[English] 日本語
Yorodumi
- PDB-7y4l: PBS of PBS-PSII-PSI-LHCs from Porphyridium purpureum. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7y4l
TitlePBS of PBS-PSII-PSI-LHCs from Porphyridium purpureum.
Components
  • (Allophycocyanin ...) x 4
  • (C-phycocyanin ...) x 2
  • (FAS1 domain-containing ...) x 2
  • (Phycobilisome ...) x 9
  • (R-phycoerythrin gamma chain, ...) x 4
  • B-phycoerythrin beta chain
  • CaRSPs1
  • CaRSPs2
  • LPP2
  • LRC5
  • Linker4
  • Lrc4
  • Phycobiliprotein ApcE
  • Phycoerythrin alpha subunit
KeywordsPHOTOSYNTHESIS / PBS
Function / homology
Function and homology information


phycobilisome / chloroplast thylakoid membrane / photosynthesis / cell adhesion molecule binding / extracellular matrix organization / extracellular matrix / macroautophagy / cell adhesion / lyase activity / extracellular space
Similarity search - Function
Allophycocyanin linker chain / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily ...Allophycocyanin linker chain / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / 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 / PHYCOERYTHROBILIN / PHYCOUROBILIN / Phycobiliprotein ApcE / Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod / Uncharacterized protein / Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod / Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod / R-phycoerythrin gamma chain, chloroplastic / Uncharacterized protein ...PHYCOCYANOBILIN / PHYCOERYTHROBILIN / PHYCOUROBILIN / Phycobiliprotein ApcE / Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod / Uncharacterized protein / Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod / Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod / R-phycoerythrin gamma chain, chloroplastic / Uncharacterized protein / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / R-phycoerythrin gamma chain, chloroplastic / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod / Uncharacterized protein / Uncharacterized protein / R-phycoerythrin gamma chain, chloroplastic / R-phycoerythrin gamma chain, chloroplastic / FAS1 domain-containing protein / Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated, rod / Uncharacterized protein / Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated, rod / Uncharacterized protein / Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod / FAS1 domain-containing protein / Phycoerythrin alpha subunit / B-phycoerythrin beta chain / C-phycocyanin alpha subunit / Allophycocyanin alpha subunit / Phycobilisome rod-core linker polypeptide / C-phycocyanin beta subunit / Allophycocyanin beta 18 subunit / Allophycocyanin gamma subunit / Allophycocyanin beta subunit
Similarity search - Component
Biological speciesPorphyridium purpureum (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYou, X. / Zhang, X. / Cheng, J. / Xiao, Y.N. / Sun, S. / Sui, S.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2023
Title: In situ structure of the red algal phycobilisome-PSII-PSI-LHC megacomplex.
Authors: Xin You / Xing Zhang / Jing Cheng / Yanan Xiao / Jianfei Ma / Shan Sun / Xinzheng Zhang / Hong-Wei Wang / Sen-Fang Sui /
Abstract: In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis. The antenna systems of red ...In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis. The antenna systems of red algae consist of soluble phycobilisomes (PBSs) and transmembrane light-harvesting complexes (LHCs). Excitation energy transfer pathways from PBS to photosystems remain unclear owing to the lack of structural information. Here we present in situ structures of PBS-PSII-PSI-LHC megacomplexes from the red alga Porphyridium purpureum at near-atomic resolution using cryogenic electron tomography and in situ single-particle analysis, providing interaction details between PBS, PSII and PSI. The structures reveal several unidentified and incomplete proteins and their roles in the assembly of the megacomplex, as well as a huge and sophisticated pigment network. This work provides a solid structural basis for unravelling the mechanisms of PBS-PSII-PSI-LHC megacomplex assembly, efficient energy transfer from PBS to the two photosystems, and regulation of energy distribution between PSII and PSI.
