7KSQ

The Structure of the moss PSI-LHCI reveals the evolution of the LHCI antenna


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structure of the Physcomitrium patens photosystem I reveals a unique Lhca2 paralogue replacing Lhca4.

Gorski, C.Riddle, R.Toporik, H.Da, Z.Dobson, Z.Williams, D.Mazor, Y.

(2022) Nat Plants 8: 307-316

  • DOI: https://doi.org/10.1038/s41477-022-01099-w
  • Primary Citation of Related Structures:  
    7KSQ, 7KU5, 7KUX

  • PubMed Abstract: 

    The moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges, which drove evolutionary processes. The photosynthetic machinery of modern flowering plants is adapted to the high light conditions on land. Red-shifted Lhca4 antennae are present in the photosystem I light-harvesting complex of many green-lineage plants but absent in P. patens. The cryo-EM structure of the P. patens photosystem I light-harvesting complex I supercomplex (PSI-LHCI) at 2.8 Å reveals that Lhca4 is replaced by a unique Lhca2 paralogue in moss. This PSI-LHCI supercomplex also retains the PsaM subunit, present in Cyanobacteria and several algal species but lost in vascular plants, and the PsaO subunit responsible for binding light-harvesting complex II. The blue-shifted Lhca2 paralogue and chlorophyll b enrichment relative to flowering plants make the P. patens PSI-LHCI spectroscopically unique among other green-lineage supercomplexes. Overall, the structure represents an evolutionary intermediate PSI with the crescent-shaped LHCI common in vascular plants, and contains a unique Lhca2 paralogue that facilitates the moss's adaptation to low-light niches.


  • Organizational Affiliation

    School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1742Physcomitrium patensMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q8MFA3 (Physcomitrium patens)
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UniProt GroupQ8MFA3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2732Physcomitrium patensMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q8MFA2 (Physcomitrium patens)
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UniProt GroupQ8MFA2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticC [auth 1]192Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JLZ3 (Physcomitrium patens)
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UniProt GroupA0A2K1JLZ3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticD [auth 2]203Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IW94 (Physcomitrium patens)
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UniProt GroupA0A2K1IW94
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticE [auth 3]218Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IB10 (Physcomitrium patens)
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UniProt GroupA0A2K1IB10
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticF [auth 4]203Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1K0E4 (Physcomitrium patens)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]80Physcomitrium patensMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXQ2 (Physcomitrium patens)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PsaDH [auth D]142Physcomitrium patensMutation(s): 0 
UniProt
Find proteins for A9REG3 (Physcomitrium patens)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PsaEI [auth E]63Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IHL7 (Physcomitrium patens)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-FJ [auth F]160Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IN36 (Physcomitrium patens)
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UniProt GroupA0A2K1IN36
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-GK [auth G]91Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JC42 (Physcomitrium patens)
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UniProt GroupA0A2K1JC42
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsaHL [auth H]87Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JDR4 (Physcomitrium patens)
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UniProt GroupA0A2K1JDR4
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]34Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXR3 (Physcomitrium patens)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]41Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXM2 (Physcomitrium patens)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PsaKO [auth K]81Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JLW2 (Physcomitrium patens)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PSI subunit VP [auth L]160Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1KIF2 (Physcomitrium patens)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIQ [auth M]30Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXK4 (Physcomitrium patens)
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UniProt GroupQ6YXK4
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PsaOR [auth O]88Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JDE1 (Physcomitrium patens)
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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SD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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AF [auth 2]
FG [auth 4]
GF [auth 2]
GG [auth 4]
HG [auth 4]
AF [auth 2],
FG [auth 4],
GF [auth 2],
GG [auth 4],
HG [auth 4],
NE [auth 1],
NF [auth 3],
NG [auth 4],
OE [auth 2],
RE [auth 2],
SE [auth 2],
TE [auth 2],
WE [auth 2],
ZD [auth 1]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth 1]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth 1],
AG [auth 4],
AH [auth G],
AI [auth O],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth 1],
BG [auth 4],
BH [auth G],
BI [auth O],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth 1],
CG [auth 4],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth 1],
DG [auth 4],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth 1],
EG [auth 4],
FA [auth A],
FC [auth B],
FD [auth B],
FE [auth 1],
FH [auth H],
GA [auth A],
GC [auth B],
GD [auth B],
GE [auth 1],
HA [auth A],
HC [auth B],
HD [auth B],
HE [auth 1],
HF [auth 3],
IA [auth A],
IC [auth B],
ID [auth B],
IF [auth 3],
IG [auth 4],
IH [auth I],
JA [auth A],
JC [auth B],
JD [auth B],
JF [auth 3],
JG [auth 4],
JH [auth J],
KA [auth A],
KC [auth B],
KF [auth 3],
KG [auth 4],
LA [auth A],
LC [auth B],
LF [auth 3],
LG [auth 4],
MA [auth A],
MC [auth B],
MF [auth 3],
MG [auth 4],
NA [auth A],
NC [auth B],
OA [auth A],
OC [auth B],
OF [auth 3],
OH [auth K],
PA [auth A],
PC [auth B],
PE [auth 2],
PF [auth 3],
PH [auth K],
QA [auth A],
QC [auth B],
QE [auth 2],
QF [auth 3],
QH [auth K],
RA [auth A],
RB [auth A],
RC [auth B],
RF [auth 3],
RH [auth K],
SA [auth A],
SB [auth A],
SC [auth B],
SF [auth 3],
T [auth A],
TA [auth A],
TB [auth A],
TC [auth B],
TF [auth 3],
TH [auth L],
U [auth A],
UA [auth A],
UB [auth A],
UC [auth B],
UE [auth 2],
UF [auth 3],
UH [auth L],
V [auth A],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth 1],
VE [auth 2],
VG [auth F],
VH [auth L],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WD [auth 1],
WG [auth F],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XD [auth 1],
XE [auth 2],
XG [auth F],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YD [auth 1],
YE [auth 2],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZE [auth 2],
ZG [auth G],
ZH [auth O]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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S [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

