9K9W | pdb_00009k9w

structure of bundle-shaped PBS with short rod

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history. 


Literature

Light-induced structural adaptation of the bundle-shaped phycobilisome from thylakoid-lacking cyanobacterium Gloeobacter violaceus.

Ma, J., You, X., Sun, S., Sui, S.F.

(2025) Nat Commun 16: 5956-5956

  • DOI: https://doi.org/10.1038/s41467-025-60673-w
  • Primary Citation of Related Structures:  
    9K9W, 9M3J

  • PubMed Abstract: 

    Gloeobacter diverged from other lineages early in cyanobacterial evolution, preferentially growing under low light intensity conditions. Among cyanobacteria, G. violaceus exhibits unique features, including lack of a thylakoid membrane and bundle-shaped antenna phycobilisomes (PBSs), densely packed and well-organized on the plasma membrane. However, without high-resolution structures, it has remained unclear how G. violaceus PBSs assemble into a bundle-shaped configuration. Here we solve the cryo-EM structures of PBSs from G. violaceus cells cultured under low (Sr-PBS) or moderate (Lr-PBS) light intensity. These structures reveal two unique linker proteins, L RC 91kDa and L RC 81kDa , that play a key role in the PBS architecture. Analysis of the bilin arrangement indicates that the bundle-shaped structure allows efficient energy transfer among rods. Moreover, comparison between Lr-PBS and Sr-PBS uncovers a distinct mode of adaption to increased light intensity wherein the ApcA 2 -ApcB 3 -ApcD layer can be blocked from binding to the core by altering structural elements exclusively found in the G. violaceus L CM . This study illustrates previously unrecognized mechanisms of assembly and adaptation to varying light intensity in the bundle-shaped PBS of G. violaceus.

