6L4T | pdb_00006l4t

Structure of the peripheral FCPI from diatom

• PDB DOI: https://doi.org/10.2210/pdb6L4T/pdb
• EM Map EMD-0834: EMDB EMDataResource

• Classification: ELECTRON TRANSPORT
• Organism(s): Chaetoceros neogracilis
• Mutation(s): No 


• Deposited: 2019-10-21 Released: 2020-05-20 
• Deposition Author(s): Nagao, R., Kato, K., Miyazaki, N., Akita, F., Shen, J.R.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of photosystem I-light-harvesting supercomplex from a red-lineage diatom

Nagao, R., Kato, K., Ifuku, K., Suzuki, T., Kumazawa, M., Uchiyama, I., Kashino, Y., Dohmae, N., Akimoto, S., Shen, J.R., Miyazaki, N., Akita, F.

(2020) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-020-16324-3

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B1C1D1E1F1G1H1I1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 401.58 kDa 
• Atom Count: 23,863 
• Modeled Residue Count: 1,851 
• Deposited Residue Count: 2,406 
• Unique protein chains: 10

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr12	A [auth 6]	208	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr10	B [auth 7]	296	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr4	C [auth 8]	270	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr3	D [auth 10]	207	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq13	E [auth 11]	229	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq3	F [auth 12]	204	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq11	G [auth 13]	244	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq10	H [auth 14]	249	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq8	I [auth 15]	281	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq5	J [auth 16]	218	Chaetoceros neogracilis	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLA	AB [auth 8], AE [auth 13], BB [auth 8], BC [auth 10], BE [auth 13], CC [auth 10], DC [auth 10], DD [auth 12], EA [auth 7], EB [auth 8], ED [auth 12], EE [auth 13], FA [auth 7], FB [auth 8], FC [auth 10], FD [auth 12], FG [auth 16], GA [auth 7], GE [auth 13], GG [auth 16], HA [auth 7], HD [auth 12], HG [auth 16], IA [auth 7], ID [auth 12], JD [auth 12], JG [auth 16], K [auth 6], KA [auth 7], KF [auth 15], KG [auth 16], L [auth 6], LA [auth 7], LD [auth 12], LF [auth 15], LG [auth 16], M [auth 6], MA [auth 7], MF [auth 15], MG [auth 16], N [auth 6], NA [auth 7], ND [auth 12], NF [auth 15], NG [auth 16], OC [auth 11], OE [auth 14], OF [auth 15], OG [auth 16], P [auth 6], PE [auth 14], PF [auth 15], Q [auth 6], QC [auth 11], QE [auth 14], QF [auth 15], RE [auth 14], RF [auth 15], SC [auth 11], SF [auth 15], TC [auth 11], TE [auth 14], TF [auth 15], U [auth 6], UC [auth 11], UF [auth 15], V [auth 6], VE [auth 14], VF [auth 15], W [auth 6], WD [auth 12], WE [auth 14], WF [auth 15], X [auth 6], XA [auth 8], XB [auth 10], YA [auth 8], YB [auth 10], YD [auth 13], YE [auth 14], ZA [auth 8], ZB [auth 10], ZD [auth 13], ZE [auth 14]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG	IF [auth 14], QB [auth 8], RB [auth 8], TB [auth 8], VA [auth 7]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	CA [auth 6]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
A86	AA [auth 6], AD [auth 11], AF [auth 14], BF [auth 14], CF [auth 14], CG [auth 15], DF [auth 14], DG [auth 15], EF [auth 14], EG [auth 15], FF [auth 14], GF [auth 14], HF [auth 14], JC [auth 10], KC [auth 10], KE [auth 13], LB [auth 8], LC [auth 10], MC [auth 11], ME [auth 13], NE [auth 14], OB [auth 8], PD [auth 12], QA [auth 7], QG [auth 16], RA [auth 7], RD [auth 12], SG [auth 16], UA [auth 7], VB [auth 10], WB [auth 10], XF [auth 15], YC [auth 11], YF [auth 15], ZC [auth 11], ZF [auth 15]	(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate C42 H58 O6 SJWWTRQNNRNTPU-XJUZQKKNSA-N
KC1	AC [auth 10], CB [auth 8], CE [auth 13], DB [auth 8], DE [auth 13], EC [auth 10], FE [auth 13], GB [auth 8], GC [auth 10], GD [auth 12], HB [auth 8], HE [auth 13], IB [auth 8], IE [auth 13], IG [auth 16], JA [auth 7], JB [auth 8], JE [auth 13], KB [auth 8], KD [auth 12], MD [auth 12], O [auth 6], OA [auth 7], OD [auth 12], PC [auth 11], PG [auth 16], R [auth 6], RC [auth 11], S [auth 6], SE [auth 14], T [auth 6], UE [auth 14], VC [auth 11], WC [auth 11], XE [auth 14]	Chlorophyll c1 C35 H30 Mg N4 O5 DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6	AG [auth 15], BA [auth 6], BG [auth 15], DA [auth 7], HC [auth 10], IC [auth 10], LE [auth 13], MB [auth 8], NB [auth 8], PA [auth 7], QD [auth 12], RG [auth 16], SA [auth 7], SD [auth 12], TA [auth 7], XC [auth 11], Y [auth 6], Z [auth 6]	(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol C40 H54 O3 OGHZCSINIMWCSB-WMTIXGNLSA-N
LMT	BD [auth 11], CD [auth 12], JF [auth 15], NC [auth 11], PB [auth 8], SB [auth 8], TD [auth 12], TG [auth 16], UB [auth 8], UD [auth 12], VD [auth 12], WA [auth 7], XD [auth 12]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3
MODEL REFINEMENT	PHENIX	1.13_2998

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Nagao, R., Kato, K., Miyazaki, N., Akita, F., Shen, J.R.

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 2.0: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2025-09-17
  Changes: Advisory, Data collection, Derived calculations
• Version 2.2: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 2.3: 2026-09-16
  Changes: Data collection, Structure summary