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- PDB-8wql: In situ PBS-PSII supercomplex from cyanobacterial Spirulina platensis -

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Basic information

Entry
Database: PDB / ID: 8wql
TitleIn situ PBS-PSII supercomplex from cyanobacterial Spirulina platensis
Components
  • (Allophycocyanin ...) x 3
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Allophycocyanin-B alpha subunit
  • C-phycocyanin alpha subunit
  • LCM
  • LPP1
  • LPP2
  • LRC1
  • Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
  • Phycocyanin beta subunit
  • PsbQ protein
  • PsbU
KeywordsPHOTOSYNTHESIS / complex
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / PHYCOCYANOBILIN / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / PHYCOCYANOBILIN / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / Phycocyanin beta subunit
Similarity search - Component
Biological speciesArthrospira sp. FACHB-439 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYou, X. / Zhang, X. / Xiao, Y.N. / Sun, S. / Sui, S.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: In situ structural determination of cyanobacterial phycobilisome-PSII supercomplex by STAgSPA strategy.
Authors: Xing Zhang / Yanan Xiao / Xin You / Shan Sun / Sen-Fang Sui /
Abstract: Photosynthesis converting solar energy to chemical energy is one of the most important chemical reactions on earth. In cyanobacteria, light energy is captured by antenna system phycobilisomes (PBSs) ...Photosynthesis converting solar energy to chemical energy is one of the most important chemical reactions on earth. In cyanobacteria, light energy is captured by antenna system phycobilisomes (PBSs) and transferred to photosynthetic reaction centers of photosystem II (PSII) and photosystem I (PSI). While most of the protein complexes involved in photosynthesis have been characterized by in vitro structural analyses, how these protein complexes function together in vivo is not well understood. Here we implemented STAgSPA, an in situ structural analysis strategy, to solve the native structure of PBS-PSII supercomplex from the cyanobacteria Arthrospira sp. FACHB439 at resolution of ~3.5 Å. The structure reveals coupling details among adjacent PBSs and PSII dimers, and the collaborative energy transfer mechanism mediated by multiple super-PBS in cyanobacteria. Our results provide insights into the diversity of photosynthesis-related systems between prokaryotic cyanobacteria and eukaryotic red algae but are also a methodological demonstration for high-resolution structural analysis in cellular or tissue samples.
History
DepositionOct 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 2.0Sep 10, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_asym.entity_id
Revision 3.0Sep 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / citation ...atom_site / citation / em_admin / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_asym.entity_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BA: LRC1
BB: LCM
CB: LCM
OB: Allophycocyanin alpha chain
PB: Allophycocyanin beta chain
QB: Allophycocyanin alpha chain
RB: Allophycocyanin beta chain
SB: Allophycocyanin alpha chain
TB: Allophycocyanin beta chain
UB: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
VB: Allophycocyanin alpha chain
WB: Allophycocyanin beta chain
XB: Allophycocyanin alpha chain
YB: Allophycocyanin beta chain
ZB: Allophycocyanin alpha chain
BC: LRC1
AD: Photosystem II protein D1
BD: Photosystem II CP47 reaction center protein
CD: Photosystem II CP43 reaction center protein