History
DepositionJun 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: Linker4
BA: B-phycoerythrin beta chain
CA: B-phycoerythrin beta chain
DA: B-phycoerythrin beta chain
EA: Linker4
FA: B-phycoerythrin beta chain
GA: B-phycoerythrin beta chain
HA: B-phycoerythrin beta chain
IA: B-phycoerythrin beta chain
JA: Phycoerythrin alpha subunit
KA: CaRSPs1
LA: B-phycoerythrin beta chain
MA: B-phycoerythrin beta chain
NA: B-phycoerythrin beta chain
OA: B-phycoerythrin beta chain
PA: B-phycoerythrin beta chain
QA: B-phycoerythrin beta chain
RA: B-phycoerythrin beta chain
SA: B-phycoerythrin beta chain
TA: Phycoerythrin alpha subunit
UA: CaRSPs1
VA: B-phycoerythrin beta chain
WA: CaRSPs2
XA: B-phycoerythrin beta chain
YA: B-phycoerythrin beta chain
ZA: B-phycoerythrin beta chain
AB: R-phycoerythrin gamma chain, chloroplastic
BB: Phycobilisome rod-core linker polypeptide
CB: C-phycocyanin alpha subunit
DB: C-phycocyanin beta subunit
EB: C-phycocyanin alpha subunit
FB: C-phycocyanin beta subunit
GB: C-phycocyanin alpha subunit
HB: C-phycocyanin beta subunit
IB: C-phycocyanin alpha subunit
JB: C-phycocyanin beta subunit
KB: C-phycocyanin alpha subunit
LB: C-phycocyanin beta subunit
MB: C-phycocyanin alpha subunit
NB: C-phycocyanin beta subunit
OB: Phycoerythrin alpha subunit
PB: B-phycoerythrin beta chain
QB: Phycoerythrin alpha subunit
RB: B-phycoerythrin beta chain
SB: Phycoerythrin alpha subunit
TB: B-phycoerythrin beta chain
UB: Phycoerythrin alpha subunit
VB: B-phycoerythrin beta chain
WB: Phycoerythrin alpha subunit
XB: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
YB: B-phycoerythrin beta chain
ZB: Phycoerythrin alpha subunit
AC: R-phycoerythrin gamma chain, chloroplastic
BC: Phycobilisome rod-core linker polypeptide
CC: C-phycocyanin alpha subunit
DC: C-phycocyanin beta subunit
EC: C-phycocyanin alpha subunit
FC: C-phycocyanin beta subunit
GC: C-phycocyanin alpha subunit
HC: C-phycocyanin beta subunit
IC: C-phycocyanin alpha subunit
JC: C-phycocyanin beta subunit
KC: C-phycocyanin alpha subunit
LC: C-phycocyanin beta subunit
MC: C-phycocyanin alpha subunit
NC: C-phycocyanin beta subunit
OC: Phycoerythrin alpha subunit
PC: B-phycoerythrin beta chain
QC: Phycoerythrin alpha subunit
RC: B-phycoerythrin beta chain
SC: Phycoerythrin alpha subunit
TC: B-phycoerythrin beta chain
UC: Phycoerythrin alpha subunit
VC: B-phycoerythrin beta chain
WC: Phycoerythrin alpha subunit
XC: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
YC: B-phycoerythrin beta chain
ZC: Phycoerythrin alpha subunit
AD: R-phycoerythrin gamma chain, chloroplastic
BD: Phycobilisome rod-core linker polypeptide
CD: C-phycocyanin alpha subunit
DD: C-phycocyanin beta subunit
ED: C-phycocyanin alpha subunit
FD: C-phycocyanin beta subunit
GD: C-phycocyanin alpha subunit
HD: C-phycocyanin beta subunit
ID: C-phycocyanin alpha subunit
JD: C-phycocyanin beta subunit
KD: C-phycocyanin alpha subunit
LD: C-phycocyanin beta subunit
MD: C-phycocyanin alpha subunit
ND: C-phycocyanin beta subunit
OD: Phycoerythrin alpha subunit
PD: B-phycoerythrin beta chain
QD: Phycoerythrin alpha subunit
RD: B-phycoerythrin beta chain
SD: Phycoerythrin alpha subunit
TD: B-phycoerythrin beta chain
UD: Phycoerythrin alpha subunit
VD: B-phycoerythrin beta chain
WD: Phycoerythrin alpha subunit
XD: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
YD: B-phycoerythrin beta chain
ZD: Phycoerythrin alpha subunit
AE: R-phycoerythrin gamma chain, chloroplastic
BE: Phycobilisome rod-core linker polypeptide
CE: C-phycocyanin alpha subunit
DE: C-phycocyanin beta subunit
EE: C-phycocyanin alpha subunit
FE: C-phycocyanin beta subunit
GE: C-phycocyanin alpha subunit
HE: C-phycocyanin beta subunit
