7KSQ | pdb_00007ksq

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

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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 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.

Macromolecule Content 

  • Total Structure Weight: 544.74 kDa 
  • Atom Count: 36,553 
  • Modeled Residue Count: 3,347 
  • Deposited Residue Count: 3,347 
  • Unique protein chains: 18

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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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)
Explore A0A2K1K0E4 
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UniProt GroupA0A2K1K0E4
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Reference Sequence
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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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UniProt GroupQ6YXQ2
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Reference Sequence
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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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Reference Sequence
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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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UniProt GroupA0A2K1IHL7
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Reference Sequence
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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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Reference Sequence
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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)
Explore A0A2K1JC42 
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UniProt GroupA0A2K1JC42
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Reference Sequence
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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)
Explore A0A2K1JDR4 
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UniProt GroupA0A2K1JDR4
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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)
Explore A0A2K1JLW2 
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Reference Sequence
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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)
Explore A0A2K1KIF2 
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UniProt GroupA0A2K1KIF2
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Reference Sequence
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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)
Explore Q6YXK4 
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UniProt GroupQ6YXK4
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Reference Sequence
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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)
Explore A0A2K1JDE1 
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UniProt GroupA0A2K1JDE1
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Reference Sequence

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
SD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
(Subject of Investigation/LOI)

Query on CHL



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



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

Query on SF4



Download:Ideal Coordinates CCD File
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

View Full Validation Report



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