DD: Photosystem II D2 protein
ED: Cytochrome b559 subunit alpha
FD: Cytochrome b559 subunit beta
HD: Photosystem II reaction center protein H
ID: Photosystem II reaction center protein I
JD: Photosystem II reaction center protein J
KD: Photosystem II reaction center protein K
LD: Photosystem II reaction center protein L
MD: Photosystem II reaction center protein M
OD: Photosystem II extrinsic protein O
QD: PsbQ protein
RD: Photosystem II reaction center protein Y
SD: LPP1
TD: Photosystem II reaction center protein T
UD: PsbU
VD: Photosystem II extrinsic protein V
XD: Photosystem II reaction center protein X
YD: Photosystem II reaction center protein Psb30
ZD: Photosystem II reaction center protein Z
AE: Photosystem II protein D1
BE: Photosystem II CP47 reaction center protein
CE: Photosystem II CP43 reaction center protein
DE: Photosystem II D2 protein
EE: Cytochrome b559 subunit alpha
FE: Cytochrome b559 subunit beta
HE: Photosystem II reaction center protein H
IE: Photosystem II reaction center protein I
JE: Photosystem II reaction center protein J
KE: Photosystem II reaction center protein K
LE: Photosystem II reaction center protein L
ME: Photosystem II reaction center protein M
OE: Photosystem II extrinsic protein O
QE: PsbQ protein
RE: Photosystem II reaction center protein Y
SE: LPP1
TE: Photosystem II reaction center protein T
UE: PsbU
VE: Photosystem II extrinsic protein V
XE: Photosystem II reaction center protein X
YE: Photosystem II reaction center protein Psb30
ZE: Photosystem II reaction center protein Z
EF: LPP2
IF: Allophycocyanin beta chain
JF: Allophycocyanin alpha chain
KF: Allophycocyanin beta chain
LF: Allophycocyanin alpha chain
MF: Allophycocyanin beta chain
NF: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
XF: Allophycocyanin alpha chain
YF: Allophycocyanin beta chain
ZF: Allophycocyanin alpha chain
AG: Allophycocyanin alpha chain
BG: LPP2
GG: Allophycocyanin alpha chain
HG: Allophycocyanin beta chain
IG: Allophycocyanin alpha chain
JG: Allophycocyanin beta chain
KG: Allophycocyanin alpha chain
LG: Allophycocyanin beta chain
MG: Allophycocyanin beta chain
NG: Allophycocyanin alpha chain
OG: Allophycocyanin beta chain
PG: Allophycocyanin alpha chain
QG: Allophycocyanin beta-18 subunit
RG: Allophycocyanin alpha chain
SG: Allophycocyanin beta chain
TG: Allophycocyanin alpha chain
UG: Allophycocyanin beta chain
VG: Allophycocyanin-B alpha subunit
WG: Allophycocyanin beta chain
BH: LRC1
BI: LRC1
BJ: LRC1
EK: LPP2
IK: Allophycocyanin beta chain
JK: Allophycocyanin alpha chain
KK: Allophycocyanin beta chain
LK: Allophycocyanin alpha chain
MK: Allophycocyanin beta chain
NK: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
XK: Allophycocyanin alpha chain
YK: Allophycocyanin beta chain
ZK: Allophycocyanin alpha chain
AL: Allophycocyanin alpha chain
BL: LPP2
GL: Allophycocyanin alpha chain
HL: Allophycocyanin beta chain
IL: Allophycocyanin alpha chain
JL: Allophycocyanin beta chain
KL: Allophycocyanin alpha chain
LL: Allophycocyanin beta chain
ML: Allophycocyanin beta chain
NL: Allophycocyanin alpha chain
OL: Allophycocyanin beta chain
PL: Allophycocyanin alpha chain
QL: Allophycocyanin beta-18 subunit
RL: Allophycocyanin alpha chain
SL: Allophycocyanin beta chain
TL: Allophycocyanin alpha chain
UL: Allophycocyanin beta chain
VL: Allophycocyanin-B alpha subunit
WL: Allophycocyanin beta chain
A1: Photosystem II protein D1
B1: Photosystem II CP47 reaction center protein
C1: Photosystem II CP43 reaction center protein
D1: Photosystem II D2 protein
E1: Cytochrome b559 subunit alpha
