8WMV | pdb_00008wmv

The structure of PSI-14CAC complex at stationary growth phase

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Rhodomonas salina
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2023-10-04 Released: 2024-05-29 
  • Deposition Author(s): Zhang, S.M., Si, L., Li, M.
  • Funding Organization(s): National Basic Research Program of China (973 Program), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8WMV

This is version 1.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 958.2 kDa 
  • Atom Count: 59,342 
  • Modeled Residue Count: 5,017 
  • Deposited Residue Count: 5,955 
  • Unique protein chains: 26

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1752Rhodomonas salinaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A6MVZ7 (Rhodomonas salina)
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UniProt GroupA6MVZ7
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2734Rhodomonas salinaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A6MVZ6 (Rhodomonas salina)
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UniProt GroupA6MVZ6
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Rhodomonas salinaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A6MVS8 (Rhodomonas salina)
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UniProt GroupA6MVS8
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II141Rhodomonas salinaMutation(s): 0 
UniProt
Find proteins for A6MVZ1 (Rhodomonas salina)
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UniProt GroupA6MVZ1
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV64Rhodomonas salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A6MW36 (Rhodomonas salina)
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UniProt GroupA6MW36
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III188Rhodomonas salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A6MVU7 (Rhodomonas salina)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]36Rhodomonas salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A6MVV1 (Rhodomonas salina)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]42Rhodomonas salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A6MVU6 (Rhodomonas salina)
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UniProt GroupA6MVU6
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII [auth L]153Rhodomonas salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A6MVV8 (Rhodomonas salina)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIJ [auth M]30Rhodomonas salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A6MVT4 (Rhodomonas salina)
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Reference Sequence
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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 
Membrane Entity: Yes 
UniProt
Find proteins for A6MVS9 (Rhodomonas salina)
Explore A6MVS9 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
chain sM [auth s]269Rhodomonas salinaMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-cN [auth c]216Rhodomonas salinaMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-aO [auth a]216Rhodomonas salinaMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-bP [auth b]223Rhodomonas salinaMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-hQ [auth h]225Rhodomonas salinaMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-m, CAC-fR [auth m],
V [auth f],
X [auth j]		212Rhodomonas salinaMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-eS [auth e]203Rhodomonas salinaMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-lT [auth l]238Rhodomonas salinaMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-kU [auth k]241Rhodomonas salinaMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-iW [auth i]218Rhodomonas salinaMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-dY [auth d]213Rhodomonas salinaMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-gZ [auth g]255Rhodomonas salinaMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaRAA [auth R]129Rhodomonas salinaMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
CAC-nBA [auth n]219Rhodomonas salinaMutation(s): 0 

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
VD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AB [auth A]
AD [auth B]
AG [auth c]
AH [auth a]
AJ [auth m]
AB [auth A],
AD [auth B],
AG [auth c],
AH [auth a],
AJ [auth m],
AK [auth l],
AN [auth j],
AP [auth n],
BB [auth A],
BC [auth A],
BD [auth B],
BG [auth c],
BH [auth a],
BJ [auth m],
BK [auth l],
BN [auth j],
BO [auth g],
BP [auth n],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth B],
CE [auth B],
CG [auth c],
CH [auth a],
CK [auth l],
CL [auth k],
CN [auth j],
CO [auth g],
CP [auth n],
DA [auth A],
DB [auth A],
DD [auth B],
DF [auth O],
DG [auth c],
DI [auth h],
DK [auth l],
DM [auth i],
DO [auth g],
DP [auth n],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth B],
EI [auth h],
EK [auth l],
EM [auth i],
EN [auth j],
EO [auth g],
EP [auth n],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth B],
FE [auth F],
FG [auth c],
FI [auth h],
FK [auth l],
FM [auth i],
FN [auth j],
FO [auth g],
FP [auth n],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GE [auth F],
GG [auth c],
GI [auth h],
GK [auth l],
GM [auth i],
GO [auth g],
GP [auth n],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth F],
HF [auth O],
HI [auth h],
HJ [auth e],
HK [auth l],
HM [auth i],
HO [auth g],
HP [auth n],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IF [auth K],
II [auth h],
IJ [auth e],
IM [auth i],
IO [auth g],
IP [auth n],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth K],
JI [auth h],
JJ [auth e],
JK [auth l],
JL [auth f],
JM [auth i],
JO [auth g],
JP [auth n],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KH [auth b],
KI [auth h],
KJ [auth e],
KL [auth f],
KM [auth i],
KO [auth g],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LH [auth b],
LJ [auth e],
LL [auth f],
LN [auth d],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MF [auth s],
MH [auth b],
MJ [auth e],
ML [auth f],
MM [auth i],
MN [auth d],
MP [auth n],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NF [auth s],
NH [auth b],
NJ [auth e],
NL [auth f],
NM [auth i],
NN [auth d],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OE [auth J],
OH [auth b],
OJ [auth e],
OL [auth f],
ON [auth d],
OO [auth g],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PH [auth b],
PI [auth h],
PL [auth f],
PN [auth d],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QE [auth J],
QF [auth s],
QH [auth b],
QI [auth m],
QJ [auth e],
QK [auth k],
QL [auth f],
QN [auth d],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RH [auth b],
RI [auth m],
RJ [auth e],
RK [auth k],
RL [auth f],
RN [auth d],
SA [auth A],
SC [auth B],
SD [auth B],
SF [auth s],
SG [auth a],
SH [auth b],
SI [auth m],
SK [auth k],
SL [auth f],
SN [auth d],
TA [auth A],
TC [auth B],
TD [auth B],
TF [auth s],
TG [auth a],
TH [auth b],
TI [auth m],
TK [auth k],
UA [auth A],
UC [auth B],
UE [auth L],
UG [auth a],
UH [auth b],
UI [auth m],
UK [auth k],
UL [auth f],
UM [auth j],
VA [auth A],
VC [auth B],
VE [auth L],
VF [auth c],
VG [auth a],
VI [auth m],
VK [auth k],
VL [auth f],
VM [auth j],
VN [auth d],
VO [auth g],
WA [auth A],
WC [auth B],
WE [auth L],
WF [auth c],
WG [auth a],
WI [auth m],
WK [auth k],
WM [auth j],
XA [auth A],
XC [auth B],
XF [auth c],
XG [auth a],
XI [auth m],
XK [auth k],
XM [auth j],
YA [auth A],
YC [auth B],
YE [auth L],
YF [auth c],
YG [auth a],
YI [auth m],
YK [auth k],
YM [auth j],
YO [auth R],
ZA [auth A],
ZC [auth B],
ZF [auth c],
ZG [auth a],
ZM [auth j]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG


