7EXT

Cryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002


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 1.0 of the entry. See complete history


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: https://doi.org/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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptide CpcG248Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: cpcG
UniProt
Find proteins for Q05238 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore Q05238 
Go to UniProtKB:  Q05238
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05238
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin subunit alpha162Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: cpcA
UniProt
Find proteins for P03943 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore P03943 
Go to UniProtKB:  P03943
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03943
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin subunit beta172Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: cpcB
UniProt
Find proteins for P03944 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore P03944 
Go to UniProtKB:  P03944
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03944
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod290Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: cpcC
UniProt
Find proteins for Q05237 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore Q05237 
Go to UniProtKB:  Q05237
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05237
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobiliprotein ApcECB [auth 03],
DB [auth 13]
886Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: apcE
EC: 4
UniProt
Find proteins for O68973 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore O68973 
Go to UniProtKB:  O68973
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68973
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core67Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: apcC
UniProt
Find proteins for O68971 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore O68971 
Go to UniProtKB:  O68971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68971
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin alpha subunit161Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: apcA
UniProt
Find proteins for B1XQM2 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore B1XQM2 
Go to UniProtKB:  B1XQM2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1XQM2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin beta subunit161Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: apcB
UniProt
Find proteins for O68970 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore O68970 
Go to UniProtKB:  O68970
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68970
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin subunit beta-18GC [auth g3],
QB [auth Q3]
169Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: apcF
UniProt
Find proteins for O68967 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore O68967 
Go to UniProtKB:  O68967
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68967
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin subunit alpha-BMC [auth m3],
VB [auth V3]
161Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: apcD
UniProt
Find proteins for O68966 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore O68966 
Go to UniProtKB:  O68966
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68966
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
AJ [auth P1]
AK [auth I2]
AL [auth 03]
AM [auth d3]
AN [auth E4]
AJ [auth P1],
AK [auth I2],
AL [auth 03],
AM [auth d3],
AN [auth E4],
AO [auth W4],
AP [auth P5],
AQ [auth I6],
AR [auth A7],
AS [auth D8],
AT [auth V8],
BJ [auth P1],
BK [auth I2],
BL [auth 03],
BM [auth e3],
BN [auth E4],
BO [auth X4],
BP [auth P5],
BQ [auth I6],
