6KAC

Cryo-EM structure of the C2S2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insight into light harvesting for photosystem II in green algae.

Sheng, X.Watanabe, A.Li, A.Kim, E.Song, C.Murata, K.Song, D.Minagawa, J.Liu, Z.

(2019) Nat.Plants 5: 1320-1330

  • DOI: 10.1038/s41477-019-0543-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Green algae and plants rely on light-harvesting complex II (LHCII) to collect photon energy for oxygenic photosynthesis. In Chlamydomonas reinhardtii, LHCII molecules associate with photosystem II (PSII) to form various supercomplexes, including the ...

    Green algae and plants rely on light-harvesting complex II (LHCII) to collect photon energy for oxygenic photosynthesis. In Chlamydomonas reinhardtii, LHCII molecules associate with photosystem II (PSII) to form various supercomplexes, including the C 2 S 2 M 2 L 2 type, which is the largest PSII-LHCII supercomplex in algae and plants that is presently known. Here, we report high-resolution cryo-electron microscopy (cryo-EM) maps and structural models of the C 2 S 2 M 2 L 2 and C 2 S 2 supercomplexes from C. reinhardtii. The C 2 S 2 supercomplex contains an LhcbM1-LhcbM2/7-LhcbM3 heterotrimer in the strongly associated LHCII, and the LhcbM1 subunit assembles with CP43 through two interfacial galactolipid molecules. The loosely and moderately associated LHCII trimers interact closely with the minor antenna complex CP29 to form an intricate subcomplex bound to CP47 in the C 2 S 2 M 2 L 2 supercomplex. A notable direct pathway is established for energy transfer from the loosely associated LHCII to the PSII reaction centre, as well as several indirect routes. Structure-based computational analysis on the excitation energy transfer within the two supercomplexes provides detailed mechanistic insights into the light-harvesting process in green algae.


    Organizational Affiliation

    Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan. minagawa@nibb.ac.jp.,University of Chinese Academy of Sciences, Beijing, China. liuzf@ibp.ac.cn.,University of Chinese Academy of Sciences, Beijing, China.,Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan. minagawa@nibb.ac.jp.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan.,National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. liuzf@ibp.ac.cn.,Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein D1
A, a
352Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbA
EC: 1.10.3.9
Find proteins for P07753 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P07753
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center protein
B, b
508Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbB
Find proteins for P37255 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P37255
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
V, v
33Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: ycf12
Find proteins for P50370 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P50370
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 reaction center protein
C, c
461Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbC
Find proteins for P10898 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P10898
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
D, d
352Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Find proteins for P06007 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P06007
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
82Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbE
Find proteins for P48268 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P48268
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
44Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbF
Find proteins for Q08363 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q08363
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
88Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbH
Find proteins for P22666 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P22666
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
37Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbI
Find proteins for P59763 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P59763
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
42Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbJ
Find proteins for O19930 (Chlamydomonas reinhardtii)
Go to UniProtKB:  O19930
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
46Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbK
Find proteins for P18263 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P18263
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
38Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbL
Find proteins for P32974 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P32974
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein M
M, m
34Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbM
Find proteins for P92277 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P92277
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Oxygen-evolving enhancer protein 1, chloroplastic
O, o
291Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSBO
Find proteins for P12853 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P12853
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Oxygen-evolving enhancer protein 2, chloroplastic
P, p
245Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSBP
Find proteins for P11471 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P11471
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Oxygen-evolving enhancer protein 3, chloroplastic
Q, q
199Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSBQ
Find proteins for P12852 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P12852
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
31Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbT (ycf8)
Find proteins for P37256 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P37256
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center W protein, chloroplastic
W, w
115Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbW
Find proteins for Q9SPI9 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q9SPI9
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
4.1 kDa photosystem II subunit
X, x
101Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSBX
Find proteins for A8I846 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8I846
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
62Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psbZ (ycf9)
Find proteins for P92276 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P92276
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein, chloroplastic
N, n
257Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcII-1.3 (LHCBM3)
Find proteins for Q93WL4 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q93WL4
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein, chloroplastic
G, g
249Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcII-3 (LHCBM2)
Find proteins for Q93WE0 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q93WE0
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein CP29
R, r
280Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: Lhcb4
Find proteins for Q93WD2 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q93WD2
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein, chloroplastic
S, s
289Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: lhcb5 (LHCB5)
Find proteins for Q9FEK6 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q9FEK6
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein, chloroplastic
Y, y
256Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcII-4 (Lhcb)
Find proteins for Q93VE0 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q93VE0
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Predicted protein
U, u
178Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CPLD45
Find proteins for A8I5A0 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8I5A0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
10 kDa photosystem II polypeptide PsbR (potential)
1, 0
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Unindentified Stromal Protein (USP)
4, 3
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 18 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

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a, A, B, b
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
LUT
Query on LUT

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g, G, n, N, S, s, Y, y
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
(3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL, LUTEIN
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
 Ligand Interaction
CLA
Query on CLA

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a, A, B, b, C, c, D, d, g, G, N, n, r, R, s, S, y, Y
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

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D, d
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
PLASTOQUINONE 9
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
XAT
Query on XAT

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G, g, n, N, R, r, Y, y
(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
VIOLAXANTHIN
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
 Ligand Interaction
OEX
Query on OEX

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a, A
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, a
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DGD
Query on DGD

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C, c
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

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A, a, b, B, c, C, d, D, h, H
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCT
Query on BCT

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d, D
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
NEX
Query on NEX

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g, G, N, n, R, r, s, S, y, Y
(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
(3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL, 9'-CIS-NEOXANTHIN
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
 Ligand Interaction
HEM
Query on HEM

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f, F
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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A, a, B, b, C, c, d, D, h, H
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

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A, a
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
FE2
Query on FE2

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A, a
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CHL
Query on CHL

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G, g, N, n, R, r, s, S, Y, y
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
 Ligand Interaction
LHG
Query on LHG

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c, C, D, d, G, g, l, L, N, n, s, S, y, Y
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
LMU
Query on LMU

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y, Y, z, Z
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFA0503702
Chinese Academy of SciencesChinaXDB27020106
Chinese Academy of SciencesChinaXDB08020302
Chinese Academy of SciencesChinaQYZDB-SSW-SMC005
National Natural Science Foundation of ChinaChina31670749

Revision History 

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-11-20
    Type: Advisory, Derived calculations
  • Version 1.2: 2019-12-11
    Type: Database references
  • Version 1.3: 2019-12-25
    Type: Database references