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- PDB-7ext: Cryo-EM structure of cyanobacterial phycobilisome from Synechococ... -

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Entry
Database: PDB / ID: 7ext
TitleCryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002
Components
  • (Allophycocyanin ...) x 4
  • (C-phycocyanin subunit ...) x 2
  • (Phycobilisome ...) x 3
  • Phycobiliprotein ApcE
KeywordsPHOTOSYNTHESIS / Phycobilisome / Synechococcus sp. PCC 7002 / Cryo-EM
Function / homology
Function and homology information


Lyases / : / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit ...Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Allophycocyanin alpha subunit / Allophycocyanin subunit alpha-B / Allophycocyanin subunit beta-18 / Allophycocyanin beta subunit / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Phycobiliprotein ApcE / C-phycocyanin subunit alpha / C-phycocyanin subunit beta / Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome rod-core linker polypeptide CpcG
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7002 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZheng, L. / Zheng, Z. / Li, X. / Wang, G. / Zhang, K. / Wei, P. / Zhao, J. / Gao, N.
Funding support1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)
CitationJournal: Nat Commun / Year: 2021
Title: Structural insight into the mechanism of energy transfer in cyanobacterial phycobilisomes.
Authors: Lvqin Zheng / Zhenggao Zheng / Xiying Li / Guopeng Wang / Kun Zhang / Peijun Wei / Jindong Zhao / Ning Gao /
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 ...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). 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.
History
DepositionMay 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
A1: Phycobilisome rod-core linker polypeptide CpcG
B1: C-phycocyanin subunit alpha
C1: C-phycocyanin subunit beta
D1: C-phycocyanin subunit alpha
E1: C-phycocyanin subunit beta
F1: C-phycocyanin subunit alpha
G1: C-phycocyanin subunit beta
H1: C-phycocyanin subunit alpha
I1: C-phycocyanin subunit beta
J1: C-phycocyanin subunit alpha
K1: C-phycocyanin subunit beta
L1: C-phycocyanin subunit alpha
M1: C-phycocyanin subunit beta
N1: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
O1: C-phycocyanin subunit alpha
P1: C-phycocyanin subunit beta
Q1: C-phycocyanin subunit alpha
R1: C-phycocyanin subunit beta
S1: C-phycocyanin subunit alpha
T1: C-phycocyanin subunit beta
U1: C-phycocyanin subunit alpha
V1: C-phycocyanin subunit beta
W1: C-phycocyanin subunit alpha
X1: C-phycocyanin subunit beta
Y1: C-phycocyanin subunit alpha
Z1: C-phycocyanin subunit beta
a1: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
A2: Phycobilisome rod-core linker polypeptide CpcG
B2: C-phycocyanin subunit alpha
C2: C-phycocyanin subunit beta
D2: C-phycocyanin subunit alpha
E2: C-phycocyanin subunit beta
F2: C-phycocyanin subunit alpha
G2: C-phycocyanin subunit beta
H2: C-phycocyanin subunit alpha
I2: C-phycocyanin subunit beta
J2: C-phycocyanin subunit alpha
K2: C-phycocyanin subunit beta
L2: C-phycocyanin subunit alpha
M2: C-phycocyanin subunit beta
N2: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
O2: C-phycocyanin subunit alpha
P2: C-phycocyanin subunit beta
Q2: C-phycocyanin subunit alpha
R2: C-phycocyanin subunit beta
S2: C-phycocyanin subunit alpha
T2: C-phycocyanin subunit beta
U2: C-phycocyanin subunit alpha
V2: C-phycocyanin subunit beta
W2: C-phycocyanin subunit alpha
X2: C-phycocyanin subunit beta
Y2: C-phycocyanin subunit alpha
Z2: C-phycocyanin subunit beta
a2: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
03: Phycobiliprotein ApcE
13: Phycobiliprotein ApcE
23: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
33: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
G3: Allophycocyanin alpha subunit
H3: Allophycocyanin beta subunit
I3: Allophycocyanin alpha subunit
J3: Allophycocyanin beta subunit
K3: Allophycocyanin alpha subunit
L3: Allophycocyanin beta subunit
M3: Allophycocyanin beta subunit
N3: Allophycocyanin alpha subunit
O3: Allophycocyanin beta subunit
P3: Allophycocyanin alpha subunit
Q3: Allophycocyanin subunit beta-18
R3: Allophycocyanin alpha subunit
S3: Allophycocyanin beta subunit
T3: Allophycocyanin alpha subunit
U3: Allophycocyanin beta subunit
V3: Allophycocyanin subunit alpha-B
W3: Allophycocyanin beta subunit
X3: Allophycocyanin alpha subunit
Y3: Allophycocyanin beta subunit
Z3: Allophycocyanin alpha subunit
a3: Allophycocyanin beta subunit
b3: Allophycocyanin alpha subunit
c3: Allophycocyanin beta subunit
d3: Allophycocyanin alpha subunit
e3: Allophycocyanin beta subunit
f3: Allophycocyanin alpha subunit
g3: Allophycocyanin subunit beta-18
h3: Allophycocyanin beta subunit
i3: Allophycocyanin alpha subunit
j3: Allophycocyanin beta subunit
k3: Allophycocyanin alpha subunit
l3: Allophycocyanin beta subunit
m3: Allophycocyanin subunit alpha-B
n3: Allophycocyanin beta subunit
o3: Allophycocyanin alpha subunit
p3: Allophycocyanin beta subunit
q3: Allophycocyanin alpha subunit
r3: Allophycocyanin beta subunit
s3: Allophycocyanin alpha subunit
