8WMW

The structure of PSI-11CAC at the stationary growth phase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Growth phase-dependent reorganization of cryptophyte photosystem I antennae.

Zhang, S.Si, L.Su, X.Zhao, X.An, X.Li, M.

(2024) Commun Biol 7: 560-560

  • DOI: https://doi.org/10.1038/s42003-024-06268-5
  • Primary Citation of Related Structures:  
    8WM6, 8WMJ, 8WMV, 8WMW, 8WNW

  • PubMed Abstract: 

    Photosynthetic cryptophytes are eukaryotic algae that utilize membrane-embedded chlorophyll a/c binding proteins (CACs) and lumen-localized phycobiliproteins (PBPs) as their light-harvesting antennae. Cryptophytes go through logarithmic and stationary growth phases, and may adjust their light-harvesting capability according to their particular growth state. How cryptophytes change the type/arrangement of the photosynthetic antenna proteins to regulate their light-harvesting remains unknown. Here we solve four structures of cryptophyte photosystem I (PSI) bound with CACs that show the rearrangement of CACs at different growth phases. We identify a cryptophyte-unique protein, PsaQ, which harbors two chlorophyll molecules. PsaQ specifically binds to the lumenal region of PSI during logarithmic growth phase and may assist the association of PBPs with photosystems and energy transfer from PBPs to photosystems.


  • Organizational Affiliation

    Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1752Rhodomonas salinaMutation(s): 0 
Gene Names: psaA
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2734Rhodomonas salinaMutation(s): 0 
Gene Names: psaB
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Rhodomonas salinaMutation(s): 0 
Gene Names: psaC
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II141Rhodomonas salinaMutation(s): 0 
Gene Names: psaD
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV64Rhodomonas salinaMutation(s): 0 
Gene Names: psaE
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III188Rhodomonas salinaMutation(s): 0 
Gene Names: psaF
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]36Rhodomonas salinaMutation(s): 0 
Gene Names: psaI
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]42Rhodomonas salinaMutation(s): 0 
Gene Names: psaJ
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII [auth L]153Rhodomonas salinaMutation(s): 0 
Gene Names: psaL
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIJ [auth M]30Rhodomonas salinaMutation(s): 0 
Gene Names: psaM
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PsaOK [auth O]146Rhodomonas salinaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKL [auth K]87Rhodomonas salinaMutation(s): 0 
Gene Names: psaK
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
CAC-cM [auth c]216Rhodomonas salinaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
CAC-aN [auth a]216Rhodomonas salinaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
CAC-bO [auth b]223Rhodomonas salinaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
CAC-hP [auth h]225Rhodomonas salinaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
CAC-eQ [auth e]203Rhodomonas salinaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
CAC-kR [auth k]241Rhodomonas salinaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
CAC-fS [auth f],
U [auth j]
212Rhodomonas salinaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
CAC-iT [auth i]218Rhodomonas salinaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
CAC-dV [auth d]213Rhodomonas salinaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
CAC-gW [auth g]255Rhodomonas salinaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
PsaRX [auth R]129Rhodomonas salinaMutation(s): 0 
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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SD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AA [auth A]
AB [auth A]
AC [auth A]
AD [auth B]
AG [auth a]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth B],
AG [auth a],
AH [auth b],
AI [auth e],
AL [auth j],
AN [auth R],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth B],
BE [auth F],
BG [auth a],
BH [auth b],
BI [auth e],
BJ [auth k],
BL [auth j],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth F],
CG [auth a],
CH [auth b],
CI [auth e],
CL [auth j],
DA [auth A],
DB [auth A],
DD [auth B],
DF [auth O],
DG [auth a],
DH [auth b],
DI [auth e],
DK [auth i],
DL [auth j],
DM [auth g],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EF [auth K],
EG [auth a],
EI [auth e],
EK [auth i],
EM [auth g],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FF [auth K],
FG [auth a],
FK [auth i],
FL [auth j],
FM [auth g],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GG [auth a],
GI [auth e],
GK [auth i],
GL [auth j],
GM [auth g],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth c],
HG [auth a],
HI [auth e],
HK [auth i],
HM [auth g],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth I],
IF [auth c],
IG [auth a],
IK [auth i],
IM [auth g],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth c],
JG [auth a],
JJ [auth f],
JK [auth i],
JM [auth g],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KF [auth c],
KG [auth a],
KJ [auth f],
KK [auth i],
KM [auth g],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LE [auth J],
LF [auth c],
LH [auth h],
LJ [auth f],
LM [auth g],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MF [auth c],
MH [auth h],
MJ [auth f],
MK [auth i],
ML [auth d],
MM [auth g],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth J],
NF [auth c],
NH [auth h],
NJ [auth f],
NK [auth i],
NL [auth d],
OA [auth A],
OC [auth B],
OD [auth B],
OF [auth c],
OH [auth h],
OI [auth k],
OJ [auth f],
OL [auth d],
PA [auth A],
PC [auth B],
PD [auth B],
PF [auth c],
PH [auth h],
PI [auth k],
PJ [auth f],
PL [auth d],
QA [auth A],
QC [auth B],
QD [auth B],
QH [auth h],
QI [auth k],
QJ [auth f],
QL [auth d],
QM [auth g],
RA [auth A],
RC [auth B],
RE [auth L],
RF [auth c],
RH [auth h],
RI [auth k],
RJ [auth f],
RL [auth d],
SA [auth A],
SC [auth B],
SE [auth L],
SF [auth c],
SI [auth k],
SJ [auth f],
SL [auth d],
TA [auth A],
TC [auth B],
TE [auth L],
TG [auth b],
TI [auth k],
TL [auth d],
UA [auth A],
UC [auth B],
UG [auth b],
UI [auth k],
UJ [auth f],
UK [auth j],
UL [auth d],
VA [auth A],
VC [auth B],
VG [auth b],
VI [auth k],
VJ [auth f],
VK [auth j],
WA [auth A],
WC [auth B],
WE [auth L],
WG [auth b],
WH [auth h],
WI [auth k],
WK [auth j],
XA [auth A],
XB [auth A],
XC [auth B],
XG [auth b],
XH [auth e],
XI [auth k],
XK [auth j],
XL [auth d],
XM [auth g],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth B],
YG [auth b],
YH [auth e],
YK [auth j],
Z [auth A],
ZA [auth A],
ZC [auth B],
ZE [auth O],
ZG [auth b],
ZH [auth e],
ZK [auth j]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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CF [auth O],
GE [auth F],
OE [auth J],
RG [auth b],
XE [auth L]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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BK [auth f]
BM [auth d]
CK [auth f]
CM [auth g]
DC [auth B]
BK [auth f],
BM [auth d],
CK [auth f],
CM [auth g],
DC [auth B],
HJ [auth k],
KH [auth b],
LL [auth j],
NI [auth e],
PB [auth A],
PE [auth J],
QB [auth A],
RK [auth i],
SG [auth b],
WM [auth g],
XF [auth c],
YF [auth c],
ZF [auth a]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
KC2
Query on KC2

