9MCC | pdb_00009mcc

Cryo-EM structure of violaxanthin-chlorophyll-a-binding protein with red shifted Chl a (rVCP) from Trachydiscus minutus at 2.4 angstrom

PDB DOI: https://doi.org/10.2210/pdb9MCC/pdb
EM Map EMD-63799: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Trachydiscus minutus
Mutation(s): No

Deposited: 2025-03-17 Released: 2025-12-31
Deposition Author(s): Seki, S., Litvin, R., Bina, D., Tanaka, H., Miyata, T., Namba, K., Kurisu, G., Polivka, T., Fujii, R.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of violaxanthin-chlorophyll a protein with red Chl: rVCP from Trachydiscus minutus.

Seki, S., Litvin, R., Bina, D., Miyata, T., Tanaka, H., Namba, K., Kurisu, G., Polivka, T., Fujii, R.

To be published.

Macromolecule Content

Total Structure Weight: 148.91 kDa
Atom Count: 8,978
Modeled Residue Count: 700
Deposited Residue Count: 900
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting complex	A, C	229	Trachydiscus minutus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
light-harvesting complex	B, D	221	Trachydiscus minutus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLA (Subject of Investigation/LOI) Query on CLA Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain IB [auth D] SDF format, chain JA [auth C] SDF format, chain JB [auth D] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain OA [auth C] SDF format, chain U [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain ZA [auth D] SDF format, chain Z [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain UA [auth C] 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 P [auth A] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain M [auth A] 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 HB [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain DB [auth D] SDF format, chain DA [auth B] SDF format, chain CB [auth D] SDF format, chain CA [auth B] SDF format, chain BB [auth D] SDF format, chain BA [auth B] SDF format, chain AB [auth D] SDF format, chain AA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth D] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth C] 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 P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] 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 HB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain AA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain GB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain JA [auth C] mmCIF format, chain JB [auth D] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth C] 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 P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] 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 HB [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CA [auth B] AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], E [auth A], EA [auth B], EB [auth D], F [auth A], FB [auth D], G [auth A], GB [auth D], H [auth A], HB [auth D], I [auth A], IB [auth D], J [auth A], JA [auth C], JB [auth D], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], U [auth B], UA [auth C], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B], ZA [auth D]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain F [auth A] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] 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 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 W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain F [auth A] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] 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 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 W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth D]
A1L1F Query on A1L1F Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain KB [auth D] SDF format, chain XA [auth C] SDF format, chain VA [auth C] SDF format, chain S [auth A] SDF format, chain Q [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain XA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain KB [auth D] mmCIF format, chain XA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth A]	FA [auth B] KB [auth D] Q [auth A] S [auth A] VA [auth C] FA [auth B], KB [auth D], Q [auth A], S [auth A], VA [auth C], XA [auth C]	[(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethenyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] octanoate C₅₀ H₇₂ O₇ JYJFYJLLQQTZBJ-AYSGSIDZSA-N		Interactions Focus chain FA [auth B] Focus chain KB [auth D] Focus chain Q [auth A] Focus chain S [auth A] Focus chain VA [auth C] Focus chain XA [auth C] Interactions & Density Focus chain FA [auth B] Focus chain KB [auth D] Focus chain Q [auth A] Focus chain S [auth A] Focus chain VA [auth C] Focus chain XA [auth C]
XAT Query on XAT Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain YA [auth C] SDF format, chain WA [auth C] SDF format, chain T [auth A] SDF format, chain NB [auth D] SDF format, chain MB [auth D] SDF format, chain LB [auth D] SDF format, chain IA [auth B] SDF format, chain HA [auth B] SDF format, chain GA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain LB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain MB [auth D] mmCIF format, chain LB [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B]	GA [auth B] HA [auth B] IA [auth B] LB [auth D] MB [auth D] GA [auth B], HA [auth B], IA [auth B], LB [auth D], MB [auth D], NB [auth D], R [auth A], T [auth A], WA [auth C], YA [auth C]	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C₄₀ H₅₆ O₄ SZCBXWMUOPQSOX-WVJDLNGLSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain R [auth A] Focus chain T [auth A] Focus chain WA [auth C] Focus chain YA [auth C] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain R [auth A] Focus chain T [auth A] Focus chain WA [auth C] Focus chain YA [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.9.4.1
MODEL REFINEMENT	PHENIX	1.19.2
RECONSTRUCTION	cryoSPARC	4.2.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121003
Japan Society for the Promotion of Science (JSPS)	Japan	K23KJ1834
Japan Science and Technology	Japan	JPMJFS2138
Japan Science and Technology	Japan	JPMJCR20E1
Japan Society for the Promotion of Science (JSPS)	Japan	23H04958