6L4T

Structure of the peripheral FCPI from diatom


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.0 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 


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr12A [auth 6]208Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr10B [auth 7]296Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr4C [auth 8]270Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcr3D [auth 10]207Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq13E [auth 11]229Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq3F [auth 12]204Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq11G [auth 13]244Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq10H [auth 14]249Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq8I [auth 15]281Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq5J [auth 16]218Chaetoceros neogracilisMutation(s): 0 
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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AB [auth 8]
AE [auth 13]
BB [auth 8]
BC [auth 10]
BE [auth 13]
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
Query on LMG

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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
Query on LHG

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CA [auth 6]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
Query on A86

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AA [auth 6]
AD [auth 11]
AF [auth 14]
BF [auth 14]
CF [auth 14]
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
Query on KC1

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AC [auth 10]
CB [auth 8]
CE [auth 13]
DB [auth 8]
DE [auth 13]
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
Query on DD6

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AG [auth 15]
BA [auth 6]
BG [auth 15]
DA [auth 7]
HC [auth 10]
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
Query on LMT

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BD [auth 11]
CD [auth 12]
JF [auth 15]
NC [auth 11]
PB [auth 8]
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:
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