t3: Allophycocyanin beta subunit
u3: Allophycocyanin alpha subunit
v3: Allophycocyanin beta subunit
w3: Allophycocyanin alpha subunit
x3: Allophycocyanin beta subunit
y3: Allophycocyanin alpha subunit
z3: Allophycocyanin beta subunit
A4: Phycobilisome rod-core linker polypeptide CpcG
B4: C-phycocyanin subunit alpha
C4: C-phycocyanin subunit beta
D4: C-phycocyanin subunit alpha
E4: C-phycocyanin subunit beta
F4: C-phycocyanin subunit alpha
G4: C-phycocyanin subunit beta
H4: C-phycocyanin subunit alpha
I4: C-phycocyanin subunit beta
J4: C-phycocyanin subunit alpha
K4: C-phycocyanin subunit beta
L4: C-phycocyanin subunit alpha
M4: C-phycocyanin subunit beta
N4: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
O4: C-phycocyanin subunit alpha
P4: C-phycocyanin subunit beta
Q4: C-phycocyanin subunit alpha
R4: C-phycocyanin subunit beta
S4: C-phycocyanin subunit alpha
T4: C-phycocyanin subunit beta
U4: C-phycocyanin subunit alpha
V4: C-phycocyanin subunit beta
W4: C-phycocyanin subunit alpha
X4: C-phycocyanin subunit beta
Y4: C-phycocyanin subunit alpha
Z4: C-phycocyanin subunit beta
a4: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
A5: Phycobilisome rod-core linker polypeptide CpcG
B5: C-phycocyanin subunit alpha
C5: C-phycocyanin subunit beta
D5: C-phycocyanin subunit alpha
E5: C-phycocyanin subunit beta
F5: C-phycocyanin subunit alpha
G5: C-phycocyanin subunit beta
H5: C-phycocyanin subunit alpha
I5: C-phycocyanin subunit beta
J5: C-phycocyanin subunit alpha
K5: C-phycocyanin subunit beta
L5: C-phycocyanin subunit alpha
M5: C-phycocyanin subunit beta
N5: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
O5: C-phycocyanin subunit alpha
P5: C-phycocyanin subunit beta
Q5: C-phycocyanin subunit alpha
R5: C-phycocyanin subunit beta
S5: C-phycocyanin subunit alpha
T5: C-phycocyanin subunit beta
U5: C-phycocyanin subunit alpha
V5: C-phycocyanin subunit beta
W5: C-phycocyanin subunit alpha
X5: C-phycocyanin subunit beta
Y5: C-phycocyanin subunit alpha
Z5: C-phycocyanin subunit beta
a5: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
A6: Phycobilisome rod-core linker polypeptide CpcG
B6: C-phycocyanin subunit alpha
C6: C-phycocyanin subunit beta
D6: C-phycocyanin subunit alpha
E6: C-phycocyanin subunit beta
F6: C-phycocyanin subunit alpha
G6: C-phycocyanin subunit beta
H6: C-phycocyanin subunit alpha
I6: C-phycocyanin subunit beta
J6: C-phycocyanin subunit alpha
K6: C-phycocyanin subunit beta
L6: C-phycocyanin subunit alpha
M6: C-phycocyanin subunit beta
N6: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
O6: C-phycocyanin subunit alpha
P6: C-phycocyanin subunit beta
Q6: C-phycocyanin subunit alpha
R6: C-phycocyanin subunit beta
S6: C-phycocyanin subunit alpha
T6: C-phycocyanin subunit beta
U6: C-phycocyanin subunit alpha
V6: C-phycocyanin subunit beta
W6: C-phycocyanin subunit alpha
X6: C-phycocyanin subunit beta
Y6: C-phycocyanin subunit alpha
Z6: C-phycocyanin subunit beta
a6: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
A7: Allophycocyanin alpha subunit
B7: Allophycocyanin beta subunit
C7: Allophycocyanin alpha subunit
D7: Allophycocyanin beta subunit
E7: Allophycocyanin alpha subunit
F7: Allophycocyanin beta subunit
G7: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
H7: Allophycocyanin alpha subunit
I7: Allophycocyanin beta subunit
J7: Allophycocyanin alpha subunit
K7: Allophycocyanin beta subunit
L7: Allophycocyanin alpha subunit
M7: Allophycocyanin beta subunit
N7: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
O7: Allophycocyanin alpha subunit
P7: Allophycocyanin beta subunit
Q7: Allophycocyanin alpha subunit
R7: Allophycocyanin beta subunit
S7: Allophycocyanin alpha subunit
T7: Allophycocyanin beta subunit
U7: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
V7: Allophycocyanin alpha subunit
W7: Allophycocyanin beta subunit
X7: Allophycocyanin alpha subunit
Y7: Allophycocyanin beta subunit
Z7: Allophycocyanin alpha subunit
a7: Allophycocyanin beta subunit
b7: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
A8: Phycobilisome rod-core linker polypeptide CpcG
B8: C-phycocyanin subunit alpha
C8: C-phycocyanin subunit beta
D8: C-phycocyanin subunit alpha
E8: C-phycocyanin subunit beta
F8: C-phycocyanin subunit alpha
G8: C-phycocyanin subunit beta
H8: C-phycocyanin subunit alpha
I8: C-phycocyanin subunit beta
J8: C-phycocyanin subunit alpha
K8: C-phycocyanin subunit beta
L8: C-phycocyanin subunit alpha
M8: C-phycocyanin subunit beta
N8: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
O8: C-phycocyanin subunit alpha
P8: C-phycocyanin subunit beta
Q8: C-phycocyanin subunit alpha
R8: C-phycocyanin subunit beta
S8: C-phycocyanin subunit alpha
T8: C-phycocyanin subunit beta
U8: C-phycocyanin subunit alpha
V8: C-phycocyanin subunit beta
W8: C-phycocyanin subunit alpha
X8: C-phycocyanin subunit beta
Y8: C-phycocyanin subunit alpha
Z8: C-phycocyanin subunit beta
a8: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,778,193528
Polymers4,608,649240
Non-polymers169,544288
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Phycobilisome ... , 3 types, 24 molecules A1A2A4A5A6A8N1a1N2a2N4a4N5a5N6a6N8a82333G7N7U7b7