F1: Cytochrome b559 subunit beta
H1: Photosystem II reaction center protein H
I1: Photosystem II reaction center protein I
J1: Photosystem II reaction center protein J
K1: Photosystem II reaction center protein K
L1: Photosystem II reaction center protein L
M1: Photosystem II reaction center protein M
O1: Photosystem II extrinsic protein O
Q1: PsbQ protein
R1: Photosystem II reaction center protein Y
T1: Photosystem II reaction center protein T
U1: PsbU
V1: Photosystem II extrinsic protein V
X1: Photosystem II reaction center protein X
Y1: Photosystem II reaction center protein Psb30
Z1: Photosystem II reaction center protein Z
a1: Photosystem II protein D1
b1: Photosystem II CP47 reaction center protein
c1: Photosystem II CP43 reaction center protein
d1: Photosystem II D2 protein
e1: Cytochrome b559 subunit alpha
f1: Cytochrome b559 subunit beta
h1: Photosystem II reaction center protein H
i1: Photosystem II reaction center protein I
j1: Photosystem II reaction center protein J
k1: Photosystem II reaction center protein K
l1: Photosystem II reaction center protein L
m1: Photosystem II reaction center protein M
o1: Photosystem II extrinsic protein O
q1: PsbQ protein
r1: Photosystem II reaction center protein Y
S1: LPP1
t1: Photosystem II reaction center protein T
u1: PsbU
v1: Photosystem II extrinsic protein V
x1: Photosystem II reaction center protein X
y1: Photosystem II reaction center protein Psb30
z1: Photosystem II reaction center protein Z
b2: C-phycocyanin alpha subunit
c2: Phycocyanin beta subunit
d2: C-phycocyanin alpha subunit
e2: Phycocyanin beta subunit
f2: C-phycocyanin alpha subunit
g2: Phycocyanin beta subunit
h2: C-phycocyanin alpha subunit
i2: Phycocyanin beta subunit
j2: C-phycocyanin alpha subunit
k2: Phycocyanin beta subunit
l2: C-phycocyanin alpha subunit
m2: Phycocyanin beta subunit
B2: LRC1
b3: C-phycocyanin alpha subunit
c3: Phycocyanin beta subunit
d3: C-phycocyanin alpha subunit
e3: Phycocyanin beta subunit
f3: C-phycocyanin alpha subunit
g3: Phycocyanin beta subunit
h3: C-phycocyanin alpha subunit
i3: Phycocyanin beta subunit
j3: C-phycocyanin alpha subunit
k3: Phycocyanin beta subunit
l3: C-phycocyanin alpha subunit
m3: Phycocyanin beta subunit
B3: LRC1
Z4: Allophycocyanin alpha chain
a4: Allophycocyanin beta chain
b4: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
S4: Allophycocyanin alpha chain
T4: Allophycocyanin beta chain
U4: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
V4: Allophycocyanin alpha chain
W4: Allophycocyanin beta chain
X4: Allophycocyanin alpha chain
Y4: Allophycocyanin beta chain
s4: Allophycocyanin alpha chain
t4: Allophycocyanin beta chain
u4: Allophycocyanin alpha chain
v4: Allophycocyanin beta chain
w4: Allophycocyanin alpha chain
o4: Allophycocyanin alpha chain
p4: Allophycocyanin beta chain
q4: Allophycocyanin alpha chain
r4: Allophycocyanin beta chain
x4: Allophycocyanin beta chain
y4: Allophycocyanin alpha chain
z4: Allophycocyanin beta chain
B4: LCM
C4: LCM
O4: Allophycocyanin alpha chain
P4: Allophycocyanin beta chain
Q4: Allophycocyanin alpha chain
R4: Allophycocyanin beta chain
B5: LRC1
b5: C-phycocyanin alpha subunit
c5: Phycocyanin beta subunit
d5: C-phycocyanin alpha subunit
e5: Phycocyanin beta subunit
f5: C-phycocyanin alpha subunit
g5: Phycocyanin beta subunit
h5: C-phycocyanin alpha subunit
i5: Phycocyanin beta subunit
j5: C-phycocyanin alpha subunit
k5: Phycocyanin beta subunit
l5: C-phycocyanin alpha subunit
m5: Phycocyanin beta subunit
b6: C-phycocyanin alpha subunit
c6: Phycocyanin beta subunit
d6: C-phycocyanin alpha subunit
e6: Phycocyanin beta subunit
