7EYD

Cryo-EM structure of cyanobacterial phycobilisome from Anabaena sp. PCC 7120


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural insight into the mechanism of energy transfer in cyanobacterial phycobilisomes.

Zheng, L.Zheng, Z.Li, X.Wang, G.Zhang, K.Wei, P.Zhao, J.Gao, N.

(2021) Nat Commun 12: 5497-5497

  • DOI: 10.1038/s41467-021-25813-y
  • Primary Citation of Related Structures:  
    7EXT, 7EYD

  • PubMed Abstract: 
  • Phycobilisomes (PBS) are the major light-harvesting machineries for photosynthesis in cyanobacteria and red algae and they have a hierarchical structure of a core and peripheral rods, with both consisting of phycobiliproteins and linker proteins. Here we report the cryo-EM structures of PBS from two cyanobacterial species, Anabaena 7120 and Synechococcus 7002 ...

    Phycobilisomes (PBS) are the major light-harvesting machineries for photosynthesis in cyanobacteria and red algae and they have a hierarchical structure of a core and peripheral rods, with both consisting of phycobiliproteins and linker proteins. Here we report the cryo-EM structures of PBS from two cyanobacterial species, Anabaena 7120 and Synechococcus 7002. Both PBS are hemidiscoidal in shape and share a common triangular core structure. While the Anabaena PBS has two additional hexamers in the core linked by the 4th linker domain of ApcE (L CM ). The PBS structures predict that, compared with the PBS from red algae, the cyanobacterial PBS could have more direct routes for energy transfer to ApcD. Structure-based systematic mutagenesis analysis of the chromophore environment of ApcD and ApcF subunits reveals that aromatic residues are critical to excitation energy transfer (EET). The structures also suggest that the linker protein could actively participate in the process of EET in both rods and the cores. These results provide insights into the organization of chromophores and the mechanisms of EET within cyanobacterial PBS.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, National Biomedical Imaging Center, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China. gaon@pku.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptide CpcG2A [auth A1],
OB [auth A4]
247Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: cpcG2alr0535
UniProt
Find proteins for P29987 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
C-phycocyanin alpha subunit163Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: cpcAalr0529
UniProt
Find proteins for P07121 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
C-phycocyanin beta subunit173Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: cpcBalr0528
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod286Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: cpcCalr0530
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptide CpcG4AA [auth A2],
OC [auth A5],
OD [auth A6],
CJ [auth AA]
253Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: cpcG4alr0537
UniProt
Find proteins for P29989 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptide CpcG1AB [auth A3],
OE [auth A7]
279Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: cpcG1alr0534
UniProt
Find proteins for P29986 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Allophycocyanin subunit alpha 1161Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: apcA1alr0021
UniProt
Find proteins for P80555 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Allophycocyanin subunit beta162Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: apcBalr0022
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core68Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: apcCasr0023
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobiliprotein ApcEXG [auth 09],
YG [auth 19]
1,132Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: apcEalr0020
EC: 4
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Allophycocyanin subunit beta-18SH [auth Q9],
II [auth g9]
169Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: apcFall2327
UniProt
Find proteins for Q7A2D6 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Allophycocyanin subunit alpha-BXH [auth V9],
OI [auth m9]
161Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: apcDall3653
UniProt
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
AL [auth S1],
AM [auth K2],
AN [auth E3],
AO [auth J4],
AP [auth A5],
AL [auth S1],
AM [auth K2],
AN [auth E3],
AO [auth J4],
AP [auth A5],
AQ [auth V5],
AR [auth N6],
AS [auth G7],
AT [auth S8],
AU [auth 09],
AV [auth T9],
AW [auth y9],
AX [auth SA],
BL [auth T1],
BM [auth L2],
BN [auth E3],
BO [auth K4],
BP [auth A5],
BQ [auth V5],
BR [auth O6],
BS [auth H7],
BT [auth T8],
