7WLM | pdb_00007wlm

The Cryo-EM structure of siphonaxanthin chlorophyll a/b type light-harvesting complex II

PDB DOI: https://doi.org/10.2210/pdb7WLM/pdb
EM Map EMD-32588: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Codium fragile
Mutation(s): No

Deposited: 2022-01-13 Released: 2022-11-23
Deposition Author(s): Seki, S., Nakaniwa, T., Castro-Hartmann, P., Sader, K., Kawamoto, A., Tanaka, H., Qian, P., Kurisu, G., Fujii, R.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural insights into blue-green light utilization by marine green algal light harvesting complex II at 2.78 angstrom.

Seki, S., Nakaniwa, T., Castro-Hartmann, P., Sader, K., Kawamoto, A., Tanaka, H., Qian, P., Kurisu, G., Fujii, R.

(2022) BBA Adv 2: 100064-100064

PubMed: 37082593 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.bbadva.2022.100064
Primary Citation Related Structures:
7WLM

PubMed Abstract:
Light-harvesting complex II (LHCII) present in plants and green algae absorbs solar energy to promote photochemical reactions. A marine green macroalga, Codium fragile , exhibits the unique characteristic of absorbing blue-green light from the sun during photochemical reactions while being underwater owing to the presence of pigment-altered LHCII called siphonaxanthin-chlorophyll a/b- binding protein (SCP). In this study, we determined the structure of SCP at a resolution of 2.78 Å using cryogenic electron microscopy. SCP has a trimeric structure, wherein each monomer containing two lutein and two chlorophyll a molecules in the plant-type LHCII are replaced by siphonaxanthin and its ester and two chlorophyll b molecules, respectively. Siphonaxanthin occupies the binding site in SCP having a polarity in the trimeric inner core, and exhibits a distorted conjugated chain comprising a carbonyl group hydrogen bonded to a cysteine residue of apoprotein. These features suggest that the siphonaxanthin molecule is responsible for the characteristic green absorption of SCP. The replaced chlorophyll b molecules extend the region of the stromal side chlorophyll b cluster, spanning two adjacent monomers.

Organizational Affiliation

Division of Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.

Macromolecule Content

Total Structure Weight: 115.87 kDa
Atom Count: 7,308
Modeled Residue Count: 603
Deposited Residue Count: 669
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
siphonaxanthin chlorophyll a/b binding light-harvesting complex II	A, B, C	223	Codium fragile	Mutation(s): 0
UniProt
Find proteins for A0A8S0G488 (Codium fragile) Explore A0A8S0G488 Go to UniProtKB: A0A8S0G488
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8S0G488
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHL (Subject of Investigation/LOI) Query on CHL Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain V [auth B] SDF format, chain UA [auth C] SDF format, chain U [auth B] SDF format, chain TA [auth C] SDF format, chain SA [auth C] SDF format, chain RA [auth C] SDF format, chain QA [auth C] SDF format, chain PA [auth C] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain D [auth A] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] D [auth A] DA [auth B] AA [auth B], BA [auth B], CA [auth B], D [auth A], DA [auth B], E [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], LA [auth C], M [auth A], MA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], U [auth B], UA [auth C], V [auth B], Y [auth B], Z [auth B]	CHLOROPHYLL B C₅₅ H₇₀ Mg N₄ O₆ MWVCRINOIIOUAU-UYSPMESUSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CLA Query on CLA Download:Ideal Coordinates CCD File SDF format, chain XA [auth C] SDF format, chain X [auth B] SDF format, chain WA [auth C] SDF format, chain W [auth B] SDF format, chain VA [auth C] SDF format, chain P [auth A] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B]	EA [auth B] F [auth A] FA [auth B] G [auth A] GA [auth B] EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], VA [auth C], W [auth B], WA [auth C], X [auth B], XA [auth C]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Interactions & Density Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C]
0UR (Subject of Investigation/LOI) Query on 0UR Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain R [auth A] SDF format, chain IA [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain IA [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain IA [auth B]	IA [auth B], R [auth A], ZA [auth C]	Siphonein C₅₂ H₇₆ O₅ UERRVASYDCUNEJ-DHYZAJTQSA-N		Interactions Focus chain IA [auth B] Focus chain R [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain IA [auth B] Focus chain R [auth A] Focus chain ZA [auth C]
LHG Query on LHG Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain KA [auth B] SDF format, chain BB [auth C] MOL2 format, chain T [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain BB [auth C] mmCIF format, chain T [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain BB [auth C]	BB [auth C], KA [auth B], T [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain BB [auth C] Focus chain KA [auth B] Focus chain T [auth A] Interactions & Density Focus chain BB [auth C] Focus chain KA [auth B] Focus chain T [auth A]
NEX Query on NEX Download:Ideal Coordinates CCD File SDF format, chain YA [auth C] SDF format, chain Q [auth A] SDF format, chain HA [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain HA [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain HA [auth B]	HA [auth B], Q [auth A], YA [auth C]	(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL C₄₀ H₅₆ O₄ PGYAYSRVSAJXTE-OQASCVKESA-N		Interactions Focus chain HA [auth B] Focus chain Q [auth A] Focus chain YA [auth C] Interactions & Density Focus chain HA [auth B] Focus chain Q [auth A] Focus chain YA [auth C]
0IE (Subject of Investigation/LOI) Query on 0IE Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain JA [auth B] SDF format, chain AB [auth C] MOL2 format, chain S [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain AB [auth C] mmCIF format, chain S [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain AB [auth C]	AB [auth C], JA [auth B], S [auth A]	Siphonaxanthin C₄₀ H₅₆ O₄ SUCKEYMKNGZJHK-ZARIWKGHSA-N		Interactions Focus chain AB [auth C] Focus chain JA [auth B] Focus chain S [auth A] Interactions & Density Focus chain AB [auth C] Focus chain JA [auth B] Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	Coot	0.9.4.1
MODEL REFINEMENT	PHENIX	1.19.2-4158

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		Sasakura Enviro-Science Foundation 2020

Revision History (Full details and data files)

Version 1.0: 2022-11-23
Type: Initial release
Version 1.1: 2023-05-03
Changes: Database references, Refinement description
Version 1.2: 2024-06-26
Changes: Data collection, Refinement description