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 7YMI | pdb_00007ymi

PSII-Pcb Dimer of Acaryochloris Marina

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history. 

Literature

Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll d -containing cyanobacterium.

Shen, L., Gao, Y., Tang, K., Qi, R., Fu, L., Chen, J.H., Wang, W., Ma, X., Li, P., Chen, M., Kuang, T., Zhang, X., Shen, J.R., Wang, P., Han, G.

(2024) Sci Adv 10: eadk7140-eadk7140

  • DOI: https://doi.org/10.1126/sciadv.adk7140
  • Primary Citation Related Structures: 
    7YMI, 7YMM

  • PubMed Abstract: 

    Acaryochloris marina is a unique cyanobacterium using chlorophyll d (Chl d ) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of A. marina associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from A. marina at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization.

    • Organizational Affiliation: 
    • Cryo-EM Centre, Southern University of Science and Technology, Shenzhen 518055, China.

Macromolecule Content 

  • Total Structure Weight: 1,079.02 kDa 
  • Atom Count: 68,428 
  • Modeled Residue Count: 6,692 
  • Deposited Residue Count: 7,498 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 2A,
U [auth a]		360Acaryochloris marina MBIC11017Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for A5A8K9 (Acaryochloris marina (strain MBIC 11017))
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UniProt GroupA5A8K9
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
V [auth b]		506Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0CFM2 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
W [auth c]		490Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C1V7 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 protein 1D,
X [auth d]		351Acaryochloris marina MBIC11017Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for B0C1V6 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]		83Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C6T2 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein YF,
Z [auth f]		99Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C2V2 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 10 kDa phosphoprotein PsbHAA [auth h],
G [auth H]		71Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0CDZ2 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein PsbIBA [auth i],
H [auth I]		34Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C5R5 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
I [auth K]		45Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
J [auth L]		38Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C6T1 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
K [auth M]		34Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0CFM0 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TFA [auth t],
L [auth T]		46Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C605 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinGA [auth x],
M [auth X]		40Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0BYW9 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12HA [auth y],
N [auth Y]		39Acaryochloris marina MBIC11017Mutation(s): 0 
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZIA [auth z],
O [auth Z]		62Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C0S7 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
High light inducible proteinJA [auth 6],
P [auth 2]		352Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C3E5 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown proteinKA [auth g],
Q [auth G]		41Acaryochloris marina MBIC11017Mutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
High light inducible proteinLA [auth 5],
R [auth 1]		356Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C576 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
High light inducible proteinMA [auth 7],
S [auth 3]		349Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C6I0 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
High light inducible proteinNA [auth 8],
T [auth 4]		353Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C3E6 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD


Download:Ideal Coordinates CCD File
MC [auth C],
MI [auth c],
SB [auth B],
UH [auth b]		DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CL7
(Subject of Investigation/LOI)