f6: C-phycocyanin alpha subunit
g6: Phycocyanin beta subunit
h6: C-phycocyanin alpha subunit
i6: Phycocyanin beta subunit
j6: C-phycocyanin alpha subunit
k6: Phycocyanin beta subunit
l6: C-phycocyanin alpha subunit
m6: Phycocyanin beta subunit
B6: LRC1
b7: C-phycocyanin alpha subunit
c7: Phycocyanin beta subunit
d7: C-phycocyanin alpha subunit
e7: Phycocyanin beta subunit
f7: C-phycocyanin alpha subunit
g7: Phycocyanin beta subunit
h7: C-phycocyanin alpha subunit
i7: Phycocyanin beta subunit
j7: C-phycocyanin alpha subunit
k7: Phycocyanin beta subunit
l7: C-phycocyanin alpha subunit
m7: Phycocyanin beta subunit
B7: LRC1
B8: LRC1
b8: C-phycocyanin alpha subunit
c8: Phycocyanin beta subunit
d8: C-phycocyanin alpha subunit
e8: Phycocyanin beta subunit
f8: C-phycocyanin alpha subunit
g8: Phycocyanin beta subunit
h8: C-phycocyanin alpha subunit
i8: Phycocyanin beta subunit
j8: C-phycocyanin alpha subunit
k8: Phycocyanin beta subunit
l8: C-phycocyanin alpha subunit
m8: Phycocyanin beta subunit
b9: C-phycocyanin alpha subunit
c9: Phycocyanin beta subunit
d9: C-phycocyanin alpha subunit
e9: Phycocyanin beta subunit
f9: C-phycocyanin alpha subunit
g9: Phycocyanin beta subunit
h9: C-phycocyanin alpha subunit
i9: Phycocyanin beta subunit
j9: C-phycocyanin alpha subunit
k9: Phycocyanin beta subunit
l9: C-phycocyanin alpha subunit
m9: Phycocyanin beta subunit
B9: LRC1
bA: C-phycocyanin alpha subunit
cA: Phycocyanin beta subunit
dA: C-phycocyanin alpha subunit
eA: Phycocyanin beta subunit
fA: C-phycocyanin alpha subunit
gA: Phycocyanin beta subunit
hA: C-phycocyanin alpha subunit
iA: Phycocyanin beta subunit
jA: C-phycocyanin alpha subunit
kA: Phycocyanin beta subunit
lA: C-phycocyanin alpha subunit
mA: Phycocyanin beta subunit
aB: Allophycocyanin beta chain
bB: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
sB: Allophycocyanin alpha chain
tB: Allophycocyanin beta chain
uB: Allophycocyanin alpha chain
vB: Allophycocyanin beta chain
wB: Allophycocyanin alpha chain
oB: Allophycocyanin alpha chain
pB: Allophycocyanin beta chain
qB: Allophycocyanin alpha chain
rB: Allophycocyanin beta chain
xB: Allophycocyanin beta chain
yB: Allophycocyanin alpha chain
zB: Allophycocyanin beta chain
bC: C-phycocyanin alpha subunit
cC: Phycocyanin beta subunit
dC: C-phycocyanin alpha subunit
eC: Phycocyanin beta subunit
fC: C-phycocyanin alpha subunit
gC: Phycocyanin beta subunit
hC: C-phycocyanin alpha subunit
iC: Phycocyanin beta subunit
jC: C-phycocyanin alpha subunit
kC: Phycocyanin beta subunit
lC: C-phycocyanin alpha subunit
mC: Phycocyanin beta subunit
aD: Photosystem II protein D1
bD: Photosystem II CP47 reaction center protein
cD: Photosystem II CP43 reaction center protein
dD: Photosystem II D2 protein
eD: Cytochrome b559 subunit alpha
fD: Cytochrome b559 subunit beta
hD: Photosystem II reaction center protein H
iD: Photosystem II reaction center protein I
jD: Photosystem II reaction center protein J
kD: Photosystem II reaction center protein K
lD: Photosystem II reaction center protein L
mD: Photosystem II reaction center protein M
oD: Photosystem II extrinsic protein O
qD: PsbQ protein
rD: Photosystem II reaction center protein Y
tD: Photosystem II reaction center protein T
uD: PsbU
vD: Photosystem II extrinsic protein V
xD: Photosystem II reaction center protein X
yD: Photosystem II reaction center protein Psb30
zD: Photosystem II reaction center protein Z
aE: Photosystem II protein D1
bE: Photosystem II CP47 reaction center protein
cE: Photosystem II CP43 reaction center protein
dE: Photosystem II D2 protein
