus chain JA [auth I] Focus chain OA [auth K] Focus chain P [auth A] Focus chain S [auth B] Focus chain TA [auth M] Focus chain Z [auth E]
QSE (Subject of Investigation/LOI) Query on QSE Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain UA [auth N] SDF format, chain T [auth C] SDF format, chain RA [auth M] SDF format, chain KA [auth J] SDF format, chain FA [auth H] SDF format, chain AA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain UA [auth N] MOL2 format, chain T [auth C] MOL2 format, chain RA [auth M] MOL2 format, chain KA [auth J] MOL2 format, chain FA [auth H] MOL2 format, chain AA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain UA [auth N] mmCIF format, chain T [auth C] mmCIF format, chain RA [auth M] mmCIF format, chain KA [auth J] mmCIF format, chain FA [auth H] mmCIF format, chain AA [auth F]	AA [auth F] FA [auth H] KA [auth J] RA [auth M] T [auth C] AA [auth F], FA [auth H], KA [auth J], RA [auth M], T [auth C], UA [auth N], X [auth E]	all-trans okenone C₄₁ H₅₄ O₂ FSQZIFSGNDUYRQ-TYKRLFMMSA-N		Interactions Focus chain AA [auth F] Focus chain FA [auth H] Focus chain KA [auth J] Focus chain RA [auth M] Focus chain T [auth C] Focus chain UA [auth N] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain FA [auth H] Focus chain KA [auth J] Focus chain RA [auth M] Focus chain T [auth C] Focus chain UA [auth N] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.38 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17.1
MODEL REFINEMENT	REFMAC
RECONSTRUCTION	RELION	3.1

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0001035
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_120117
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--