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 6L4U | pdb_00006l4u

Structure of the PSI-FCPI supercomplex from diatom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 3.1 of the entry. See complete history. 

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 

Macromolecule Content 

  • Total Structure Weight: 997.68 kDa 
  • Atom Count: 62,199 
  • Modeled Residue Count: 5,205 
  • Deposited Residue Count: 6,198 
  • Unique protein chains: 28

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1751Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2733Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II139Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV67Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III185Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]36Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]41Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII [auth L]151Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIJ [auth M]30Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown protein 1K [auth 1u]130Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit Psa28L [auth 2u]121Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr15M [auth 1]227Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr8N [auth 2]205Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr2O [auth 3]200Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr9P [auth 4]215Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr11Q [auth 5]266Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr12R [auth 6]208Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr10S [auth 7]296Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr4T [auth 8]270Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcf6U [auth 9]214Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr3V [auth 10]207Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq13W [auth 11]229Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq3X [auth 12]204Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq11Y [auth 13]244Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq10Z [auth 14]249Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq8AA [auth 15]281Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq5BA [auth 16]218Chaetoceros neogracilisMutation(s): 0 
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Reference Sequence

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AB [auth A]
AD [auth B]
AG [auth 2]
AH [auth 4]
AI [auth 5]
AB [auth A],
AD [auth B],
AG [auth 2],
AH [auth 4],
AI [auth 5],
AK [auth 8],
AL [auth 9],
AQ [auth 16],
BB [auth A],
BD [auth B],
BH [auth 4],
BK [auth 8],
BL [auth 9],
BN [auth 12],
CB [auth A],
CD [auth B],
CH [auth 4],
CK [auth 8],
CL [auth 9],
CN [auth 12],
CP [auth 15],
CQ [auth 16],
DA [auth A],
DB [auth A],
DD [auth B],
DF [auth 1],
DH [auth 4],
DK [auth 8],
DL [auth 9],
DN [auth 12],
DP [auth 15],
DQ [auth 16],
EA [auth A],
EB [auth A],
ED [auth B],
EF [auth 1],
EH [auth 4],
EP [auth 15],
EQ [auth 16],
FA [auth A],
FB [auth A],
FD [auth B],
FE [auth B],
FF [auth 1],
FN [auth 12],
FP [auth 15],
FQ [auth 16],
GA [auth A],
GB [auth A],
GD [auth B],
GF [auth 1],
GJ [auth 7],
GK [auth 8],
GP [auth 15],
GQ [auth 16],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth 1],
HH [auth 4],
HJ [auth 7],
HK [auth 8],
HM [auth 11],
HN [auth 12],
HO [auth 14],
HP [auth 15],
HQ [auth 16],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IG [auth 3],
IJ [auth 7],
IO [auth 14],
IP [auth 15],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JE [auth F],
JF [auth 1],
JG [auth 3],
JH [auth 4],
JJ [auth 7],
JM [auth 11],
JO [auth 14],
JP [auth 15],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KE [auth F],
KG [auth 3],
KJ [auth 7],
KO [auth 14],
KP [auth 15],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LE [auth F],
LI [auth 6],
LM [auth 11],
LP [auth 15],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MG [auth 3],
MI [auth 6],
MJ [auth 7],
MM [auth 11],
MO [auth 14],
MP [auth 15],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NG [auth 3],
NI [auth 6],
NJ [auth 7],
NM [auth 11],
NP [auth 15],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OF [auth 2],
OG [auth 3],
OI [auth 6],
OJ [auth 7],
OO [auth 14],
OP [auth 15],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth J],
PJ [auth 7],
PL [auth 10],
PO [auth 14],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QF [auth 2],
QG [auth 3],
QI [auth 6],
QL [auth 10],
QN [auth 12],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RF [auth 2],
RG [auth 3],
RH [auth 5],
RI [auth 6],
RL [auth 10],
RN [auth 13],
RO [auth 14],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SF [auth 2],
SH [auth 5],
SN [auth 13],
SO [auth 14],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TE [auth L],
TH [auth 5],
TL [auth 10],
TN [auth 13],
UA [auth A],
UC [auth B],
UE [auth L],
UF [auth 2],
UL [auth 10],
UN [auth 13],
VA [auth A],
VC [auth B],
VF [auth 2],
VI [auth 6],
VK [auth 9],
VL [auth 10],
WA [auth A],
WC [auth B],
WF [auth 2],
WH [auth 5],
WI [auth 6],
WK [auth 9],
XA [auth A],
XC [auth B],
XF [auth 2],
XH [auth 5],
XI [auth 6],
XK [auth 9],
XL [auth 10],
XM [auth 12],
XN [auth 13],
YA [auth A],
YC [auth B],
YF [auth 2],
YH [auth 5],
YI [auth 6],
YM [auth 12],
YP [auth 16],
ZA [auth A],
ZC [auth B],
ZE [auth 2u],
ZG [auth 4],
ZJ [auth 8],
ZK [auth 9],
ZM [auth 12],
ZN [auth 13],
ZP [auth 16]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0



Download:Ideal Coordinates CCD File
CA [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
AP [auth 14]
BE [auth B]
BF [auth 2u]
DE [auth B]
FC [auth A]
AP [auth 14],
BE [auth B],
BF [auth 2u],
DE [auth B],
FC [auth A],
HI [auth 5],
II [auth 6],
NE [auth F],
RK [auth 8],
SK [auth 8],
TK [auth 8],
XJ [auth 7],
YG [auth 3]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