eE: Cytochrome b559 subunit alpha
fE: Cytochrome b559 subunit beta
hE: Photosystem II reaction center protein H
iE: Photosystem II reaction center protein I
jE: Photosystem II reaction center protein J
kE: Photosystem II reaction center protein K
lE: Photosystem II reaction center protein L
mE: Photosystem II reaction center protein M
oE: Photosystem II extrinsic protein O
qE: PsbQ protein
rE: Photosystem II reaction center protein Y
tE: Photosystem II reaction center protein T
uE: PsbU
vE: Photosystem II extrinsic protein V
xE: Photosystem II reaction center protein X
yE: Photosystem II reaction center protein Psb30
zE: Photosystem II reaction center protein Z
aF: Allophycocyanin beta chain
bF: Allophycocyanin alpha chain
cF: Allophycocyanin beta chain
dF: Allophycocyanin alpha chain
eF: Allophycocyanin beta chain
3F: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
fF: Allophycocyanin alpha chain
gF: Allophycocyanin beta-18 subunit
hF: Allophycocyanin beta chain
iF: Allophycocyanin alpha chain
jF: Allophycocyanin beta chain
kF: Allophycocyanin alpha chain
lF: Allophycocyanin beta chain
mF: Allophycocyanin-B alpha subunit
nF: Allophycocyanin beta chain
9F: Allophycocyanin alpha chain
2G: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
1G: Allophycocyanin beta chain
4G: Allophycocyanin alpha chain
5G: Allophycocyanin beta chain
6G: Allophycocyanin alpha chain
7G: Allophycocyanin beta chain
8G: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
bH: C-phycocyanin alpha subunit
cH: Phycocyanin beta subunit
dH: C-phycocyanin alpha subunit
eH: Phycocyanin beta subunit
fH: C-phycocyanin alpha subunit
gH: Phycocyanin beta subunit
hH: C-phycocyanin alpha subunit
iH: Phycocyanin beta subunit
jH: C-phycocyanin alpha subunit
kH: Phycocyanin beta subunit
lH: C-phycocyanin alpha subunit
mH: Phycocyanin beta subunit
bI: C-phycocyanin alpha subunit
cI: Phycocyanin beta subunit
dI: C-phycocyanin alpha subunit
eI: Phycocyanin beta subunit
fI: C-phycocyanin alpha subunit
gI: Phycocyanin beta subunit
hI: C-phycocyanin alpha subunit
iI: Phycocyanin beta subunit
jI: C-phycocyanin alpha subunit
kI: Phycocyanin beta subunit
lI: C-phycocyanin alpha subunit
mI: Phycocyanin beta subunit
bJ: C-phycocyanin alpha subunit
cJ: Phycocyanin beta subunit
dJ: C-phycocyanin alpha subunit
eJ: Phycocyanin beta subunit
fJ: C-phycocyanin alpha subunit
gJ: Phycocyanin beta subunit
hJ: C-phycocyanin alpha subunit
iJ: Phycocyanin beta subunit
jJ: C-phycocyanin alpha subunit
kJ: Phycocyanin beta subunit
lJ: C-phycocyanin alpha subunit
mJ: Phycocyanin beta subunit
aK: Allophycocyanin beta chain
bK: Allophycocyanin alpha chain
cK: Allophycocyanin beta chain
dK: Allophycocyanin alpha chain
eK: Allophycocyanin beta chain
3K: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
fK: Allophycocyanin alpha chain
gK: Allophycocyanin beta-18 subunit
hK: Allophycocyanin beta chain
iK: Allophycocyanin alpha chain
jK: Allophycocyanin beta chain
kK: Allophycocyanin alpha chain
lK: Allophycocyanin beta chain
mK: Allophycocyanin-B alpha subunit
nK: Allophycocyanin beta chain
9K: Allophycocyanin alpha chain
2L: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
1L: Allophycocyanin beta chain
4L: Allophycocyanin alpha chain
5L: Allophycocyanin beta chain
6L: Allophycocyanin alpha chain
7L: Allophycocyanin beta chain
8L: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,522,4961327
Polymers7,937,928445
Non-polymers584,569882
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 9 types, 192 molecules BABCBHBIBJB2B3B5B6B7B8B9BBCBB4C4UBNFNKb4U4bB3F2G8G3K2L8LQDQE...