    • Organizational Affiliation: 
    • State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China. majf@nankai.edu.cn.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin beta subunit161Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7NL79 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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UniProt GroupQ7NL79
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phycocyanin alpha chain162Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7M7F7 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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UniProt GroupQ7M7F7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phycocyanin beta chain172Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7M7C7 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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UniProt GroupQ7M7C7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phycocyanin-associated rod linker protein274Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7NGF2 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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UniProt GroupQ7NGF2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phycocyanin-associated rod linker protein275Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7NM19 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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UniProt GroupQ7NM19
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Glr2806 proteinBE [auth M6],
TA [auth M2]		729Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7NGT2 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
CpcD proteinCE [auth N6],
UA [auth N2]		70Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7NL59 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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UniProt GroupQ7NL59
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin alpha subunit161Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7NL80 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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UniProt GroupQ7NL80
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core68Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7NL78 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobiliprotein ApcEGE [auth j5],
HE [auth k5]		1,155Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7NL81 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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UniProt GroupQ7NL81
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Glr1262 proteinUI [auth a9],
VI [auth aA]		824Gloeobacter violaceus PCC 7421Mutation(s): 0 
UniProt
Find proteins for Q7NL64 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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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 
AK [auth GA]
AL [auth ZA]
AM [auth A3]
AN [auth T3]
AO [auth J4]
AK [auth GA],
AL [auth ZA],
AM [auth A3],
AN [auth T3],
AO [auth J4],
AP [auth G5],
AQ [auth L6],
AR [auth R7],
AS [auth a7],
AT [auth W8],
AU [auth O9],
AV [auth T9],
AW [auth W1],
BK [auth HA],
BL [auth O1],
BM [auth B3],
BN [auth T3],
BO [auth J4],
BP [auth H5],
BQ [auth N6],
BR [auth S7],
BS [auth b7],
BT [auth W8],
BU [auth P9],
BV [auth T9],
BW [auth X1],
CK [auth HA],
CL [auth P1],
CM [auth B3],
CN [auth U3],
CO [auth K4],
CP [auth I5],
CQ [auth A7],
CR [auth B7],
CS [auth c7],
CT [auth X8],
CU [auth P9],
CV [auth U9],
CW [auth X1],
DK [auth IA],
DL [auth P1],
DM [auth C3],
DN [auth V3],
DO [auth L4],
DP [auth J5],
DQ [auth j5],
DR [auth C7],
DS [auth d7],
DT [auth F8],
DU [auth Q9],
DV [auth V9],
DW [auth Y1],
EK [auth JA],
EL [auth Q1],
EM [auth D3],
EN [auth V3],
EO [auth L4],
EP [auth C1],
EQ [auth j5],
ER [auth D7],
ES [auth e7],
ET [auth F8],
EU [auth Y8],
EV [auth V9],
EW [auth Z1],
FK [auth JA],
FL [auth R1],
FM [auth D3],
FN [auth W3],
FO [auth M4],
FP [auth c5],
FQ [auth k5],
FR [auth E7],
FS [auth f7],
FT [auth G8],
FU [auth Z8],
FV [auth W9],
FW [auth Z1],
GK [auth KA],
GL [auth R1],
GM [auth E3],
GN [auth X3],
GO [auth N4],
GP [auth d5],
GQ [auth k5],
GR [auth F7],
GS [auth E1],
GT [auth H8],
GU [auth A9],
GV [auth X9],
GW [auth A2],
HK [auth LA],
HL [auth S1],
HM [auth F3],
HN [auth X3],
HO [auth O4],
