7VEA

Pentacylindrical allophycocyanin core from Thermosynechococcus vulcanus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.

Kawakami, K.Hamaguchi, T.Hirose, Y.Kosumi, D.Miyata, M.Kamiya, N.Yonekura, K.

(2022) Nat Commun 13: 3389-3389

  • DOI: https://doi.org/10.1038/s41467-022-30962-9
  • Primary Citation of Related Structures:  
    7VEA, 7VEB

  • PubMed Abstract: 

    Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are compositionally and structurally diverse, and exceedingly complex, all of which pose a challenge for a comprehensive understanding of their function. To date, three detailed architectures of PBSs by cryo-electron microscopy (cryo-EM) have been described: a hemiellipsoidal type, a block-type from rhodophytes, and a cyanobacterial hemidiscoidal-type. Here, we report cryo-EM structures of a pentacylindrical allophycocyanin core and phycocyanin-containing rod of a thermophilic cyanobacterial hemidiscoidal PBS. The structures define the spatial arrangement of protein subunits and chromophores, crucial for deciphering the energy transfer mechanism. They reveal how the pentacylindrical core is formed, identify key interactions between linker proteins and the bilin chromophores, and indicate pathways for unidirectional energy transfer.


  • Organizational Affiliation

    Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1, Sayo, Hyogo, 679-5148, Japan. kawakami.k@spring8.or.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin alpha chain161Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P50030 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P50030 
Go to UniProtKB:  P50030
Entity Groups  
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UniProt GroupP50030
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin beta chain161Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P50031 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P50031 
Go to UniProtKB:  P50031
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50031
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobiliprotein ApcEFB [auth dM],
M [auth aM]
1,139Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DGF2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DGF2 
Go to UniProtKB:  Q8DGF2
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UniProt GroupQ8DGF2
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome core componentKB [auth dR],
R [auth aR]
169Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DHC5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DHC5 
Go to UniProtKB:  Q8DHC5
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UniProt GroupQ8DHC5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core67Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P50036 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P50036 
Go to UniProtKB:  P50036
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UniProt GroupP50036
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  • 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 
AD [auth aM]
AE [auth cL]
AF [auth eQ]
BD [auth aM]
BE [auth cM]
AD [auth aM],
AE [auth cL],
AF [auth eQ],
BD [auth aM],
BE [auth cM],
BF [auth eR],
CD [auth aN],
CE [auth dA],
CF [auth eS],
DD [auth aO],
DE [auth dB],
DF [auth eT],
ED [auth aP],
EE [auth dC],
EF [auth eU],
FD [auth aQ],
FE [auth dD],
FF [auth eV],
GD [auth bM],
GE [auth dE],
GF [auth eW],
HD [auth bN],
HE [auth dF],
HF [auth eX],
ID [auth bO],
IE [auth dG],
IF [auth fB],
JD [auth bP],
JE [auth dH],
JF [auth fD],
KD [auth bQ],
KE [auth dI],
KF [auth fD],
LD [auth bR],
LE [auth dJ],
LF [auth fF],
MC [auth aA],
MD [auth bS],
ME [auth dK],
MF [auth fF],
NC [auth aB],
ND [auth bT],
NE [auth dL],
NF [auth fG],
OC [auth aC],
OD [auth bU],
OE [auth dM],
OF [auth fI],
PC [auth aD],
PD [auth bV],
PE [auth dM],
PF [auth fJ],
QC [auth aE],
QD [auth bW],
QE [auth dM],
QF [auth fL],
RC [auth aF],
RD [auth bX],
RE [auth dN],
RF [auth fM],
SC [auth aG],
SD [auth cB],
SE [auth dO],
TC [auth aH],
TD [auth cD],
TE [auth dP],
UC [auth aI],
UD [auth cD],
UE [auth dQ],
VC [auth aJ],
VD [auth cF],
VE [auth dR],
WC [auth aK],
WD [auth cF],
WE [auth eM],
XC [auth aL],
XD [auth cG],
XE [auth eN],
YC [auth aM],
YD [auth cI],
YE [auth eO],
ZC [auth aM],
ZD [auth cJ],
ZE [auth eP]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
AA [auth bT]
AB [auth dH]
AC [auth fB]
B [auth aB]
CA [auth bV]
AA [auth bT],
AB [auth dH],
AC [auth fB],
B [auth aB],
CA [auth bV],
CB [auth dJ],
CC [auth fD],
D [auth aD],
EA [auth bX],
EB [auth dL],
EC [auth fF],
F [auth aF],
GB [auth dN],
GC [auth fH],
H [auth aH],
HA [auth cB],
IB [auth dP],
IC [auth fJ],
J [auth aJ],
JA [auth cD],
KC [auth fL],
L [auth aL],
LA [auth cF],
N [auth aN],
NA [auth cH],
NB [auth eN],
P [auth aP],
PA [auth cJ],
PB [auth eP],
RA [auth cL],
RB [auth eR],
TB [auth eT],
U [auth bN],
UA [auth dB],
VB [auth eV],
W [auth bP],
WA [auth dD],
XB [auth eX],
Y [auth bR],
YA [auth dF]
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2
RECONSTRUCTIONRELION3.1.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20H05109
Japan Society for the Promotion of Science (JSPS)Japan20K06528
Japan Society for the Promotion of Science (JSPS)Japan17H06434

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references