#1: Protein
LRC1


Mass: 29443.213 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria)
#2: Protein
LCM


Mass: 102100.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria)
#5: Protein
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core


Mass: 7775.107 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcC / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZBQ2
#19: Protein
PsbQ protein


Mass: 18641.410 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbQ / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZQ11
#23: Protein
PsbU


Mass: 10733.153 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria)
#28: Protein
LPP2


Mass: 15788.175 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZJ52
#30: Protein
Allophycocyanin-B alpha subunit


Mass: 18022.709 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcD / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZH43
#31: Protein ...
C-phycocyanin alpha subunit


Mass: 17616.848 Da / Num. of mol.: 72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: cpcA / Production host: Arthrospira sp. FACHB-439 (bacteria)
#32: Protein ...
Phycocyanin beta subunit


Mass: 18062.441 Da / Num. of mol.: 72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: cpcB / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A9UKJ0

-
Allophycocyanin ... , 3 types, 136 molecules OBQBSBVBXBZBJFLFXFZFAGGGIGKGNGPGRGTGJKLKXKZKALGLILKLNLPLRLTL...

#3: Protein ...
Allophycocyanin alpha chain


Mass: 17409.799 Da / Num. of mol.: 64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcA / Production host: Arthrospira sp. FACHB-439 (bacteria)
#4: Protein ...
Allophycocyanin beta chain


Mass: 17345.748 Da / Num. of mol.: 68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcB / Production host: Arthrospira sp. FACHB-439 (bacteria)
#29: Protein
Allophycocyanin beta-18 subunit


Mass: 18446.771 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcF / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZN25

-
Photosystem II ... , 17 types, 102 molecules ADAEA1a1aDaEBDBEB1b1bDbECDCEC1c1cDcEDDDED1d1dDdEHDHEH1h1hDhE...

#6: Protein
Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein


Mass: 39675.184 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbA1 / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4ENJ6, photosystem II
#7: Protein
Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56256.766 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbB / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EP29
#8: Protein
Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 51545.973 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbC / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EL13
#9: Protein
Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39521.270 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbD1, psbD / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EL11, photosystem II
#12: Protein
Photosystem II reaction center protein H / PSII-H


Mass: 7636.935 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbH / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZFR1
#13: Protein/peptide
Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4414.285 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbI / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EN47
#14: Protein/peptide
Photosystem II reaction center protein J / PSII-J


Mass: 3914.632 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbJ / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZEX7
#15: Protein/peptide
Photosystem II reaction center protein K / PSII-K


Mass: 4979.012 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbK / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EP73
#16: Protein/peptide
Photosystem II reaction center protein L / PSII-L


Mass: 4581.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbL / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZAC5
#17: Protein/peptide
Photosystem II reaction center protein M / PSII-M


Mass: 4128.829 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbM / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZMZ9
#18: Protein
Photosystem II extrinsic protein O / Photosystem II manganese-stabilizing polypeptide


Mass: 30064.770 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbO / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZRB6
#20: Protein/peptide
Photosystem II reaction center protein Y


Mass: 4189.124 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbY / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZG21
#22: Protein/peptide
Photosystem II reaction center protein T / PSII-T


Mass: 3439.182 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbTc, psbT / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EP38
#24: Protein
Photosystem II extrinsic protein V / PsbV / Cytochrome c-550 / Cytochrome c550 / Low-potential cytochrome c


Mass: 18165.770 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbV1, psbV / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4ELM7
#25: Protein/peptide
Photosystem II reaction center protein X


Mass: 5427.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbX / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZPA1
#26: Protein/peptide
Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein Ycf12


Mass: 4692.648 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psb30 / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZL09
#27: Protein
Photosystem II reaction center protein Z / PSII-Z


Mass: 6848.350 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbZ / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZFP8

-
Cytochrome b559 subunit ... , 2 types, 12 molecules EDEEE1e1eDeEFDFEF1f1fDfE

#10: Protein
Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 9344.573 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbE / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EIR1
#11: Protein/peptide
Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4994.852 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbF / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZAF8

-
Protein/peptide , 1 types, 3 molecules SDSES1

#21: Protein/peptide LPP1


Mass: 4017.944 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria)

-
Sugars , 2 types, 78 molecules

#40: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#44: Sugar...
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 14 types, 804 molecules

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


Mass: 588.694 Da / Num. of mol.: 348 / Source method: obtained synthetically / Formula: C33H40N4O6
#34: Chemical
ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CaMn4O5
#35: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#36: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 210 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#37: Chemical
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C53H80O2
#38: Chemical...
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C41H78O12S
#39: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C45H86O10
#41: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CHO3
#42: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#43: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#45: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C55H74N4O5
#46: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#47: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#48: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: In situ PBS-PSII supercomplex / Type: CELL / Entity ID: #1-#32 / Source: NATURAL
Source (natural)Organism: Arthrospira platensis (bacteria)
Buffer solutionpH: 7.6
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 / Calibrated defocus min: 6000 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168000 / Symmetry type: POINT

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