5ZGH

Cryo-EM structure of the red algal PSI-LHCR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Unique organization of photosystem I-light-harvesting supercomplex revealed by cryo-EM from a red alga

Pi, X.Tian, L.Dai, H.E.Qin, X.Cheng, L.Kuang, T.Sui, S.F.Shen, J.R.

(2018) Proc Natl Acad Sci U S A 115: 4423-4428

  • DOI: https://doi.org/10.1073/pnas.1722482115
  • Primary Citation of Related Structures:  
    5ZGB, 5ZGH

  • PubMed Abstract: 

    Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic algae and higher plants, PSI consists of a core surrounded by variable species and numbers of light-harvesting complex (LHC)I proteins, forming a PSI-LHCI supercomplex. Here, we report cryo-EM structures of PSI-LHCR from the red alga Cyanidioschyzon merolae in two forms, one with three Lhcr subunits attached to the side, similar to that of higher plants, and the other with two additional Lhcr subunits attached to the opposite side, indicating an ancient form of PSI-LHCI. Furthermore, the red algal PSI core showed features of both cyanobacterial and higher plant PSI, suggesting an intermediate type during evolution from prokaryotes to eukaryotes. The structure of PsaO, existing in eukaryotic organisms, was identified in the PSI core and binds three chlorophylls a and may be important in harvesting energy and in mediating energy transfer from LHCII to the PSI core under state-2 conditions. Individual attaching sites of LHCRs with the core subunits were identified, and each Lhcr was found to contain 11 to 13 chlorophylls a and 5 zeaxanthins, which are apparently different from those of LHCs in plant PSI-LHCI. Together, our results reveal unique energy transfer pathways different from those of higher plant PSI-LHCI, its adaptation to the changing environment, and the possible changes of PSI-LHCI during evolution from prokaryotes to eukaryotes.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lhcr1A [auth 1]175Cyanidioschyzon merolae strain 10DMutation(s): 0 
UniProt
Find proteins for M1VKK5 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore M1VKK5 
Go to UniProtKB:  M1VKK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1VKK5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lhcr2B [auth 2]199Cyanidioschyzon merolae strain 10DMutation(s): 0 
UniProt
Find proteins for M1UU36 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore M1UU36 
Go to UniProtKB:  M1UU36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1UU36
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Lhcr3C [auth 3]188Cyanidioschyzon merolae strain 10DMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PsaAD [auth A]748Cyanidioschyzon merolae strain 10DMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q85FY7 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85FY7 
Go to UniProtKB:  Q85FY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85FY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PsaBE [auth B]732Cyanidioschyzon merolae strain 10DMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q85FY6 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85FY6 
Go to UniProtKB:  Q85FY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85FY6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PsaCF [auth C]81Cyanidioschyzon merolae strain 10DMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q85G47 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85G47 
Go to UniProtKB:  Q85G47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85G47
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PsaDG [auth D]139Cyanidioschyzon merolae strain 10DMutation(s): 0 
UniProt
Find proteins for Q85FY0 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85FY0 
Go to UniProtKB:  Q85FY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85FY0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PsaEH [auth E]94Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85FZ1 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85FZ1 
Go to UniProtKB:  Q85FZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85FZ1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PsaFI [auth F]185Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85FS9 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85FS9 
Go to UniProtKB:  Q85FS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85FS9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PsaIJ [auth I]32Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85FQ6 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85FQ6 
Go to UniProtKB:  Q85FQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85FQ6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PsaJK [auth J]38Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85FS8 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85FS8 
Go to UniProtKB:  Q85FS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85FS8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsaKL [auth K]60Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85G51 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85G51 
Go to UniProtKB:  Q85G51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85G51
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PsaLM [auth L]140Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85FP8 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85FP8 
Go to UniProtKB:  Q85FP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85FP8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PsaMN [auth M]29Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85G73 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore Q85G73 
Go to UniProtKB:  Q85G73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ85G73
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PsaO155Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for M1VFJ4 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
Explore M1VFJ4 
Go to UniProtKB:  M1VFJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1VFJ4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
OF [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CL0
Query on CL0