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BC [auth A]
CC [auth A]
CE [auth B]
DJ [auth 6]
GI [auth 5]
BC [auth A],
CC [auth A],
CE [auth B],
DJ [auth 6],
GI [auth 5],
HG [auth 2],
ML [auth 9]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86

Query on A86



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AF [auth 2u]
BJ [auth 6]
BM [auth 10]
CF [auth 2u]
CM [auth 10]
AF [auth 2u],
BJ [auth 6],
BM [auth 10],
CF [auth 2u],
CM [auth 10],
DM [auth 10],
DO [auth 13],
EI [auth 5],
EM [auth 11],
FG [auth 2],
FI [auth 5],
FO [auth 13],
GG [auth 2],
GO [auth 14],
HL [auth 9],
JL [auth 9],
JN [auth 12],
JQ [auth 16],
KH [auth 4],
KL [auth 9],
LF [auth 1],
LN [auth 12],
LQ [auth 16],
MH [auth 4],
NH [auth 4],
NK [auth 8],
NL [auth 10],
OL [auth 10],
PF [auth 2],
PH [auth 4],
PP [auth 15],
QH [auth 5],
QK [auth 8],
QP [auth 15],
RM [auth 11],
RP [auth 15],
SJ [auth 7],
SM [auth 11],
TJ [auth 7],
TM [auth 11],
TO [auth 14],
UO [auth 14],
UP [auth 15],
VG [auth 3],
VO [auth 14],
VP [auth 15],
WG [auth 3],
WJ [auth 7],
WO [auth 14],
WP [auth 15],
XO [auth 14],
XP [auth 15],
YO [auth 14],
ZO [auth 14]
(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

Query on KC1



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AN [auth 12]
AO [auth 13]
BG [auth 2]
BI [auth 5]
BO [auth 13]
AN [auth 12],
AO [auth 13],
BG [auth 2],
BI [auth 5],
BO [auth 13],
BQ [auth 16],
CO [auth 13],
EK [auth 8],
EL [auth 9],
EN [auth 12],
FH [auth 4],
FK [auth 8],
FL [auth 9],
GH [auth 4],
GL [auth 9],
GN [auth 12],
IF [auth 1],
IH [auth 4],
IK [auth 8],
IM [auth 11],
IN [auth 12],
IQ [auth 16],
JK [auth 8],
KF [auth 1],
KK [auth 8],
KM [auth 11],
LG [auth 3],
LJ [auth 7],
LK [auth 8],
LO [auth 14],
MK [auth 8],
NO [auth 14],
OM [auth 11],
PG [auth 3],
PI [auth 6],
PM [auth 11],
QJ [auth 7],
QO [auth 14],
SG [auth 3],
SI [auth 6],
SL [auth 10],
TF [auth 2],
TI [auth 6],
UH [auth 5],
UI [auth 6],
VH [auth 5],
VN [auth 13],
WL [auth 10],
WN [auth 13],
YK [auth 9],
YL [auth 10],
YN [auth 13],
ZF [auth 2],
ZH [auth 5]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6

Query on DD6



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AJ [auth 6]
AM [auth 10]
CG [auth 2]
CI [auth 5]
CJ [auth 6]
AJ [auth 6],
AM [auth 10],
CG [auth 2],
CI [auth 5],
CJ [auth 6],
DG [auth 2],
DI [auth 5],
EG [auth 2],
EO [auth 13],
FJ [auth 7],
IL [auth 9],
KI [auth 6],
KN [auth 12],
KQ [auth 16],
LH [auth 4],
MF [auth 1],
MN [auth 12],
OH [auth 4],
OK [auth 8],
PK [auth 8],
QM [auth 11],
RJ [auth 7],
SP [auth 15],
TG [auth 3],
TP [auth 15],
UG [auth 3],
UJ [auth 7],
VJ [auth 7],
XG [auth 3],
ZI [auth 6],
ZL [auth 10]
(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
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AC [auth A]
AE [auth B]
ME [auth F]
OE [auth I]
QE [auth J]
AC [auth A],
AE [auth B],
ME [auth F],
OE [auth I],
QE [auth J],
RE [auth J],
SE [auth L],
VD [auth B],
VE [auth L],
WB [auth A],
WD [auth B],
WE [auth L],
XB [auth A],
XD [auth B],
XE [auth M],
YB [auth A],
YD [auth B],
YE [auth 2u],
ZB [auth A],
ZD [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
BP [auth 15]
DC [auth A]
EC [auth A]
EE [auth B]
EJ [auth 7]
BP [auth 15],
DC [auth A],
EC [auth A],
EE [auth B],
EJ [auth 7],
FM [auth 11],
GC [auth A],
GE [auth B],
GM [auth 11],
JI [auth 6],
LL [auth 9],
MQ [auth 16],
NF [auth 1],
NN [auth 12],
ON [auth 12],
PN [auth 12],
UK [auth 8],
UM [auth 11],
VM [auth 11],
WM [auth 12],
YJ [auth 7]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
UB [auth A],
UD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
HE [auth C],
IE [auth C],
VB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UNK
Query on UNK
K [auth 1u]L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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, Structure summary
  • Version 3.0: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2026-09-16
    Changes: Data collection, Structure summary