IE: C-phycocyanin alpha subunit
JE: C-phycocyanin beta subunit
KE: C-phycocyanin alpha subunit
LE: C-phycocyanin beta subunit
ME: C-phycocyanin alpha subunit
NE: C-phycocyanin beta subunit
OE: Phycoerythrin alpha subunit
PE: B-phycoerythrin beta chain
QE: Phycoerythrin alpha subunit
RE: B-phycoerythrin beta chain
SE: Phycoerythrin alpha subunit
TE: B-phycoerythrin beta chain
UE: Phycoerythrin alpha subunit
VE: B-phycoerythrin beta chain
WE: Phycoerythrin alpha subunit
XE: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
YE: B-phycoerythrin beta chain
ZE: Phycoerythrin alpha subunit
AF: Phycoerythrin alpha subunit
BF: B-phycoerythrin beta chain
CF: Phycoerythrin alpha subunit
DF: B-phycoerythrin beta chain
EF: Phycoerythrin alpha subunit
FF: B-phycoerythrin beta chain
GF: Phycoerythrin alpha subunit
HF: B-phycoerythrin beta chain
IF: Phycoerythrin alpha subunit
JF: B-phycoerythrin beta chain
KF: Phycoerythrin alpha subunit
LF: B-phycoerythrin beta chain
MF: Phycoerythrin alpha subunit
NF: B-phycoerythrin beta chain
OF: Phycoerythrin alpha subunit
PF: B-phycoerythrin beta chain
QF: Phycoerythrin alpha subunit
RF: B-phycoerythrin beta chain
SF: Phycoerythrin alpha subunit
TF: B-phycoerythrin beta chain
UF: Phycoerythrin alpha subunit
VF: B-phycoerythrin beta chain
WF: Phycoerythrin alpha subunit
XF: B-phycoerythrin beta chain
YF: Phycoerythrin alpha subunit
ZF: B-phycoerythrin beta chain
AG: Phycoerythrin alpha subunit
BG: B-phycoerythrin beta chain
CG: Phycoerythrin alpha subunit
DG: B-phycoerythrin beta chain
EG: Phycoerythrin alpha subunit
FG: B-phycoerythrin beta chain
GG: Phycoerythrin alpha subunit
HG: B-phycoerythrin beta chain
IG: Phycoerythrin alpha subunit
JG: B-phycoerythrin beta chain
KG: Phycoerythrin alpha subunit
LG: B-phycoerythrin beta chain
MG: Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated, rod
NG: Phycoerythrin alpha subunit
OG: B-phycoerythrin beta chain
PG: Phycoerythrin alpha subunit
QG: B-phycoerythrin beta chain
RG: Phycoerythrin alpha subunit
SG: B-phycoerythrin beta chain
TG: Phycoerythrin alpha subunit
UG: B-phycoerythrin beta chain
VG: Phycoerythrin alpha subunit
WG: B-phycoerythrin beta chain
XG: Phycoerythrin alpha subunit
YG: B-phycoerythrin beta chain
ZG: Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated, rod
AH: R-phycoerythrin gamma chain, chloroplastic
BH: R-phycoerythrin gamma chain, chloroplastic
CH: Phycoerythrin alpha subunit
DH: B-phycoerythrin beta chain
EH: Phycoerythrin alpha subunit
FH: B-phycoerythrin beta chain
GH: Phycoerythrin alpha subunit
HH: B-phycoerythrin beta chain
IH: Phycoerythrin alpha subunit
JH: B-phycoerythrin beta chain
KH: Phycoerythrin alpha subunit
LH: B-phycoerythrin beta chain
MH: Phycoerythrin alpha subunit
NH: B-phycoerythrin beta chain
OH: Phycoerythrin alpha subunit
PH: B-phycoerythrin beta chain
QH: Phycoerythrin alpha subunit
RH: B-phycoerythrin beta chain
SH: Phycoerythrin alpha subunit
TH: B-phycoerythrin beta chain
UH: Phycoerythrin alpha subunit
VH: B-phycoerythrin beta chain
WH: Phycoerythrin alpha subunit
XH: B-phycoerythrin beta chain
YH: Phycoerythrin alpha subunit
ZH: B-phycoerythrin beta chain
AI: Phycoerythrin alpha subunit
BI: B-phycoerythrin beta chain
CI: Phycoerythrin alpha subunit
DI: B-phycoerythrin beta chain
EI: Phycoerythrin alpha subunit
FI: B-phycoerythrin beta chain
GI: Phycoerythrin alpha subunit
HI: B-phycoerythrin beta chain
II: Phycoerythrin alpha subunit
JI: B-phycoerythrin beta chain
KI: Phycoerythrin alpha subunit
LI: B-phycoerythrin beta chain
MI: R-phycoerythrin gamma chain, chloroplastic
NI: Phycoerythrin alpha subunit
OI: B-phycoerythrin beta chain
PI: Phycoerythrin alpha subunit
QI: B-phycoerythrin beta chain
RI: Phycoerythrin alpha subunit
SI: B-phycoerythrin beta chain
TI: Phycoerythrin alpha subunit
UI: B-phycoerythrin beta chain
VI: Phycoerythrin alpha subunit
WI: B-phycoerythrin beta chain
XI: Phycoerythrin alpha subunit