Download Ideal Coordinates CCD File 
QB [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth 1]
AB [auth 3]
AC [auth A]
AD [auth A]
AE [auth B]
AA [auth 1],
AB [auth 3],
AC [auth A],
AD [auth A],
AE [auth B],
AF [auth B],
AG [auth K],
BB [auth 3],
BC [auth A],
BD [auth A],
BE [auth B],
BF [auth B],
BG [auth K],
CB [auth 3],
CC [auth A],
CD [auth A],
CE [auth B],
CF [auth B],
DB [auth 3],
DC [auth A],
DE [auth B],
DF [auth B],
DG [auth L],
EB [auth 3],
EC [auth A],
EE [auth B],
EF [auth B],
FB [auth 3],
FC [auth A],
FE [auth B],
FF [auth B],
FG [auth L],
GA [auth 2],
GB [auth 3],
GC [auth A],
GE [auth B],
GF [auth B],
GG [auth L],
HA [auth 2],
HB [auth 3],
HC [auth A],
HE [auth B],
HG [auth L],
IA [auth 2],
IB [auth 3],
IC [auth A],
IE [auth B],
JA [auth 2],
JB [auth 3],
JC [auth A],
JE [auth B],
KA [auth 2],
KC [auth A],
KE [auth B],
KG [auth O],
LA [auth 2],
LC [auth A],
LE [auth B],
LG [auth O],
MA [auth 2],
MC [auth A],
ME [auth B],
MG [auth O],
NA [auth 2],
NC [auth A],
ND [auth A],
NE [auth B],
NG [auth O],
OA [auth 2],
OC [auth A],
OD [auth A],
OE [auth B],
P [auth 1],
PA [auth 2],
PC [auth A],
PD [auth A],
PE [auth B],
Q [auth 1],
QA [auth 2],
QC [auth A],
QE [auth B],
R [auth 1],
RA [auth 2],
RB [auth A],
RC [auth A],
RD [auth B],
RE [auth B],
S [auth 1],
SA [auth 2],
SB [auth A],
SC [auth A],
SD [auth B],
SE [auth B],
SF [auth F],
T [auth 1],
TB [auth A],
TC [auth A],
TD [auth B],
TE [auth B],
TF [auth F],
U [auth 1],
UB [auth A],
UC [auth A],
UD [auth B],
UE [auth B],
V [auth 1],
VB [auth A],
VC [auth A],
VD [auth B],
VE [auth B],
W [auth 1],
WB [auth A],
WC [auth A],
WD [auth B],
WE [auth B],
WF [auth J],
X [auth 1],
XB [auth A],
XC [auth A],
XD [auth B],
XE [auth B],
Y [auth 1],
YA [auth 3],
YB [auth A],
YC [auth A],
YD [auth B],
YE [auth B],
Z [auth 1],
ZA [auth 3],
ZB [auth A],
ZC [auth A],
ZD [auth B],
ZE [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LHG
Query on LHG

Download Ideal Coordinates CCD File 
ED [auth A],
FD [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
ZEX
Query on ZEX

Download Ideal Coordinates CCD File 
BA [auth 1]
CA [auth 1]
DA [auth 1]
EA [auth 1]
FA [auth 1]
BA [auth 1],
CA [auth 1],
DA [auth 1],
EA [auth 1],
FA [auth 1],
KB [auth 3],
LB [auth 3],
MB [auth 3],
NB [auth 3],
OB [auth 3],
TA [auth 2],
UA [auth 2],
VA [auth 2],
WA [auth 2],
XA [auth 3]
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
C40 H56 O2
YRMDXLDAZBQLBK-WIHRHFSMSA-N
BCR
Query on BCR

Download Ideal Coordinates CCD File 
CG [auth K]
EG [auth L]
GD [auth A]
HD [auth A]
ID [auth A]
CG [auth K],
EG [auth L],
GD [auth A],
HD [auth A],
ID [auth A],
IF [auth B],
IG [auth L],
JD [auth A],
JF [auth B],
JG [auth L],
KD [auth A],
KF [auth B],
LF [auth B],
MD [auth A],
MF [auth B],
NF [auth B],
RF [auth F],
UF [auth F],
VF [auth I],
XF [auth J],
YF [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

Download Ideal Coordinates CCD File 
DD [auth A],
HF [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
3XQ
Query on 3XQ

Download Ideal Coordinates CCD File 
ZF [auth J](2S)-2,3-dihydroxypropyl octadecanoate
C21 H42 O4
VBICKXHEKHSIBG-FQEVSTJZSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
LD [auth A],
PF [auth C],
QF [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
1DO
Query on 1DO

Download Ideal Coordinates CCD File 
PB [auth 3]1-DODECANOL
C12 H26 O
LQZZUXJYWNFBMV-UHFFFAOYSA-N
BGC
Query on BGC

Download Ideal Coordinates CCD File 
QD [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2018-04-11 
  • Deposition Author(s): Pi, X.

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary