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 1.0 of the entry. See complete history


Literature

Core and rod structures of a cyanobacterial light-harvesting phycobilisome

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

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Allophycocyanin alpha chain161Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: apcAtll0957
UniProt
Find proteins for P50030 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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Go to UniProtKB:  P50030
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UniProt GroupP50030
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Allophycocyanin beta chain161Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: apcBtll0956
UniProt
Find proteins for P50031 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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UniProt GroupP50031
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobiliprotein ApcEM [auth aM],
FB [auth dM]
1139Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: apcE
UniProt
Find proteins for Q8DGF2 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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UniProt GroupQ8DGF2
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobilisome core componentR [auth aR],
KB [auth dR]
169Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: apcF
UniProt
Find proteins for Q8DHC5 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core67Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: apcCtsl0955
UniProt
Find proteins for P50036 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
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Go to UniProtKB:  P50036
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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 
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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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 

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