YI: B-phycoerythrin beta chain
ZI: R-phycoerythrin gamma chain, chloroplastic
AJ: R-phycoerythrin gamma chain, chloroplastic
BJ: Phycoerythrin alpha subunit
CJ: B-phycoerythrin beta chain
DJ: Phycoerythrin alpha subunit
EJ: B-phycoerythrin beta chain
FJ: Phycoerythrin alpha subunit
GJ: B-phycoerythrin beta chain
HJ: Phycoerythrin alpha subunit
IJ: B-phycoerythrin beta chain
JJ: Phycoerythrin alpha subunit
KJ: B-phycoerythrin beta chain
LJ: Phycoerythrin alpha subunit
MJ: B-phycoerythrin beta chain
NJ: Phycoerythrin alpha subunit
OJ: B-phycoerythrin beta chain
PJ: Phycoerythrin alpha subunit
QJ: B-phycoerythrin beta chain
RJ: Phycoerythrin alpha subunit
SJ: B-phycoerythrin beta chain
TJ: Phycoerythrin alpha subunit
UJ: B-phycoerythrin beta chain
VJ: Phycoerythrin alpha subunit
WJ: B-phycoerythrin beta chain
XJ: Phycoerythrin alpha subunit
YJ: B-phycoerythrin beta chain
AK: Phycoerythrin alpha subunit
BK: B-phycoerythrin beta chain
CK: Phycoerythrin alpha subunit
DK: B-phycoerythrin beta chain
EK: Phycoerythrin alpha subunit
FK: B-phycoerythrin beta chain
GK: Phycoerythrin alpha subunit
HK: B-phycoerythrin beta chain
IK: Phycoerythrin alpha subunit
JK: B-phycoerythrin beta chain
KK: Phycoerythrin alpha subunit
LK: B-phycoerythrin beta chain
MK: Phycoerythrin alpha subunit
NK: B-phycoerythrin beta chain
OK: Phycoerythrin alpha subunit
PK: B-phycoerythrin beta chain
QK: Phycoerythrin alpha subunit
RK: B-phycoerythrin beta chain
SK: Phycoerythrin alpha subunit
TK: B-phycoerythrin beta chain
UK: Phycoerythrin alpha subunit
VK: B-phycoerythrin beta chain
WK: Phycoerythrin alpha subunit
XK: B-phycoerythrin beta chain
YK: R-phycoerythrin gamma chain, chloroplastic
A1: Phycoerythrin alpha subunit
B1: B-phycoerythrin beta chain
C1: Phycoerythrin alpha subunit
D1: B-phycoerythrin beta chain
E1: Phycoerythrin alpha subunit
F1: B-phycoerythrin beta chain
G1: Phycoerythrin alpha subunit
H1: B-phycoerythrin beta chain
I1: Phycoerythrin alpha subunit
J1: B-phycoerythrin beta chain
K1: Phycoerythrin alpha subunit
L1: B-phycoerythrin beta chain
M1: Phycoerythrin alpha subunit
N1: B-phycoerythrin beta chain
O1: Phycoerythrin alpha subunit
P1: B-phycoerythrin beta chain
Q1: Phycoerythrin alpha subunit
R1: B-phycoerythrin beta chain
S1: Phycoerythrin alpha subunit
T1: B-phycoerythrin beta chain
U1: Phycoerythrin alpha subunit
V1: B-phycoerythrin beta chain
W1: Phycoerythrin alpha subunit
X1: B-phycoerythrin beta chain
Y1: R-phycoerythrin gamma chain, chloroplastic
e1: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
L2: C-phycocyanin beta subunit
M2: C-phycocyanin alpha subunit
N2: C-phycocyanin beta subunit
O2: Phycoerythrin alpha subunit
P2: B-phycoerythrin beta chain
Q2: Phycoerythrin alpha subunit
R2: B-phycoerythrin beta chain
S2: Phycoerythrin alpha subunit
T2: B-phycoerythrin beta chain
U2: Phycoerythrin alpha subunit
A2: R-phycoerythrin gamma chain, chloroplastic
B2: Phycobilisome rod-core linker polypeptide
C2: C-phycocyanin alpha subunit
D2: C-phycocyanin beta subunit
E2: C-phycocyanin alpha subunit
F2: C-phycocyanin beta subunit
G2: C-phycocyanin alpha subunit
H2: C-phycocyanin beta subunit
I2: C-phycocyanin alpha subunit
J2: C-phycocyanin beta subunit
K2: C-phycocyanin alpha subunit
V2: B-phycoerythrin beta chain
W2: Phycoerythrin alpha subunit
X2: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
Y2: B-phycoerythrin beta chain
Z2: Phycoerythrin alpha subunit
f2: Phycoerythrin alpha subunit
g2: B-phycoerythrin beta chain
h2: Phycoerythrin alpha subunit
i2: B-phycoerythrin beta chain
j2: Phycoerythrin alpha subunit
k2: B-phycoerythrin beta chain
l2: Phycoerythrin alpha subunit
m2: B-phycoerythrin beta chain
a2: B-phycoerythrin beta chain
b2: Phycoerythrin alpha subunit
c2: B-phycoerythrin beta chain
d2: Phycoerythrin alpha subunit
e2: B-phycoerythrin beta chain
23: Lrc4
33: LRC5
43: FAS1 domain-containing protein
A3: Allophycocyanin alpha subunit
B3: Allophycocyanin beta subunit
