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


Experimental Data Snapshot

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

Starting Model: experimental
View more details

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex
A, C
229Trachydiscus minutusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting complex
B, D
221Trachydiscus minutusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
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
A1L1F
Query on A1L1F

Download Ideal Coordinates CCD File 
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
XAT
Query on XAT

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9.4.1
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONcryoSPARC4.2.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP23ama121003
Japan Society for the Promotion of Science (JSPS)JapanK23KJ1834
Japan Science and TechnologyJapanJPMJFS2138
Japan Science and TechnologyJapanJPMJCR20E1
Japan Society for the Promotion of Science (JSPS)Japan23H04958

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-31
    Type: Initial release