Query on CL7


Download:Ideal Coordinates CCD File
AB [auth B]
AC [auth C]
AF [auth 3]
AG [auth 4]
AH [auth b]
AB [auth B],
AC [auth C],
AF [auth 3],
AG [auth 4],
AH [auth b],
AI [auth c],
AK [auth 5],
AL [auth 7],
AM [auth 8],
BB [auth B],
BC [auth C],
BD [auth 2],
BE [auth 1],
BF [auth 3],
BG [auth 4],
BH [auth b],
BI [auth c],
BJ [auth 6],
BK [auth 5],
BL [auth 7],
BM [auth 8],
CB [auth B],
CC [auth C],
CD [auth 2],
CE [auth 1],
CF [auth 3],
CG [auth 4],
CH [auth b],
CI [auth c],
CJ [auth 6],
CK [auth 5],
CL [auth 7],
CM [auth 8],
DB [auth B],
DC [auth C],
DD [auth 2],
DE [auth 1],
DF [auth 3],
DG [auth 4],
DH [auth b],
DI [auth c],
DJ [auth 6],
DK [auth 5],
DL [auth 7],
DM [auth 8],
EB [auth B],
EC [auth C],
ED [auth 2],
EE [auth 1],
EF [auth 3],
EG [auth 4],
EH [auth b],
EI [auth c],
EJ [auth 6],
EK [auth 5],
EL [auth 7],
EM [auth 8],
FB [auth B],
FC [auth C],
FD [auth 2],
FE [auth 1],
FF [auth 3],
FG [auth 4],
FH [auth b],
FI [auth c],
FJ [auth 6],
FK [auth 5],
FL [auth 7],
FM [auth 8],
GB [auth B],
GC [auth C],
GD [auth 2],
GE [auth 1],
GF [auth 3],
GG [auth 4],
GH [auth b],
GI [auth c],
GJ [auth 6],
GK [auth 5],
GL [auth 7],
GM [auth 8],
HB [auth B],
HC [auth C],
HD [auth 2],
HE [auth 1],
HF [auth 3],
HG [auth 4],
HH [auth b],
HI [auth c],
HJ [auth 6],
HK [auth 5],
HL [auth 7],
HM [auth 8],
IB [auth B],
IC [auth C],
ID [auth 2],
IE [auth 1],
IF [auth 3],
IG [auth 4],
IH [auth b],
II [auth c],
IJ [auth 6],
IK [auth 5],
IL [auth 7],
IM [auth 8],
JB [auth B],
JC [auth C],
JD [auth 2],
JE [auth 1],
JF [auth 3],
JG [auth 4],
JH [auth b],
JI [auth c],
JJ [auth 6],
JK [auth 5],
JL [auth 7],
JM [auth 8],
KB [auth B],
KD [auth 2],
KE [auth 1],
KF [auth 3],
KG [auth 4],
KH [auth b],
KJ [auth 6],
KK [auth 5],
KL [auth 7],
KM [auth 8],
LD [auth 2],
LE [auth 1],
LF [auth 3],
LG [auth 4],
LH [auth b],
LJ [auth 6],
LK [auth 5],
LL [auth 7],
MD [auth 2],
ME [auth 1],
MF [auth 3],
MG [auth 4],
MH [auth b],
MJ [auth 6],
MK [auth 5],
ML [auth 7],
NC [auth C],
ND [auth 2],
NE [auth 1],
NF [auth 3],
NI [auth c],
NJ [auth 6],
NK [auth 5],
NL [auth 7],
OA [auth A],
OD [auth 2],
OE [auth 1],
OF [auth 3],
OJ [auth 6],
OK [auth 5],
PD [auth 2],
PE [auth 1],
PJ [auth 6],
PK [auth 5],
QA [auth A],
QB [auth B],
QC [auth D],
QD [auth 2],
QE [auth 1],
QG [auth a],
QI [auth d],
QJ [auth 6],
QK [auth 5],
RD [auth 2],
RE [auth 1],
RJ [auth 6],
RK [auth 5],
SC [auth D],
SD [auth 2],
SE [auth 1],
SG [auth a],
SH [auth b],
SI [auth d],
SJ [auth 6],
SK [auth 5],
TA [auth A],
TC [auth D],
TE [auth 1],
TI [auth d],
UG [auth a],
VA [auth B],
WA [auth B],
WK [auth 7],
XA [auth B],
XB [auth C],
XE [auth 3],
XG [auth b],
XH [auth c],
XK [auth 7],
XL [auth 8],
YA [auth B],
YB [auth C],
YE [auth 3],
YG [auth b],
YH [auth c],
YK [auth 7],
YL [auth 8],
ZA [auth B],
ZB [auth C],
ZE [auth 3],
ZF [auth 4],
ZG [auth b],
ZH [auth c],
ZK [auth 7],
ZL [auth 8]
CHLOROPHYLL D
C54 H70 Mg N4 O6
FBCRYORFRGRJBC-ACDPFEIMSA-L
PHO
(Subject of Investigation/LOI)

Query on PHO


Download:Ideal Coordinates CCD File
PA [auth A],
RG [auth a],
WC [auth D],
WI [auth d]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
(Subject of Investigation/LOI)