C3: Allophycocyanin alpha subunit
D3: Allophycocyanin beta subunit
E3: Allophycocyanin alpha subunit
F3: Allophycocyanin beta subunit
G3: Allophycocyanin alpha subunit
H3: Allophycocyanin beta subunit
I3: Allophycocyanin beta subunit
J3: Allophycocyanin alpha 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 beta subunit
R3: Allophycocyanin alpha subunit
S3: Allophycocyanin beta subunit
T3: Allophycocyanin alpha subunit
U3: Allophycocyanin beta subunit
V3: Allophycocyanin gamma subunit
W3: Allophycocyanin beta 18 subunit
X3: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
Z3: Lrc4
a3: LRC5
b3: FAS1 domain-containing protein
c3: Allophycocyanin alpha subunit
d3: Allophycocyanin beta subunit
e3: Allophycocyanin alpha subunit
f3: Allophycocyanin beta subunit
g3: Allophycocyanin alpha subunit
h3: Allophycocyanin beta subunit
i3: Allophycocyanin alpha subunit
j3: Allophycocyanin beta subunit
k3: Allophycocyanin beta subunit
l3: Allophycocyanin alpha subunit
m3: Allophycocyanin alpha subunit
n3: Allophycocyanin beta subunit
o3: Allophycocyanin beta subunit
p3: Allophycocyanin alpha subunit
q3: Allophycocyanin beta subunit
r3: Allophycocyanin alpha subunit
s3: Allophycocyanin beta subunit
t3: Allophycocyanin alpha subunit
u3: Allophycocyanin beta subunit
v3: Allophycocyanin alpha subunit
w3: Allophycocyanin beta subunit
x3: Allophycocyanin gamma subunit
y3: Allophycocyanin beta 18 subunit
z3: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
63: Phycobiliprotein ApcE
73: Phycobiliprotein ApcE
A4: R-phycoerythrin gamma chain, chloroplastic
B4: R-phycoerythrin gamma chain, chloroplastic
C4: Phycoerythrin alpha subunit
D4: B-phycoerythrin beta chain
E4: Phycoerythrin alpha subunit
F4: B-phycoerythrin beta chain
G4: Phycoerythrin alpha subunit
H4: B-phycoerythrin beta chain
I4: Phycoerythrin alpha subunit
J4: B-phycoerythrin beta chain
K4: Phycoerythrin alpha subunit
L4: B-phycoerythrin beta chain
M4: Phycoerythrin alpha subunit
N4: B-phycoerythrin beta chain
O4: Phycoerythrin alpha subunit
P4: B-phycoerythrin beta chain
Q4: Phycoerythrin alpha subunit
R4: B-phycoerythrin beta chain
S4: Phycoerythrin alpha subunit
T4: B-phycoerythrin beta chain
U4: Phycoerythrin alpha subunit
V4: B-phycoerythrin beta chain
W4: Phycoerythrin alpha subunit
X4: B-phycoerythrin beta chain
Y4: Phycoerythrin alpha subunit
Z4: B-phycoerythrin beta chain
a4: Phycoerythrin alpha subunit
c4: B-phycoerythrin beta chain
d4: Phycoerythrin alpha subunit
e4: B-phycoerythrin beta chain
f4: Phycoerythrin alpha subunit
g4: B-phycoerythrin beta chain
h4: Phycoerythrin alpha subunit
i4: B-phycoerythrin beta chain
j4: Phycoerythrin alpha subunit
k4: B-phycoerythrin beta chain
l4: Phycoerythrin alpha subunit
m4: B-phycoerythrin beta chain
b4: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
L5: Phycoerythrin alpha subunit
M5: B-phycoerythrin beta chain
N5: Phycoerythrin alpha subunit
O5: B-phycoerythrin beta chain
P5: Phycoerythrin alpha subunit
Q5: B-phycoerythrin beta chain
R5: Phycoerythrin alpha subunit
S5: B-phycoerythrin beta chain
T5: Phycoerythrin alpha subunit
U5: B-phycoerythrin beta chain
d5: Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated, rod
A5: R-phycoerythrin gamma chain, chloroplastic
B5: Phycoerythrin alpha subunit
C5: B-phycoerythrin beta chain
D5: Phycoerythrin alpha subunit
E5: B-phycoerythrin beta chain
F5: Phycoerythrin alpha subunit
G5: B-phycoerythrin beta chain
H5: Phycoerythrin alpha subunit
I5: B-phycoerythrin beta chain
J5: Phycoerythrin alpha subunit
K5: B-phycoerythrin beta chain
V5: Phycoerythrin alpha subunit
W5: B-phycoerythrin beta chain
X5: Phycoerythrin alpha subunit
Y5: B-phycoerythrin beta chain
F6: C-phycocyanin beta subunit
G6: C-phycocyanin alpha subunit
H6: C-phycocyanin beta subunit
I6: C-phycocyanin alpha subunit
J6: C-phycocyanin beta subunit
K6: C-phycocyanin alpha subunit
L6: C-phycocyanin beta subunit
M6: C-phycocyanin alpha subunit
N6: C-phycocyanin beta subunit