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FF [auth 2],
MH [auth J],
NH [auth J],
OB [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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EF [auth 2]
LE [auth 1]
NB [auth A]
PB [auth A]
RG [auth 4]
EF [auth 2],
LE [auth 1],
NB [auth A],
PB [auth A],
RG [auth 4],
TD [auth B],
ZF [auth 3]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
LUT (Subject of Investigation/LOI)
Query on LUT

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BF [auth 2]
CF [auth 2]
DF [auth 2]
IE [auth 1]
JE [auth 1]
BF [auth 2],
CF [auth 2],
DF [auth 2],
IE [auth 1],
JE [auth 1],
OG [auth 4],
PG [auth 4],
QG [auth 4],
VF [auth 3],
WF [auth 3]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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CH [auth G]
CI [auth O]
GH [auth I]
HB [auth A]
HH [auth I]
CH [auth G],
CI [auth O],
GH [auth I],
HB [auth A],
HH [auth I],
IB [auth A],
JB [auth A],
KB [auth A],
KE [auth 1],
KH [auth J],
LB [auth A],
LD [auth B],
LH [auth J],
MB [auth A],
MD [auth B],
ND [auth B],
OD [auth B],
PD [auth B],
QD [auth B],
SH [auth K],
UD [auth B],
WH [auth L],
XF [auth 3],
XH [auth L],
YF [auth 3],
YG [auth F],
YH [auth M]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT (Subject of Investigation/LOI)
Query on LMT

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DH [auth G]
EH [auth G]
ME [auth 1]
QB [auth A]
RD [auth B]
DH [auth G],
EH [auth G],
ME [auth 1],
QB [auth A],
RD [auth B],
SG [auth 4]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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

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GB [auth A],
TG [auth C],
UG [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary