8AM5

RCII/PSI complex, class 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 II protein D1 2344Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psbA2psbA-2slr1311psbA3psbA-3sll1867
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinB [auth D]336Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psbDsll0849
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaC [auth E]81Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psbEssr3451
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaD [auth F]44Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psbFsmr0006
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IE [auth I]38Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psbIsml0001
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II assembly lipoprotein Ycf48F [auth S]342Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: ycf48slr2034
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1G [auth a]751Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaAslr1834
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2H [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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerI [auth c]81Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaCssl0563
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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UniProt GroupP32422
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIJ [auth d]141Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaDslr0737
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVK [auth e]74Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaEssr2831
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIL [auth f]165Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaFsll0819
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth i]40Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaIsmr0004
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth j]40Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaJsml0008
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 1O [auth k]86Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaK1psaKssr0390
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIP [auth l]157Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaLslr1655
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIQ [auth m]31Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: psaMsmr0005
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL0
Query on CL0

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CA [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 D]
AB [auth a]
AD [auth b]
BB [auth a]
BD [auth b]
AA [auth D],
AB [auth a],
AD [auth b],
BB [auth a],
BD [auth b],
CB [auth a],
CD [auth b],
CF [auth l],
DA [auth a],
DB [auth a],
DD [auth b],
DF [auth l],
EA [auth a],
EB [auth a],
ED [auth b],
EF [auth l],
FA [auth a],
FB [auth a],
FC [auth a],
FD [auth b],
GA [auth a],
GB [auth a],
GC [auth a],
GD [auth b],
HA [auth a],
HB [auth a],
HD [auth b],
IA [auth a],
IB [auth a],
ID [auth b],
JA [auth a],
JB [auth a],
JC [auth a],
JD [auth b],
KA [auth a],
KB [auth a],
KC [auth b],
KD [auth b],
LA [auth a],
LB [auth a],
LC [auth b],
LD [auth b],
MA [auth a],
MB [auth a],
MC [auth b],
MD [auth b],
ME [auth f],
NA [auth a],
NB [auth a],
NC [auth b],
ND [auth b],
OA [auth a],
OB [auth a],
OC [auth b],
OD [auth b],
OE [auth f],
PA [auth a],
PB [auth a],
PC [auth b],
PD [auth b],
PE [auth f],
QA [auth a],
QB [auth a],
QC [auth b],
QD [auth b],
RA [auth a],
RB [auth a],
RC [auth b],
RD [auth b],
S [auth A],
SA [auth a],
SB [auth a],
SC [auth b],
SD [auth b],
T [auth A],
TA [auth a],
TC [auth b],
TD [auth b],
UA [auth a],
UC [auth b],
UD [auth b],
V [auth A],
VA [auth a],
VC [auth b],
VD [auth b],
WA [auth a],
WC [auth b],
WD [auth b],
WE [auth j],
X [auth A],
XA [auth a],
XC [auth b],
XD [auth b],
XE [auth j],
YA [auth a],
YC [auth b],
YE [auth k],
Z [auth D],
ZA [auth a],
ZC [auth b],
ZE [auth k]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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U [auth A],
Y [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
LMG
Query on LMG

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BF [auth l],
DC [auth a],
FE [auth b],
HE [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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BC [auth a],
CC [auth a],
EC [auth a],
GE [auth b],
RE [auth f]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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BA [auth E]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZEX
Query on ZEX

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JE [auth b],
QE [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

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IE [auth b](3'R)-3'-hydroxy-beta,beta-caroten-4-one
C40 H54 O2
ZRCXVNZZDQGBQT-BANQPSJHSA-N
45D
Query on 45D

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HC [auth a]beta,beta-carotene-4,4'-dione
C40 H52 O2
FDSDTBUPSURDBL-DKLMTRRASA-N
ECH
Query on ECH

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BE [auth b],
GF [auth m]
beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
BCR
Query on BCR

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AC [auth a]
AE [auth b]
AF [auth k]
CE [auth b]
DE [auth b]
AC [auth a],
AE [auth b],
AF [auth k],
CE [auth b],
DE [auth b],
EE [auth b],
FF [auth l],
IC [auth a],
NE [auth f],
SE [auth i],
TE [auth i],
UE [auth j],
VB [auth a],
W [auth A],
WB [auth a],
XB [auth a],
YB [auth a],
ZB [auth a],
ZD [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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

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

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KE [auth c],
LE [auth c],
UB [auth a]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
R [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.19

Structure Validation

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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