O6: Phycoerythrin alpha subunit
A6: R-phycoerythrin gamma chain, chloroplastic
B6: Phycobilisome rod-core linker polypeptide
C6: C-phycocyanin alpha subunit
D6: C-phycocyanin beta subunit
E6: C-phycocyanin alpha subunit
P6: B-phycoerythrin beta chain
Q6: Phycoerythrin alpha subunit
R6: B-phycoerythrin beta chain
S6: Phycoerythrin alpha subunit
T6: B-phycoerythrin beta chain
U6: Phycoerythrin alpha subunit
V6: B-phycoerythrin beta chain
W6: Phycoerythrin alpha subunit
X6: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
Y6: B-phycoerythrin beta chain
Z6: Phycoerythrin alpha subunit
i6: B-phycoerythrin beta chain
j6: Phycoerythrin alpha subunit
k6: B-phycoerythrin beta chain
l6: Phycoerythrin alpha subunit
m6: B-phycoerythrin beta chain
a6: B-phycoerythrin beta chain
b6: Phycoerythrin alpha subunit
c6: B-phycoerythrin beta chain
d6: Phycoerythrin alpha subunit
e6: B-phycoerythrin beta chain
f6: Phycoerythrin alpha subunit
g6: B-phycoerythrin beta chain
h6: Phycoerythrin alpha subunit
A7: Phycoerythrin alpha subunit
B7: B-phycoerythrin beta chain
C7: Phycoerythrin alpha subunit
D7: B-phycoerythrin beta chain
E7: Phycoerythrin alpha subunit
F7: B-phycoerythrin beta chain
G7: Phycoerythrin alpha subunit
H7: B-phycoerythrin beta chain
I7: Phycoerythrin alpha subunit
J7: B-phycoerythrin beta chain
K7: Phycoerythrin alpha subunit
L7: B-phycoerythrin beta chain
b7: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
M7: Phycoerythrin alpha subunit
N7: B-phycoerythrin beta chain
O7: Phycoerythrin alpha subunit
P7: B-phycoerythrin beta chain
Q7: Phycoerythrin alpha subunit
R7: B-phycoerythrin beta chain
S7: Phycoerythrin alpha subunit
T7: B-phycoerythrin beta chain
U7: Phycoerythrin alpha subunit
V7: B-phycoerythrin beta chain
W7: Phycoerythrin alpha subunit
X7: B-phycoerythrin beta chain
Y7: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
V8: B-phycoerythrin beta chain
W8: Phycoerythrin alpha subunit
X8: B-phycoerythrin beta chain
Y8: Phycoerythrin alpha subunit
Z8: B-phycoerythrin beta chain
A8: Phycoerythrin alpha subunit
B8: B-phycoerythrin beta chain
C8: Phycoerythrin alpha subunit
D8: B-phycoerythrin beta chain
E8: Phycoerythrin alpha subunit
F8: B-phycoerythrin beta chain
G8: Phycoerythrin alpha subunit
H8: B-phycoerythrin beta chain
I8: Phycoerythrin alpha subunit
J8: B-phycoerythrin beta chain
K8: Phycoerythrin alpha subunit
L8: B-phycoerythrin beta chain
M8: Phycoerythrin alpha subunit
N8: B-phycoerythrin beta chain
O8: Phycoerythrin alpha subunit
P8: B-phycoerythrin beta chain
Q8: Phycoerythrin alpha subunit
R8: B-phycoerythrin beta chain
S8: Phycoerythrin alpha subunit
T8: B-phycoerythrin beta chain
U8: Phycoerythrin alpha subunit
a8: Phycoerythrin alpha subunit
b8: B-phycoerythrin beta chain
c8: Phycoerythrin alpha subunit
d8: B-phycoerythrin beta chain
e8: Phycoerythrin alpha subunit
f8: B-phycoerythrin beta chain
g8: Phycoerythrin alpha subunit
h8: B-phycoerythrin beta chain
i8: Phycoerythrin alpha subunit
j8: B-phycoerythrin beta chain
k8: Phycoerythrin alpha subunit
l8: B-phycoerythrin beta chain
m8: Phycoerythrin alpha subunit
n8: B-phycoerythrin beta chain
o8: Phycoerythrin alpha subunit
p8: B-phycoerythrin beta chain
q8: Phycoerythrin alpha subunit
r8: B-phycoerythrin beta chain
s8: Phycoerythrin alpha subunit
t8: B-phycoerythrin beta chain
u8: Phycoerythrin alpha subunit
v8: B-phycoerythrin beta chain
w8: R-phycoerythrin gamma chain, chloroplastic
x8: R-phycoerythrin gamma chain, chloroplastic
y8: R-phycoerythrin gamma chain, chloroplastic
z8: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
A9: Phycoerythrin alpha subunit
B9: B-phycoerythrin beta chain
C9: Phycoerythrin alpha subunit
D9: B-phycoerythrin beta chain
E9: Phycoerythrin alpha subunit
F9: B-phycoerythrin beta chain
G9: Phycoerythrin alpha subunit
H9: B-phycoerythrin beta chain
I9: Phycoerythrin alpha subunit
J9: B-phycoerythrin beta chain
K9: Phycoerythrin alpha subunit
L9: B-phycoerythrin beta chain