BR [auth B7],
BS [auth E8],
BT [auth V8],
CJ [auth Q1],
CK [auth I2],
CL [auth 13],
CM [auth f3],
CN [auth F4],
CO [auth X4],
CP [auth Q5],
CQ [auth J6],
CR [auth C7],
CS [auth E8],
CT [auth W8],
DJ [auth R1],
DK [auth K2],
DL [auth 13],
DM [auth g3],
DN [auth G4],
DO [auth Y4],
DP [auth R5],
DQ [auth K6],
DR [auth D7],
DS [auth E8],
DT [auth X8],
EJ [auth R1],
EK [auth K2],
EL [auth 13],
EM [auth i3],
EN [auth G4],
EO [auth Z4],
EP [auth R5],
EQ [auth K6],
ER [auth E7],
ES [auth F8],
ET [auth X8],
FJ [auth S1],
FK [auth K2],
FL [auth 13],
FM [auth j3],
FN [auth I4],
FO [auth Z4],
FP [auth S5],
FQ [auth L6],
FR [auth F7],
FS [auth G8],
FT [auth Y8],
GI [auth A1],
GJ [auth T1],
GK [auth M2],
GL [auth G3],
GM [auth k3],
GN [auth I4],
GO [auth A5],
GP [auth T5],
GQ [auth M6],
GR [auth H7],
GS [auth G8],
GT [auth Z8],
HI [auth A1],
HJ [auth U1],
HK [auth M2],
HL [auth H3],
HM [auth l3],
HN [auth I4],
HO [auth A5],
HP [auth U5],
HQ [auth M6],
HR [auth I7],
HS [auth I8],
HT [auth Z8],
II [auth B1],
IJ [auth U1],
IK [auth N2],
IL [auth I3],
IM [auth m3],
IN [auth K4],
IO [auth B5],
IP [auth U5],
IQ [auth N6],
IR [auth J7],
IS [auth I8],
JI [auth C1],
JJ [auth V1],
JK [auth N2],
JL [auth J3],
JM [auth n3],
JN [auth K4],
JO [auth C5],
JP [auth V5],
JQ [auth N6],
JR [auth K7],
JS [auth I8],
KI [auth C1],
KJ [auth V1],
KK [auth P2],
KL [auth K3],
KM [auth o3],
KN [auth L4],
KO [auth C5],
KP [auth V5],
KQ [auth O6],
KR [auth L7],
KS [auth K8],
LI [auth D1],
LJ [auth X1],
LK [auth P2],
LL [auth M3],
LM [auth p3],
LN [auth L4],
LO [auth D5],
LP [auth X5],
LQ [auth P6],
LR [auth M7],
LS [auth K8],
MI [auth F1],
MJ [auth X1],
MK [auth Q2],
ML [auth N3],
MM [auth q3],
MN [auth M4],
MO [auth F5],
MP [auth X5],
MQ [auth P6],
MR [auth O7],
MS [auth L8],
NI [auth G1],
NJ [auth X1],
NK [auth R2],
NL [auth O3],
NM [auth r3],
NN [auth M4],
NO [auth G5],
NP [auth X5],
NQ [auth Q6],
NR [auth P7],
NS [auth L8],
OI [auth G1],
OJ [auth Z1],
OK [auth S2],
OL [auth P3],
OM [auth s3],
ON [auth N4],
OO [auth G5],
OP [auth Z5],
OQ [auth R6],
OR [auth Q7],
OS [auth M8],
PI [auth H1],
PJ [auth Z1],
PK [auth T2],
PL [auth Q3],
PM [auth t3],
PN [auth O4],
PO [auth H5],
PP [auth Z5],
PQ [auth R6],
PR [auth R7],
PS [auth M8],
QI [auth I1],
QJ [auth A2],
QK [auth T2],
QL [auth R3],
QM [auth u3],
QN [auth P4],
QO [auth I5],
QP [auth A6],
QQ [auth T6],
QR [auth S7],
QS [auth N8],
RI [auth I1],
RJ [auth B2],
RK [auth V2],
RL [auth S3],
RM [auth v3],
RN [auth P4],
RO [auth I5],
RP [auth B6],
RQ [auth U6],
RR [auth T7],
RS [auth O8],
SI [auth J1],
SJ [auth C2],
SK [auth V2],
SL [auth T3],
SM [auth w3],
SN [auth P4],
SO [auth J5],
SP [auth C6],
SQ [auth V6],
SR [auth V7],
SS [auth P8],
TI [auth K1],
TJ [auth C2],
TK [auth W2],
TL [auth U3],
TM [auth x3],
TN [auth R4],
TO [auth K5],
TP [auth C6],
TQ [auth V6],
TR [auth W7],
TS [auth P8],
UI [auth K1],
UJ [auth D2],
UK [auth X2],
UL [auth V3],
UM [auth y3],
UN [auth S4],
UO [auth K5],
UP [auth C6],
UQ [auth W6],
UR [auth X7],
US [auth P8],
VI [auth L1],
VJ [auth E2],
VK [auth X2],
VL [auth W3],
VM [auth z3],
VN [auth T4],
VO [auth L5],
VP [auth E6],
VQ [auth X6],
VR [auth Y7],
VS [auth R8],
WI [auth M1],
WJ [auth E2],
WK [auth X2],
WL [auth X3],
WM [auth A4],
WN [auth T4],
WO [auth M5],
WP [auth E6],
WQ [auth X6],
WR [auth Z7],
WS [auth S8],
XI [auth M1],
XJ [auth E2],
XK [auth Z2],
XL [auth Z3],
XM [auth C4],
XN [auth U4],
XO [auth M5],
XP [auth F6],
XQ [auth Y6],
XR [auth a7],
XS [auth T8],
YI [auth N1],
YJ [auth G2],
YK [auth Z2],
YL [auth b3],
YM [auth D4],
YN [auth V4],
YO [auth N5],
YP [auth G6],
YQ [auth Z6],
YR [auth A8],
YS [auth T8],
ZI [auth O1],
ZJ [auth H2],
ZK [auth Z2],
ZL [auth c3],
ZM [auth E4],
ZN [auth V4],
ZO [auth O5],
ZP [auth H6],
ZQ [auth Z6],
ZR [auth C8],
ZS [auth U8]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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