8ASP

RCII/PSI complex, focused refinement of PSI


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis.

Zhao, Z.Vercellino, I.Knoppova, J.Sobotka, R.Murray, J.W.Nixon, P.J.Sazanov, L.A.Komenda, J.

(2023) Nat Commun 14: 4681-4681

  • DOI: https://doi.org/10.1038/s41467-023-40388-6
  • Primary Citation of Related Structures:  
    8AM5, 8ASL, 8ASP

  • PubMed Abstract: 

    Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn 4 CaO 5 cluster, thereby preventing the premature binding of Mn 2+ and Ca 2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn 4 CaO 5 cluster.


  • Organizational Affiliation

    Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, S. Kensington Campus, London, SW7 2AZ, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth a]751Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaAslr1834
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29254 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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UniProt GroupP29254
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth b]731Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaBslr1835
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC [auth c]81Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaCssl0563
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P32422 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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UniProt GroupP32422
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID [auth d]141Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaDslr0737
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVE [auth e]74Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaEssr2831
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIF [auth f]165Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaFsll0819
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth i]40Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaIsmr0004
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth j]40Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaJsml0008
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 1I [auth k]88Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaK1psaKssr0390
Membrane Entity: Yes 
UniProt
Find proteins for P72712 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIJ [auth l]157Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaLslr1655
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIK [auth m]31Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaMsmr0005
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL0
Query on CL0

Download Ideal Coordinates CCD File 
L [auth a]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth a]
AB [auth a]
AC [auth b]
AD [auth b]
BA [auth a]
AA [auth a],
AB [auth a],
AC [auth b],
AD [auth b],
BA [auth a],
BC [auth b],
BD [auth b],
CA [auth a],
CC [auth b],
CD [auth b],
DA [auth a],
DC [auth b],
DD [auth b],
DE [auth j],
EA [auth a],
EC [auth b],
ED [auth b],
EE [auth j],
FA [auth a],
FC [auth b],
GA [auth a],
GC [auth b],
HA [auth a],
HC [auth b],
HE [auth k],
IA [auth a],
IC [auth b],
IE [auth k],
JA [auth a],
JC [auth b],
JE [auth k],
KA [auth a],
KC [auth b],
LA [auth a],
LC [auth b],
LE [auth l],
M [auth a],
MA [auth a],
MB [auth a],
MC [auth b],
ME [auth l],
N [auth a],
NA [auth a],
NB [auth a],
NC [auth b],
NE [auth l],
O [auth a],
OA [auth a],
OC [auth b],
P [auth a],
PA [auth a],
PB [auth b],
PC [auth b],
Q [auth a],
QA [auth a],
QC [auth b],
R [auth a],
RA [auth a],
RB [auth b],
RC [auth b],
S [auth a],
SA [auth a],
SB [auth b],
SC [auth b],
T [auth a],
TA [auth a],
TB [auth b],
TC [auth b],
TD [auth f],
U [auth a],
UA [auth a],
UB [auth b],
UC [auth b],
V [auth a],
VA [auth a],
VB [auth b],
VC [auth b],
VD [auth f],
W [auth a],
WA [auth a],
WB [auth b],
WC [auth b],
WD [auth f],
X [auth a],
XA [auth a],
XB [auth b],
XC [auth b],
Y [auth a],
YA [auth a],
YB [auth b],
YC [auth b],
Z [auth a],
ZA [auth a],
ZB [auth b],
ZC [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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IB [auth a],
KB [auth a],
MD [auth b],
OD [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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HB [auth a],
JB [auth a],
LB [auth a],
ND [auth b],
YD [auth f]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
ZEX
Query on ZEX

Download Ideal Coordinates CCD File 
QD [auth b],
XD [auth f]
(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
EQ3
Query on EQ3

Download Ideal Coordinates CCD File 
PD [auth b](3'R)-3'-hydroxy-beta,beta-caroten-4-one
C40 H54 O2
ZRCXVNZZDQGBQT-BANQPSJHSA-N
45D
Query on 45D

Download Ideal Coordinates CCD File 
OB [auth a]beta,beta-carotene-4,4'-dione
C40 H52 O2
FDSDTBUPSURDBL-DKLMTRRASA-N
ECH
Query on ECH

Download Ideal Coordinates CCD File 
ID [auth b],
OE [auth m]
beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
BCR
Query on BCR

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AE [auth i]
BE [auth j]
CB [auth a]
DB [auth a]
EB [auth a]
AE [auth i],
BE [auth j],
CB [auth a],
DB [auth a],
EB [auth a],
FB [auth a],
FE [auth j],
GB [auth a],
GD [auth b],
GE [auth k],
HD [auth b],
JD [auth b],
KD [auth b],
KE [auth k],
LD [auth b],
UD [auth f],
ZD [auth i]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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CE [auth j]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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BB [auth a],
FD [auth b]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
QB [auth b],
RD [auth c],
SD [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONRELION3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L003260/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P00931X/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P00931X/1
European Research Council (ERC)European Union854126
Czech Science FoundationCzech Republic19-29225X

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release