M9: R-phycoerythrin gamma chain, chloroplastic
N9: Phycoerythrin alpha subunit
O9: B-phycoerythrin beta chain
P9: Phycoerythrin alpha subunit
Q9: B-phycoerythrin beta chain
R9: Phycoerythrin alpha subunit
S9: B-phycoerythrin beta chain
T9: Phycoerythrin alpha subunit
U9: B-phycoerythrin beta chain
V9: Phycoerythrin alpha subunit
W9: B-phycoerythrin beta chain
X9: Phycoerythrin alpha subunit
Y9: B-phycoerythrin beta chain
Z9: R-phycoerythrin gamma chain, chloroplastic
fA: FAS1 domain-containing protein
aA: B-phycoerythrin beta chain
bA: B-phycoerythrin beta chain
cA: CaRSPs2
dA: B-phycoerythrin beta chain
eA: B-phycoerythrin beta chain
gA: B-phycoerythrin beta chain
hA: FAS1 domain-containing protein
iB: B-phycoerythrin beta chain
jB: Phycoerythrin alpha subunit
kB: B-phycoerythrin beta chain
lB: Phycoerythrin alpha subunit
mB: B-phycoerythrin beta chain
aB: B-phycoerythrin beta chain
bB: Phycoerythrin alpha subunit
cB: B-phycoerythrin beta chain
dB: Phycoerythrin alpha subunit
eB: B-phycoerythrin beta chain
fB: Phycoerythrin alpha subunit
gB: B-phycoerythrin beta chain
hB: Phycoerythrin alpha subunit
fC: Phycoerythrin alpha subunit
gC: B-phycoerythrin beta chain
hC: Phycoerythrin alpha subunit
iC: B-phycoerythrin beta chain
jC: Phycoerythrin alpha subunit
kC: B-phycoerythrin beta chain
lC: Phycoerythrin alpha subunit
mC: B-phycoerythrin beta chain
aC: B-phycoerythrin beta chain
bC: Phycoerythrin alpha subunit
cC: B-phycoerythrin beta chain
dC: Phycoerythrin alpha subunit
eC: B-phycoerythrin beta chain
aD: B-phycoerythrin beta chain
bD: Phycoerythrin alpha subunit
cD: B-phycoerythrin beta chain
dD: Phycoerythrin alpha subunit
eD: B-phycoerythrin beta chain
fD: Phycoerythrin alpha subunit
gD: B-phycoerythrin beta chain
hD: Phycoerythrin alpha subunit
iD: B-phycoerythrin beta chain
jD: Phycoerythrin alpha subunit
kD: B-phycoerythrin beta chain
lD: Phycoerythrin alpha subunit
mD: B-phycoerythrin beta chain
aE: B-phycoerythrin beta chain
bE: Phycoerythrin alpha subunit
cE: B-phycoerythrin beta chain
dE: Phycoerythrin alpha subunit
eE: B-phycoerythrin beta chain
fE: Phycoerythrin alpha subunit
gE: B-phycoerythrin beta chain
hE: Phycoerythrin alpha subunit
iE: B-phycoerythrin beta chain
jE: Phycoerythrin alpha subunit
kE: B-phycoerythrin beta chain
lE: Phycoerythrin alpha subunit
mE: B-phycoerythrin beta chain
aF: Phycoerythrin alpha subunit
bF: B-phycoerythrin beta chain
cF: Phycoerythrin alpha subunit
dF: B-phycoerythrin beta chain
eF: Phycoerythrin alpha subunit
fF: B-phycoerythrin beta chain
gF: Phycoerythrin alpha subunit
hF: B-phycoerythrin beta chain
iF: Phycoerythrin alpha subunit
jF: B-phycoerythrin beta chain
kF: Phycoerythrin alpha subunit
lF: B-phycoerythrin beta chain
mF: Phycoerythrin alpha subunit
nF: B-phycoerythrin beta chain
oF: Phycoerythrin alpha subunit
pF: B-phycoerythrin beta chain
qF: Phycoerythrin alpha subunit
rF: B-phycoerythrin beta chain
sF: Phycoerythrin alpha subunit
tF: B-phycoerythrin beta chain
uF: Phycoerythrin alpha subunit
vF: B-phycoerythrin beta chain
wF: R-phycoerythrin gamma chain, chloroplastic
xF: R-phycoerythrin gamma chain, chloroplastic
yF: R-phycoerythrin gamma chain, chloroplastic
zF: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
aH: Phycoerythrin alpha subunit
cH: B-phycoerythrin beta chain
dH: Phycoerythrin alpha subunit
eH: B-phycoerythrin beta chain
fH: Phycoerythrin alpha subunit
gH: B-phycoerythrin beta chain
hH: Phycoerythrin alpha subunit
iH: B-phycoerythrin beta chain
jH: Phycoerythrin alpha subunit
kH: B-phycoerythrin beta chain
lH: Phycoerythrin alpha subunit
mH: B-phycoerythrin beta chain
bH: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
dJ: Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated, rod
eK: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod
Y3: LPP2
53: LPP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,003,4942318
Polymers14,060,310716
Non-polymers943,1851602
Water00
1