Download:Ideal Coordinates CCD File
AF [auth L]
CI [auth b]
GF [auth O]
KE [auth F]
NG [auth c]
AF [auth L],
CI [auth b],
GF [auth O],
KE [auth F],
NG [auth c],
RE [auth J],
UF [auth s]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG


Download:Ideal Coordinates CCD File
AI [auth b]
AO [auth g]
BI [auth b]
BM [auth f]
GJ [auth m]
AI [auth b],
AO [auth g],
BI [auth b],
BM [auth f],
GJ [auth m],
IH [auth a],
IL [auth k],
KN [auth j],
MG [auth c],
PG [auth c],
PK [auth l],
QG [auth a],
RM [auth i],
SE [auth J],
SP [auth n],
TB [auth A],
UB [auth A],
UO [auth g],
XJ [auth e],
ZB [auth A],
ZE [auth L],
ZN [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
KC2

Query on KC2


Download:Ideal Coordinates CCD File
AL [auth k]
BL [auth k]
DN [auth j]
EG [auth c]
IK [auth l]
AL [auth k],
BL [auth k],
DN [auth j],
EG [auth c],
IK [auth l],
KP [auth n],
LF [auth s],
LM [auth i],
LO [auth g],
LP [auth n],
MO [auth g],
NO [auth g],
OF [auth s],
PJ [auth e],
SM [auth i],
TL [auth f],
TN [auth d],
UN [auth d],
ZI [auth m],
ZK [auth k]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
II0

Query on II0


Download:Ideal Coordinates CCD File
AM [auth f]
CJ [auth m]
DH [auth a]
DJ [auth m]
DL [auth k]
AM [auth f],
CJ [auth m],
DH [auth a],
DJ [auth m],
DL [auth k],
EF [auth O],
EH [auth a],
EJ [auth m],
EL [auth k],
FH [auth a],
FL [auth k],
GN [auth j],
HG [auth c],
HH [auth a],
HL [auth k],
HN [auth j],
IG [auth c],
IN [auth j],
JG [auth c],
KK [auth l],
LG [auth c],
LK [auth l],
MI [auth h],
MK [auth l],
NI [auth h],
NP [auth n],
OI [auth h],
OK [auth l],
OM [auth i],
OP [auth n],
PE [auth J],
PM [auth i],
PO [auth g],
PP [auth n],
QO [auth g],
RO [auth g],
RP [auth n],
SJ [auth e],
TJ [auth e],
TM [auth i],
TO [auth g],
UJ [auth e],
VH [auth b],
WH [auth b],
WJ [auth e],
WL [auth f],
WN [auth d],
XL [auth f],
XN [auth d],
YH [auth b],
YL [auth f],
YN [auth d],
ZJ [auth l]
(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


Download:Ideal Coordinates CCD File
FF [auth O]
FJ [auth m]
GH [auth a]
GL [auth k]
JN [auth j]
FF [auth O],
FJ [auth m],
GH [auth a],
GL [auth k],
JN [auth j],
KG [auth c],
OG [auth c],
QP [auth n],
SO [auth g],
XH [auth b],
ZL [auth f],
ZO [auth R]
(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
(Subject of Investigation/LOI)

Query on WVN


Download:Ideal Coordinates CCD File
AE [auth B]
BE [auth B]
BF [auth M]
CF [auth O]
IE [auth F]
AE [auth B],
BE [auth B],
BF [auth M],
CF [auth O],
IE [auth F],
JE [auth F],
KF [auth K],
LE [auth I],
LI [auth h],
ME [auth J],
NE [auth J],
NK [auth l],
PF [auth s],
QM [auth i],
RF [auth s],
TE [auth L],
VB [auth A],
VJ [auth e],
WB [auth A],
WD [auth B],
WO [auth R],
XB [auth A],
XD [auth B],
XE [auth L],
XO [auth R],
YB [auth A],
YD [auth B],
YJ [auth l],
ZD [auth B]
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


Download:Ideal Coordinates CCD File
CM [auth i]DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
LMT

Query on LMT


Download:Ideal Coordinates CCD File
AC [auth A],
JH [auth a],
RG [auth a],
ZH [auth b]		DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN


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

Query on SF4


Download:Ideal Coordinates CCD File
DC [auth A],
DE [auth C],
EE [auth C]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Advisory, Data collection, Derived calculations, Structure summary