Query on SQD


Download:Ideal Coordinates CCD File
OB [auth B]
QH [auth b]
QL [auth 7]
RF [auth 3]
SA [auth A]
OB [auth B],
QH [auth b],
QL [auth 7],
RF [auth 3],
SA [auth A],
SL [auth 7],
TF [auth 3],
UB [auth B],
VJ [auth 6],
VK [auth 5],
WD [auth 2],
WE [auth 1],
XJ [auth 6],
YD [auth 2]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
(Subject of Investigation/LOI)

Query on LMG


Download:Ideal Coordinates CCD File
AE [auth 1]
PB [auth B]
RH [auth b]
WB [auth C]
WH [auth c]
AE [auth 1],
PB [auth B],
RH [auth b],
WB [auth C],
WH [auth c],
YC [auth D],
YI [auth d],
ZJ [auth 5]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
(Subject of Investigation/LOI)

Query on PL9


Download:Ideal Coordinates CCD File
VC [auth D],
VI [auth d]		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
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG


Download:Ideal Coordinates CCD File
RB [auth B]
TB [auth B]
TH [auth b]
TL [auth 7]
UA [auth A]
RB [auth B],
TB [auth B],
TH [auth b],
TL [auth 7],
UA [auth A],
UF [auth 3],
UL [auth 8],
VG [auth a],
VH [auth b],
WF [auth 4],
XC [auth D],
XI [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
(Subject of Investigation/LOI)

Query on HEM


Download:Ideal Coordinates CCD File
ZC [auth F],
ZI [auth f]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZEX
(Subject of Investigation/LOI)

Query on ZEX


Download:Ideal Coordinates CCD File
LM [auth 8]
MM [auth 8]
NG [auth 4]
NM [auth 8]
OG [auth 4]
LM [auth 8],
MM [auth 8],
NG [auth 4],
NM [auth 8],
OG [auth 4],
OL [auth 7],
PF [auth 3],
PG [auth 4],
PL [auth 7],
QF [auth 3],
RL [auth 7],
SF [auth 3],
TD [auth 2],
TJ [auth 6],
TK [auth 5],
UD [auth 2],
UE [auth 1],
UJ [auth 6],
UK [auth 5],
VD [auth 2],
VE [auth 1],
VF [auth 3],
WJ [auth 6],
WL [auth 8],
XD [auth 2],
YF [auth 4],
YJ [auth 6],
ZD [auth 2]
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
C40 H56 O2
YRMDXLDAZBQLBK-WIHRHFSMSA-N
8CT
(Subject of Investigation/LOI)

Query on 8CT


Download:Ideal Coordinates CCD File
AD [auth K]
AJ [auth k]
KC [auth C]
KI [auth c]
LB [auth B]
AD [auth K],
AJ [auth k],
KC [auth C],
KI [auth c],
LB [auth B],
LC [auth C],
LI [auth c],
MB [auth B],
NB [auth B],
NH [auth b],
OC [auth C],
OH [auth b],
OI [auth c],
PH [auth b],
RA [auth A],
TG [auth a],
UC [auth D],
UI [auth d],
VB [auth B],
VL [auth 8],
WG [auth b],
XF [auth 4]
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
C40 H56
ANVAOWXLWRTKGA-GZSHKXEASA-N
BCT
(Subject of Investigation/LOI)

Query on BCT


Download:Ideal Coordinates CCD File
RC [auth D],
RI [auth d]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
(Subject of Investigation/LOI)

Query on FE2


Download:Ideal Coordinates CCD File
PC [auth D],
PI [auth d]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UNK
Query on UNK		KA [auth g],
Q [auth G]		L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaQYZDY-SSW-SMC003
Chinese Academy of SciencesChinaXDB17000000
National Basic Research Program of China (973 Program)China2015CB150100

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Data collection, Database references
  • Version 2.0: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2026-09-16
    Changes: Data collection, Structure summary
  • Version 2.2: 2026-09-23
    Changes: Data collection