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

-
Components

-
Protein , 9 types, 544 molecules AAEABACADAFAGAHAIALAMANAOAPAQARASAVAXAYAZAPBRBTBVBYBPCRCTCVC...

#1: Protein Linker4


Mass: 14749.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_1598 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YXP2
#2: Protein ...
B-phycoerythrin beta chain


Mass: 18584.182 Da / Num. of mol.: 276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: cpeB / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: P11393
#3: Protein ...
Phycoerythrin alpha subunit / R-phycoerythrin alpha subunit


Mass: 17824.029 Da / Num. of mol.: 254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: peA, cpeA / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: E2IH77
#4: Protein CaRSPs1


Mass: 28151.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_9475 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YJY8
#5: Protein CaRSPs2


Mass: 35163.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_1715 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YX67
#16: Protein Lrc4


Mass: 16915.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_4247 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YTV6
#17: Protein LRC5


Mass: 30272.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_5140 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z2M2
#24: Protein Phycobiliprotein ApcE / Anchor polypeptide / PBS-anchor protein / Phycobilisome linker polypeptide


Mass: 99484.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: apcE / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A343KPB8
#30: Protein LPP2


Mass: 17273.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_5305 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z365

-
R-phycoerythrin gamma chain, ... , 4 types, 24 molecules ABACADAEAJYKY1A2A5A6AHA4w8x8wFxFBHB4y8yFMIZIM9Z9

#6: Protein
R-phycoerythrin gamma chain, chloroplastic


Mass: 31792.982 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_2041 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YX19
#12: Protein
R-phycoerythrin gamma chain, chloroplastic


Mass: 29453.639 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_2042 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YZM7
#13: Protein
R-phycoerythrin gamma chain, chloroplastic


Mass: 31358.787 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_2309 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YZH3
#14: Protein
R-phycoerythrin gamma chain, chloroplastic


Mass: 36924.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_9240 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YNU6

-
Phycobilisome ... , 9 types, 26 molecules BBBCBDBEB2B6XBXCXDXEX2X6MGZGe1eKX3z3b4bHd5dJb7Y7z8zF

#7: Protein
Phycobilisome rod-core linker polypeptide


Mass: 26996.689 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: cpcG / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0RZ90
#10: Protein
Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod


Mass: 39727.625 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_8023 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YM59
#11: Protein Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated, rod


Mass: 34958.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_0816 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z323
#15: Protein Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod


Mass: 32886.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_7221 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z7F4
#23: Protein Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core


Mass: 10428.983 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_2818 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YVZ2
#25: Protein Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod


Mass: 53601.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_2314 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YX63
#26: Protein Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associated, rod


Mass: 36321.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_0729 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z162
#27: Protein Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod


Mass: 45655.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_8365 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YMI8
#28: Protein Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod


Mass: 55146.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_9810 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YI31

-
C-phycocyanin ... , 2 types, 72 molecules CBEBGBIBKBMBCCECGCICKCMCCDEDGDIDKDMDCEEEGEIEKEMEM2C2E2G2I2K2...

#8: Protein ...
C-phycocyanin alpha subunit


Mass: 17478.664 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: cpcA / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0RYI4
#9: Protein ...
C-phycocyanin beta subunit


Mass: 18242.705 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: cpcB / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0RZB2

-
FAS1 domain-containing ... , 2 types, 4 molecules 43b3fAhA

#18: Protein FAS1 domain-containing protein


Mass: 26620.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_7258 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4ZA95
#29: Protein FAS1 domain-containing protein


Mass: 31332.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: FVE85_0141 / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4Z027

-
Allophycocyanin ... , 4 types, 46 molecules A3C3E3G3J3K3N3P3R3T3c3e3g3i3l3m3p3r3t3v3B3D3F3H3I3L3M3O3Q3S3...

#19: Protein
Allophycocyanin alpha subunit


Mass: 17639.123 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: apcA / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0RYM0
#20: Protein ...
Allophycocyanin beta subunit


Mass: 17415.797 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: apcB / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0S279
#21: Protein Allophycocyanin gamma subunit


Mass: 18126.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: apcD / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0S1U6
#22: Protein Allophycocyanin beta 18 subunit


Mass: 19778.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Gene: apcF / Production host: Porphyridium purpureum (eukaryote) / References: UniProt: W0RZE2

-
Non-polymers , 3 types, 1602 molecules

#31: Chemical...
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 1434 / Source method: obtained synthetically / Formula: C33H40N4O6
#32: Chemical...
ChemComp-PUB / PHYCOUROBILIN


Mass: 590.710 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C33H42N4O6 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 120 / Source method: obtained synthetically / Formula: C33H40N4O6

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: In situ PBS from Porphyridium purpureum / Type: CELL / Entity ID: #1-#30 / Source: RECOMBINANT
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Source (recombinant)Organism: Porphyridium purpureum (eukaryote)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215000 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more