BU [auth 19],
BV [auth U9],
BW [auth z9],
BX [auth TA],
CK [auth B1],
CL [auth T1],
CM [auth M2],
CN [auth F3],
CO [auth K4],
CP [auth B5],
CQ [auth W5],
CR [auth P6],
CS [auth I7],
CT [auth V8],
CU [auth 19],
CV [auth V9],
CW [auth AA],
CX [auth TA],
DK [auth C1],
DL [auth U1],
DM [auth N2],
DN [auth G3],
DO [auth L4],
DP [auth C5],
DQ [auth X5],
DR [auth Q6],
DS [auth I7],
DT [auth W8],
DU [auth 19],
DV [auth X9],
DW [auth AA],
DX [auth UA],
EK [auth C1],
EL [auth V1],
EM [auth N2],
EN [auth G3],
EO [auth M4],
EP [auth D5],
EQ [auth X5],
ER [auth R6],
ES [auth J7],
ET [auth X8],
EU [auth 19],
EV [auth Z9],
EW [auth AA],
EX [auth VA],
FK [auth D1],
FL [auth V1],
FM [auth O2],
FN [auth H3],
FO [auth M4],
FP [auth E5],
FQ [auth Y5],
FR [auth S6],
FS [auth K7],
FT [auth Y8],
FU [auth 19],
FV [auth b9],
FW [auth AA],
FX [auth VA],
GK [auth E1],
GL [auth W1],
GM [auth P2],
GN [auth I3],
GO [auth O4],
GP [auth E5],
GQ [auth Z5],
GR [auth T6],
GS [auth K7],
GT [auth Z8],
GU [auth 29],
GV [auth c9],
GW [auth CA],
GX [auth WA],
HK [auth E1],
HL [auth X1],
HM [auth Q2],
HN [auth I3],
HO [auth P4],
HP [auth G5],
HQ [auth Z5],
HR [auth U6],
HS [auth L7],
HT [auth b8],
HU [auth 39],
HV [auth d9],
HW [auth DA],
HX [auth XA],
IK [auth F1],
IL [auth X1],
IM [auth R2],
IN [auth J3],
IO [auth P4],
IP [auth I5],
IQ [auth B6],
IR [auth U6],
IS [auth M7],
IT [auth c8],
IU [auth A9],
IV [auth e9],
IW [auth EA],
IX [auth XA],
JK [auth G1],
JL [auth Y1],
JM [auth S2],
JN [auth K3],
JO [auth Q4],
JP [auth I5],
JQ [auth C6],
JR [auth V6],
JS [auth N7],
JT [auth d8],
JU [auth B9],
JV [auth f9],
JW [auth EA],
JX [auth YA],
KK [auth G1],
KL [auth Z1],
KM [auth T2],
KN [auth K3],
KO [auth Q4],
KP [auth J5],
KQ [auth C6],
KR [auth V6],
KS [auth A8],
KT [auth e8],
KU [auth C9],
KV [auth g9],
KW [auth GA],
KX [auth ZA],
LK [auth H1],
LL [auth Z1],
LM [auth U2],
LN [auth L3],
LO [auth R4],
LP [auth K5],
LQ [auth D6],
LR [auth W6],
LS [auth B8],
LT [auth f8],
LU [auth D9],
LV [auth i9],
LW [auth GA],
LX [auth ZA],
MK [auth I1],
ML [auth B2],
MM [auth U2],
MN [auth M3],
MO [auth S4],
MP [auth L5],
MQ [auth E6],
MR [auth W6],
MS [auth C8],
MT [auth g8],
MU [auth E9],
MV [auth j9],
MW [auth IA],
NK [auth I1],
NL [auth C2],
NM [auth V2],
NN [auth N3],
NO [auth T4],
NP [auth M5],
NQ [auth E6],
NR [auth X6],
NS [auth D8],
NT [auth h8],
NU [auth F9],
NV [auth k9],
NW [auth IA],
OK [auth J1],
OL [auth C2],
OM [auth V2],
ON [auth B4],
OO [auth T4],
OP [auth M5],
OQ [auth F6],
OR [auth X6],
OS [auth E8],
OT [auth j8],
OU [auth G9],
OV [auth l9],
OW [auth JA],
PK [auth K1],
PL [auth D2],
PM [auth W2],
PN [auth C4],
PO [auth U4],
PP [auth M5],
PQ [auth G6],
PR [auth Y6],
PS [auth F8],
PT [auth k8],
PU [auth H9],
PV [auth m9],
PW [auth KA],
QK [auth K1],
QL [auth E2],
QM [auth W2],
QN [auth C4],
QO [auth V4],
QP [auth N5],
QQ [auth G6],
QR [auth Z6],
QS [auth H8],
QT [auth l8],
QU [auth I9],
QV [auth o9],
QW [auth LA],
RK [auth L1],
RL [auth E2],
RM [auth W2],
RN [auth D4],
RO [auth V4],
RP [auth O5],
RQ [auth H6],
RR [auth Z6],
RS [auth I8],
RT [auth n8],
RU [auth J9],
RV [auth p9],
RW [auth MA],
SK [auth M1],
SL [auth F2],
SM [auth X2],
SN [auth E4],
SO [auth W4],
SP [auth P5],
SQ [auth I6],
SR [auth A7],
SS [auth J8],
ST [auth o8],
SU [auth K9],
SV [auth q9],
SW [auth MA],
TK [auth M1],
TL [auth G2],
TM [auth Y2],
TN [auth E4],
TO [auth X4],
TP [auth P5],
TQ [auth I6],
TR [auth B7],
TS [auth K8],
TT [auth p8],
TU [auth L9],
TV [auth r9],
TW [auth MA],
UK [auth O1],
UL [auth G2],
UM [auth Z2],
UN [auth F4],
UO [auth X4],
UP [auth P5],
UQ [auth J6],
UR [auth C7],
US [auth L8],
UT [auth q8],
UU [auth N9],
UV [auth s9],
UW [auth NA],
VK [auth P1],
VL [auth H2],
VM [auth Z2],
VN [auth G4],
VO [auth Y4],
VP [auth R5],
VQ [auth K6],
VR [auth D7],
VS [auth M8],
VT [auth r8],
VU [auth O9],
VV [auth t9],
VW [auth OA],
WK [auth P1],
WL [auth I2],
WM [auth A3],
WN [auth G4],
WO [auth Z4],
WP [auth S5],
WQ [auth K6],
WR [auth E7],
WS [auth O8],
WT [auth s8],
WU [auth P9],
WV [auth u9],
WW [auth PA],
XK [auth Q1],
XL [auth I2],
XM [auth B3],
XN [auth H4],
XO [auth Z4],
XP [auth T5],
XQ [auth L6],
XR [auth E7],
XS [auth P8],
XT [auth t8],
XU [auth Q9],
XV [auth v9],
XW [auth PA],
YK [auth Q1],
YL [auth J2],
YM [auth C3],
YN [auth I4],
YO [auth A5],
YP [auth T5],
YQ [auth M6],
YR [auth F7],
YS [auth Q8],
YT [auth 09],
YU [auth R9],
YV [auth w9],
YW [auth PA],
ZK [auth R1],
ZL [auth K2],
ZM [auth D3],
ZN [auth I4],
ZO [auth A5],
ZP [auth U5],
ZQ [auth N6],
ZR [auth G7],
ZS [auth R8],
ZT [auth 09],
ZU [auth S9],
ZV [auth x9],
ZW [auth RA]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)--

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release