6L35 | pdb_00006l35

PSI-LHCI Supercomplex from Physcometrella patens


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

Antenna arrangement and energy-transfer pathways of PSI-LHCI from the moss Physcomitrella patens.

Yan, Q.Zhao, L.Wang, W.Pi, X.Han, G.Wang, J.Cheng, L.He, Y.K.Kuang, T.Qin, X.Sui, S.F.Shen, J.R.

(2021) Cell Discov 7: 10-10

  • DOI: https://doi.org/10.1038/s41421-021-00242-9
  • Primary Citation Related Structures: 
    6L35

  • PubMed Abstract: 

    Plants harvest light energy utilized for photosynthesis by light-harvesting complex I and II (LHCI and LHCII) surrounding photosystem I and II (PSI and PSII), respectively. During the evolution of green plants, moss is at an evolutionarily intermediate position from aquatic photosynthetic organisms to land plants, being the first photosynthetic organisms that landed. Here, we report the structure of the PSI-LHCI supercomplex from the moss Physcomitrella patens (Pp) at 3.23 Å resolution solved by cryo-electron microscopy. Our structure revealed that four Lhca subunits are associated with the PSI core in an order of Lhca1-Lhca5-Lhca2-Lhca3. This number is much decreased from 8 to 10, the number of subunits in most green algal PSI-LHCI, but the same as those of land plants. Although Pp PSI-LHCI has a similar structure as PSI-LHCI of land plants, it has Lhca5, instead of Lhca4, in the second position of Lhca, and several differences were found in the arrangement of chlorophylls among green algal, moss, and land plant PSI-LHCI. One chlorophyll, PsaF-Chl 305, which is found in the moss PSI-LHCI, is located at the gap region between the two middle Lhca subunits and the PSI core, and therefore may make the excitation energy transfer from LHCI to the core more efficient than that of land plants. On the other hand, energy-transfer paths at the two side Lhca subunits are relatively conserved. These results provide a structural basis for unravelling the mechanisms of light-energy harvesting and transfer in the moss PSI-LHCI, as well as important clues on the changes of PSI-LHCI after landing.


  • Organizational Affiliation
    • Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.

Macromolecule Content 

  • Total Structure Weight: 527.15 kDa 
  • Atom Count: 34,822 
  • Modeled Residue Count: 3,260 
  • Deposited Residue Count: 3,267 
  • Unique protein chains: 17

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 A2733Physcomitrium 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
Photosystem I iron-sulfur center80Physcomitrium 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: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Predicted protein PsaD141Physcomitrium patensMutation(s): 0 
UniProt
Find proteins for A0A2K1JKF2 (Physcomitrium patens)
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UniProt GroupA0A2K1JKF2
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaE62Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IKE2 (Physcomitrium patens)
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UniProt GroupA0A2K1IKE2
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI-F159Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1J0L9 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Predicted protein PsaG98Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JC42 (Physcomitrium patens)
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UniProt GroupA0A2K1JC42
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaH photosystem I reaction center subunit90Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9SL09 (Physcomitrium patens)
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UniProt GroupA9SL09
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII34Physcomitrium 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: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX41Physcomitrium 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: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaK79Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1KU02 (Physcomitrium patens)
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UniProt GroupA0A2K1KU02
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI subunit V159Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IAD0 (Physcomitrium patens)
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UniProt GroupA0A2K1IAD0
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII29Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXK4 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 2]210Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1K0C7 (Physcomitrium patens)
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UniProt GroupA0A2K1K0C7
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 6]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: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticP [auth 3]213Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IB10 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticQ [auth 5]205Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1KN29 (Physcomitrium patens)
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



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

Query on CHL



Download:Ideal Coordinates CCD File
AH [auth 5]
BH [auth 5]
CH [auth 5]
GF [auth 2]
JG [auth 3]
AH [auth 5],
BH [auth 5],
CH [auth 5],
GF [auth 2],
JG [auth 3],
JH [auth 5],
NF [auth 6],
SF [auth 6],
TE [auth 2],
XE [auth 2],
YE [auth 2],
ZE [auth 2]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth G]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth G],
AF [auth 2],
AG [auth 6],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth G],
BF [auth 2],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CF [auth 2],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DF [auth 2],
DH [auth 5],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth J],
EF [auth 2],
EG [auth 3],
EH [auth 5],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FF [auth 2],
FG [auth 3],
FH [auth 5],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GG [auth 3],
GH [auth 5],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HG [auth 3],
HH [auth 5],
IA [auth A],
IC [auth B],
ID [auth B],
IE [auth K],
IG [auth 3],
IH [auth 5],
JA [auth A],
JB [auth A],
JC [auth B],
KA [auth A],
KC [auth B],
KE [auth K],
KG [auth 3],
LA [auth A],
LC [auth B],
LE [auth K],
LG [auth 3],
MA [auth A],
MC [auth B],
ME [auth K],
MG [auth 3],
NA [auth A],
NC [auth B],
NG [auth 3],
OA [auth A],
OC [auth B],
OF [auth 6],
OG [auth 3],
PA [auth A],
PC [auth B],
PE [auth L],
PF [auth 6],
PG [auth 3],
QA [auth A],
QC [auth B],
QE [auth L],
QF [auth 6],
QG [auth 3],
R [auth A],
RA [auth A],
RC [auth B],
RE [auth L],
RF [auth 6],
RG [auth 3],
S [auth A],
SA [auth A],
SB [auth A],
SC [auth B],
T [auth A],
TA [auth A],
TC [auth B],
TF [auth 6],
U [auth A],
UA [auth A],
UC [auth B],
UD [auth F],
UE [auth 2],
UF [auth 6],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VE [auth 2],
VF [auth 6],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WD [auth F],
WE [auth 2],
WF [auth 6],
WG [auth 5],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XD [auth F],
XF [auth 6],
XG [auth 5],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YD [auth F],
YF [auth 6],
YG [auth 5],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth G],
ZF [auth 6],
ZG [auth 5]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
HE [auth J],
HF [auth 2],
IF [auth 2]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



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DG [auth 6]
KB [auth A]
LB [auth A]
MF [auth 2]
NH [auth 5]
DG [auth 6],
KB [auth A],
LB [auth A],
MF [auth 2],
NH [auth 5],
RD [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT

Query on XAT



Download:Ideal Coordinates CCD File
CG [auth 6],
KF [auth 2],
LH [auth 5],
TG [auth 3]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT

Query on LUT



Download:Ideal Coordinates CCD File
BG [auth 6],
JF [auth 2],
KH [auth 5],
SG [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

Query on BCR



Download:Ideal Coordinates CCD File
CE [auth G]
DE [auth I]
FE [auth J]
GE [auth J]
JE [auth K]
CE [auth G],
DE [auth I],
FE [auth J],
GE [auth J],
JE [auth K],
KD [auth B],
LD [auth B],
LF [auth 2],
MB [auth A],
MD [auth B],
MH [auth 5],
NB [auth A],
ND [auth B],
NE [auth K],
OB [auth A],
OD [auth B],
OE [auth L],
PB [auth A],
PD [auth B],
QB [auth A],
SE [auth L],
TB [auth A],
UB [auth B],
UG [auth 3],
VD [auth F],
VG [auth 3]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN



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

Query on SF4



Download:Ideal Coordinates CCD File
RB [auth A],
SD [auth C],
TD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.13

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 2.0: 2025-04-09
    Changes: Data collection, Database references, Non-polymer description, Structure summary
  • Version 2.1: 2025-09-17
    Changes: Advisory, Data collection, Derived calculations, Structure summary