#1: Protein
Phycobilisome rod-core linker polypeptide CpcG / L-RC 28.5


Mass: 28540.152 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: cpcG / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: Q05238
#4: Protein
Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod / L-R 32.3


Mass: 32308.896 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: cpcC / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: Q05237
#6: Protein
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core


Mass: 7806.188 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcC / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: O68971

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C-phycocyanin subunit ... , 2 types, 144 molecules B1D1F1H1J1L1O1Q1S1U1W1Y1B2D2F2H2J2L2O2Q2S2U2W2Y2B4D4F4H4J4L4...

#2: Protein ...
C-phycocyanin subunit alpha / alpha-PC


Mass: 17637.695 Da / Num. of mol.: 72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: cpcA / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: P03943
#3: Protein ...
C-phycocyanin subunit beta / beta-PC


Mass: 18353.852 Da / Num. of mol.: 72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: cpcB / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: P03944

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Allophycocyanin ... , 4 types, 70 molecules G3I3K3N3P3R3T3X3Z3b3d3f3i3k3o3q3s3u3w3y3A7C7E7H7J7L7O7Q7S7V7...

#7: Protein ...
Allophycocyanin alpha subunit


Mass: 17302.660 Da / Num. of mol.: 32
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcA / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: B1XQM2
#8: Protein ...
Allophycocyanin beta subunit


Mass: 17237.590 Da / Num. of mol.: 34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcB / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: O68970
#9: Protein Allophycocyanin subunit beta-18 / Allophycocyanin subunit B18


Mass: 18742.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcF / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: O68967
#10: Protein Allophycocyanin subunit alpha-B / alpha-AP-B


Mass: 17721.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcD / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: O68966

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Protein / Non-polymers , 2 types, 290 molecules 0313

#11: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 288 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Protein Phycobiliprotein ApcE / Phycobilisome core-membrane linker phycobiliprotein ApcE


Mass: 99391.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcE / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: O68973, Lyases

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002
Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightValue: 6 MDa
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64268 / Symmetry type: POINT

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