HP [auth e5],
HQ [auth k5],
HR [auth G7],
HS [auth A8],
HT [auth H8],
HU [auth B9],
HV [auth X9],
HW [auth B2],
IK [auth LA],
IL [auth A1],
IM [auth F3],
IN [auth Y3],
IO [auth O4],
IP [auth f5],
IQ [auth k5],
IR [auth H7],
IS [auth B8],
IT [auth I8],
IU [auth B9],
IV [auth Y9],
IW [auth C2],
JK [auth OA],
JL [auth G3],
JM [auth Z3],
JN [auth B1],
JO [auth P4],
JP [auth P5],
JQ [auth A6],
JR [auth I7],
JS [auth B8],
JT [auth J8],
JU [auth C9],
JV [auth Z9],
JW [auth D2],
KK [auth PA],
KL [auth H3],
KM [auth Z3],
KN [auth B1],
KO [auth Q4],
KP [auth Q5],
KQ [auth B6],
KR [auth J7],
KS [auth C8],
KT [auth J8],
KU [auth D9],
KV [auth Z9],
KW [auth D2],
LK [auth PA],
LL [auth H3],
LM [auth A4],
LN [auth S4],
LO [auth R4],
LP [auth R5],
LQ [auth C6],
LR [auth K7],
LS [auth D8],
LT [auth K8],
LU [auth D9],
LV [auth G1],
LW [auth E2],
MK [auth QA],
ML [auth I3],
MM [auth B4],
MN [auth S4],
MO [auth K5],
MP [auth S5],
MQ [auth D6],
MR [auth L7],
MS [auth D8],
MT [auth L8],
MU [auth E9],
MV [auth a9],
MW [auth F2],
NK [auth RA],
NL [auth J3],
NM [auth B4],
NN [auth T4],
NO [auth L5],
NP [auth T5],
NQ [auth D6],
NR [auth M7],
NS [auth E8],
NT [auth M8],
NU [auth F9],
NV [auth aA],
NW [auth F2],
OK [auth RA],
OL [auth J3],
OM [auth C4],
ON [auth U4],
OO [auth M5],
OP [auth U5],
OQ [auth E6],
OR [auth N7],
OS [auth m7],
OT [auth M8],
OU [auth F9],
OV [auth aA],
PK [auth SA],
PL [auth K3],
PM [auth D4],
PN [auth U4],
PO [auth N5],
PP [auth V5],
PQ [auth F6],
PR [auth g7],
PS [auth o7],
PT [auth N8],
PU [auth F9],
PV [auth H1],
QJ [auth A],
QK [auth TA],
QL [auth G2],
QM [auth D4],
QN [auth V4],
QO [auth O5],
QP [auth W5],
QQ [auth F6],
QR [auth h7],
QS [auth p7],
QT [auth O8],
QU [auth G9],
QV [auth H1],
RJ [auth Z],
RK [auth TA],
RL [auth H2],
RM [auth L3],
RN [auth W4],
RO [auth X4],
RP [auth X5],
RQ [auth G6],
RR [auth i7],
RS [auth q7],
RT [auth O8],
RU [auth H9],
RV [auth I1],
SJ [auth AA],
SK [auth UA],
SL [auth H2],
SM [auth L3],
SN [auth W4],
SO [auth Y4],
SP [auth Y5],
SQ [auth H6],
SR [auth j7],
SS [auth r7],
ST [auth P8],
SU [auth H9],
SV [auth J1],
TJ [auth BA],
TK [auth VA],
TL [auth I2],
TM [auth O3],
TN [auth E4],
TO [auth Z4],
TP [auth Z5],
TQ [auth H6],
TR [auth k7],
TS [auth s7],
TT [auth Q8],
TU [auth I9],
TV [auth K1],
UJ [auth BA],
UK [auth VA],
UL [auth J2],
UM [auth P3],
UN [auth F4],
UO [auth A5],
UP [auth a5],
UQ [auth I6],
UR [auth T7],
US [auth u7],
UT [auth R8],
UU [auth J9],
UV [auth L1],
VJ [auth CA],
VK [auth WA],
VL [auth J2],
VM [auth P3],
VN [auth F4],
VO [auth B5],
VP [auth b5],
VQ [auth D1],
VR [auth U7],
VS [auth v7],
VT [auth S8],
VU [auth J9],
VV [auth T1],
WJ [auth DA],
WK [auth XA],
WL [auth K2],
WM [auth Q3],
WN [auth G4],
WO [auth C5],
WP [auth J6],
WQ [auth D1],
WR [auth V7],
WS [auth T8],
WT [auth F1],
WU [auth K9],
WV [auth T1],
XJ [auth DA],
XK [auth XA],
XL [auth L2],
XM [auth R3],
XN [auth H4],
XO [auth D5],
XP [auth J6],
XQ [auth O7],
XR [auth W7],
XS [auth U8],
XT [auth F1],
XU [auth R9],
XV [auth U1],
YJ [auth EA],
YK [auth YA],
YL [auth L2],
YM [auth R3],
YN [auth H4],
YO [auth E5],
YP [auth K6],
YQ [auth P7],
YR [auth X7],
YS [auth U8],
YT [auth L9],
YU [auth R9],
YV [auth V1],
ZJ [auth FA],
ZK [auth ZA],
ZL [auth N2],
ZM [auth S3],
ZN [auth I4],
ZO [auth F5],
ZP [auth L6],
ZQ [auth Q7],
ZR [auth Y7],
ZS [auth V8],
ZT [auth L9],
ZU [auth S9],
ZV [auth V1]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
A
B [auth Z]
BD [auth F5]
BF [auth F7]
BG [auth f7]
A,
B [auth Z],
BD [auth F5],
BF [auth F7],
BG [auth f7],
DD [auth H5],
DF [auth H7],
FD [auth J5],
FF [auth J7],
HF [auth L7],
ID [auth d5],
IG [auth l7],
JF [auth N7],
KD [auth f5],
KG [auth n7],
LD [auth P5],
LF [auth h7],
MG [auth p7],
ND [auth R5],
NF [auth j7],
OG [auth r7],
PC [auth L5],
PD [auth T5],
PF [auth T7],
QG [auth t7],
RC [auth N5],
RD [auth V5],
RF [auth V7],
SG [auth v7],
TD [auth X5],
TE [auth P7],
TF [auth X7],
VD [auth Z5],
VE [auth R7],
VF [auth Z7],
XC [auth B5],
XD [auth b5],
XE [auth B7],
XF [auth b7],
ZC [auth D5],
ZE [auth D7],
ZF [auth d7]
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1beta
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31670745
National Natural Science Foundation of China (NSFC)China31861143048

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Data collection, Database references