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AJ [auth k]
EL [auth j]
FI [auth e]
LK [auth i]
NM [auth g]
AJ [auth k],
EL [auth j],
FI [auth e],
LK [auth i],
NM [auth g],
OM [auth g],
PM [auth g],
QF [auth c],
SK [auth i],
TJ [auth f],
VL [auth d],
WL [auth d],
YI [auth k],
ZI [auth k]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
II0 (Subject of Investigation/LOI)
Query on II0

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AF [auth O]
AK [auth f]
AM [auth d]
CJ [auth k]
DJ [auth k]
AF [auth O],
AK [auth f],
AM [auth d],
CJ [auth k],
DJ [auth k],
EH [auth b],
EJ [auth k],
FH [auth b],
GJ [auth k],
HL [auth j],
IH [auth b],
II [auth e],
IJ [auth k],
IL [auth j],
JI [auth e],
KI [auth e],
KL [auth j],
LG [auth a],
ME [auth J],
MG [auth a],
MI [auth e],
NG [auth a],
OK [auth i],
PG [auth a],
PK [auth i],
QK [auth i],
RM [auth g],
SM [auth g],
TF [auth c],
TH [auth h],
TM [auth g],
UF [auth c],
UH [auth h],
VH [auth h],
VM [auth g],
WF [auth c],
WJ [auth f],
XJ [auth f],
YJ [auth f],
YL [auth d],
ZL [auth d]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
C40 H52 O2
DVICWXUADSCSLL-DDEWRDOISA-N
IHT
Query on IHT

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BF [auth O]
BN [auth R]
FJ [auth k]
GH [auth b]
HH [auth b]
BF [auth O],
BN [auth R],
FJ [auth k],
GH [auth b],
HH [auth b],
JL [auth j],
OG [auth a],
UM [auth g],
VF [auth c],
ZJ [auth f]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
C40 H54 O
UNJKJDIRJWIHLL-BQLQDKTLSA-N
WVN
Query on WVN

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EE [auth F]
FE [auth F]
GF [auth K]
HE [auth I]
JE [auth J]
EE [auth F],
FE [auth F],
GF [auth K],
HE [auth I],
JE [auth J],
KE [auth J],
LI [auth e],
QE [auth L],
RB [auth A],
SB [auth A],
SH [auth h],
TB [auth A],
TK [auth j],
UB [auth A],
UD [auth B],
UE [auth L],
VB [auth A],
VD [auth B],
VE [auth L],
WD [auth B],
XD [auth B],
YD [auth B],
YE [auth M],
YM [auth R],
ZM [auth R]
1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene
C40 H56
ANVAOWXLWRTKGA-NTXLUARGSA-N
LMU
Query on LMU

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TD [auth B]DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
LMT
Query on LMT

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DE [auth F],
JH [auth b],
QG [auth a],
WB [auth A]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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OB [auth A],
RD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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AE [auth C],
ZB [auth A],
ZD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--
National Basic Research Program of China (973 Program)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release