5ZJI

Structure of photosystem I supercomplex with light-harvesting complexes I and II


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the maize photosystem I supercomplex with light-harvesting complexes I and II.

Pan, X.Ma, J.Su, X.Cao, P.Chang, W.Liu, Z.Zhang, X.Li, M.

(2018) Science 360: 1109-1113

  • DOI: https://doi.org/10.1126/science.aat1156
  • Primary Citation of Related Structures:  
    5ZJI

  • PubMed Abstract: 

    Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light-harvesting complex II (LHCII), is phosphorylated and forms a supercomplex with PSI core and the PSI antenna, light-harvesting complex I (LHCI). Both LHCI and LHCII then transfer excitation energy to the PSI core. We report the structure of maize PSI-LHCI-LHCII solved by cryo-electron microscopy, revealing the recognition site between LHCII and PSI. The PSI subunits PsaN and PsaO are observed at the PSI-LHCI interface and the PSI-LHCII interface, respectively. Each subunit relays excitation to PSI core through a pair of chlorophyll molecules, thus revealing previously unseen paths for energy transfer between the antennas and the PSI core.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth 1]245Zea maysMutation(s): 0 
UniProt
Find proteins for B6SSN3 (Zea mays)
Explore B6SSN3 
Go to UniProtKB:  B6SSN3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6SSN3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticB [auth 2]270Zea maysMutation(s): 0 
UniProt
Find proteins for B6T892 (Zea mays)
Explore B6T892 
Go to UniProtKB:  B6T892
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6T892
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticC [auth 3]267Zea maysMutation(s): 0 
UniProt
Find proteins for B6SUC4 (Zea mays)
Explore B6SUC4 
Go to UniProtKB:  B6SUC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6SUC4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticD [auth 4]252Zea maysMutation(s): 0 
UniProt
Find proteins for B6SZR1 (Zea mays)
Explore B6SZR1 
Go to UniProtKB:  B6SZR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6SZR1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]750Zea maysMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P04966 (Zea mays)
Explore P04966 
Go to UniProtKB:  P04966
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04966
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]734Zea mays subsp. maysMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A059Q6U2 (Zea mays subsp. mays)
Explore A0A059Q6U2 
Go to UniProtKB:  A0A059Q6U2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059Q6U2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
photosystem I subunit VIIG [auth C]81Zea mays subsp. maysMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A172FJJ4 (Zea mays subsp. huehuetenangensis)
Explore A0A172FJJ4 
Go to UniProtKB:  A0A172FJJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A172FJJ4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIH [auth D]199Zea maysMutation(s): 0 
UniProt
Find proteins for B4FAW3 (Zea mays)
Explore B4FAW3 
Go to UniProtKB:  B4FAW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4FAW3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV AI [auth E]136Zea maysMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1D6HY75 (Zea mays)
Explore A0A1D6HY75 
Go to UniProtKB:  A0A1D6HY75
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D6HY75
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIJ [auth F]225Zea maysMutation(s): 0 
UniProt
Find proteins for B6SRI3 (Zea mays)
Explore B6SRI3 
Go to UniProtKB:  B6SRI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6SRI3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VK [auth G]145Zea maysMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6U534 (Zea mays)
Explore B6U534 
Go to UniProtKB:  B6U534
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6U534
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplasticL [auth H]142Zea maysMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O65101 (Zea mays)
Explore O65101 
Go to UniProtKB:  O65101
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO65101
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]36Zea maysMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P30980 (Zea mays)
Explore P30980 
Go to UniProtKB:  P30980
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30980
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]42Zea maysMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P62596 (Zea mays)
Explore P62596 
Go to UniProtKB:  P62596
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62596
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaKO [auth K]134Zea maysMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6TR16 (Zea mays)
Explore B6TR16 
Go to UniProtKB:  B6TR16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6TR16
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIP [auth L]211Zea maysMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6STT2 (Zea mays)
Explore B6STT2 
Go to UniProtKB:  B6STT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6STT2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
16kDa membrane proteinQ [auth O]127Zea maysMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6SQZ7 (Zea mays)
Explore B6SQZ7 
Go to UniProtKB:  B6SQZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6SQZ7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit NR [auth N]145Zea maysMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6TXS5 (Zea mays)
Explore B6TXS5 
Go to UniProtKB:  B6TXS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6TXS5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 1, chloroplasticS [auth X],
U [auth Z]
232Zea maysMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12329 (Zea mays)
Explore P12329 
Go to UniProtKB:  P12329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12329
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticT [auth Y]228Zea maysMutation(s): 0 
UniProt
Find proteins for B6SZT9 (Zea mays)
Explore B6SZT9 
Go to UniProtKB:  B6SZT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6SZT9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
KH [auth J],
TG [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

Download Ideal Coordinates CCD File 
AA [auth 1]
AJ [auth Y]
BI [auth X]
BJ [auth Y]
CB [auth 2]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0
Query on CL0

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

Download Ideal Coordinates CCD File 
AB [auth 2]
AC [auth 4]
AD [auth A]
AE [auth A]
AF [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

Download Ideal Coordinates CCD File 
CH [auth G],
HB [auth 2],
OA [auth 1],
QC [auth 4],
RC [auth 4]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
FK [auth Z]
GB [auth 2]
LE [auth A]
MA [auth 1]
ME [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX
Query on NEX

Download Ideal Coordinates CCD File 
EK [auth Z],
LJ [auth Y],
RI [auth X]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
XAT
Query on XAT

Download Ideal Coordinates CCD File 
BK [auth Z]
EB [auth 2]
IJ [auth Y]
KA [auth 1]
OC [auth 4]
(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 
CK [auth Z]
DB [auth 2]
DK [auth Z]
JA [auth 1]
JJ [auth Y]
(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 
AH [auth F]
FB [auth 2]
FH [auth G]
HH [auth I]
JH [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

Download Ideal Coordinates CCD File 
SG [auth B],
VE [auth A]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
Query on PQN

Download Ideal Coordinates CCD File 
JE [auth A],
LG [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
SE [auth A],
VG [auth C],
WG [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
T [auth Y]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the National Key R&D Program of ChinaChina2017YFA0503702
the National Key R&D Program of ChinaChina2017YFA0504700
the National Key R&D Program of ChinaChina2016YFA0502900
the Strategic Priority Research Program of CASChinaXDB08020302
the Strategic Priority Research Program of CASChinaXDB08030204
the Key Research Program of Frontier Sciences of CASChinaQYZDB-SSW-SMC005
National Natural Science Foundation of ChinaChina31770778
National Natural Science Foundation of ChinaChina31700649
National Natural Science Foundation of ChinaChina31600609
National Thousand (Young) Talents ProgramChina--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Advisory, Data collection
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other