5XNO

Structure of M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure and assembly mechanism of plant C2S2M2-type PSII-LHCII supercomplex

Su, X.Ma, J.Wei, X.Cao, P.Zhu, D.Chang, W.Liu, Z.Zhang, X.Li, M.

(2017) Science 357: 815-820

  • DOI: https://doi.org/10.1126/science.aan0327
  • Primary Citation of Related Structures:  
    5XNL, 5XNM, 5XNN, 5XNO

  • PubMed Abstract: 

    In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a dimeric core and two strongly bound and two moderately bound LHCIIs (C 2 S 2 M 2 ), is the dominant form in plants acclimated to limited light. Here we report cryo-electron microscopy structures of two forms of C 2 S 2 M 2 (termed stacked and unstacked) from Pisum sativum at 2.7- and 3.2-angstrom resolution, respectively. In each C 2 S 2 M 2 , the moderately bound LHCII assembles specifically with a peripheral antenna complex CP24-CP29 heterodimer and the strongly bound LHCII, to establish a pigment network that facilitates light harvesting at the periphery and energy transfer into the core. The high mobility of peripheral antennae, including the moderately bound LHCII and CP24, provides insights into functional regulation of plant PSII.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), 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 8, chloroplasticA [auth 1],
B [auth 2]
232Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P27490 (Pisum sativum)
Explore P27490 
Go to UniProtKB:  P27490
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27490
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticC [auth 3]243Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q04918 (Pisum sativum)
Explore Q04918 
Go to UniProtKB:  Q04918
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04918
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24D [auth 4]210Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2D0TCJ3 (Pisum sativum)
Explore A0A2D0TCJ3 
Go to UniProtKB:  A0A2D0TCJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D0TCJ3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHL
Query on CHL

Download Ideal Coordinates CCD File 
BA [auth 2]
CA [auth 2]
DA [auth 2]
E [auth 1]
EA [auth 2]
BA [auth 2],
CA [auth 2],
DA [auth 2],
E [auth 1],
EA [auth 2],
FA [auth 2],
I [auth 1],
J [auth 1],
JB [auth 4],
K [auth 1],
L [auth 1],
M [auth 1],
NB [auth 4],
OB [auth 4],
PB [auth 4],
QA [auth 3],
QB [auth 4],
UA [auth 3],
VA [auth 3],
WA [auth 3],
X [auth 2],
XA [auth 3],
YA [auth 3]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AA [auth 2]
AB [auth 3]
BB [auth 3]
CB [auth 3]
DB [auth 3]
AA [auth 2],
AB [auth 3],
BB [auth 3],
CB [auth 3],
DB [auth 3],
F [auth 1],
G [auth 1],
GA [auth 2],
H [auth 1],
HA [auth 2],
IA [auth 2],
JA [auth 2],
KA [auth 2],
KB [auth 4],
LB [auth 4],
MB [auth 4],
N [auth 1],
O [auth 1],
P [auth 1],
Q [auth 1],
R [auth 1],
RA [auth 3],
RB [auth 4],
SA [auth 3],
SB [auth 4],
TA [auth 3],
TB [auth 4],
Y [auth 2],
Z [auth 2],
ZA [auth 3]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LHG
Query on LHG

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IB [auth 3],
PA [auth 2],
W [auth 1],
XB [auth 4]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX
Query on NEX

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HB [auth 3],
OA [auth 2],
V [auth 1]
(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

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GB [auth 3],
NA [auth 2],
U [auth 1],
VB [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

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EB [auth 3]
FB [auth 3]
LA [auth 2]
MA [auth 2]
S [auth 1]
EB [auth 3],
FB [auth 3],
LA [auth 2],
MA [auth 2],
S [auth 1],
T [auth 1],
UB [auth 4]
(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

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WB [auth 4]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Strategic Priority Research Program of CASChinaXDB08020302
The Key Research Program of Frontier Sciences of CASChinaQYZDB-SSW-SMC005
National 973 project grantChina2011CBA00900
National Natural Science Foundation of ChinaChina31570724 and 31270793

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Advisory, Data collection, Other, Structure summary
  • Version 2.0: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary