9HYU | pdb_00009hyu

Cryo-EM structure of the Chromera velia PSI supercomplex at 1.84 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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

Literature

The cryo-EM structure of Photosystem I from Chromera velia with a bound superoxide dismutase heterodimer.

Yuan, X.Lukes, M.Qian, P.Charras, Q.Smrcka, T.Man, P.Kovarova, L.Konik, P.Heilmann, E.Al-Amoudi, A.Sobotka, R.Naschberger, A.

(2025) Nat Commun 17: 913-913

  • DOI: https://doi.org/10.1038/s41467-025-67637-0
  • Primary Citation Related Structures: 
    9HYU

  • PubMed Abstract: 

    Photosystem I is a key component of the solar energy conversion machinery in oxygenic photosynthesis, and its core, where photochemistry occurs, is highly conserved. However, the coral-associated alga Chromera velia that is evolutionary linked to parasitic apicomplexans, exhibits Photosystem I with unusual features. These include the splitting of the central PsaA subunit and the binding of superoxide dismutases as regular subunits. The organization of such a unique Photosystem I was enigmatic. Here, we present the cryo-EM structure of Chromera velia Photosystem I at 1.84 Å resolution. Our work reveals a superoxide dismutase heterodimer bound to the stromal side of the core, stabilized by extensions of canonical subunits, a novel protein PsaV, and a reduced light-harvesting apparatus. We elucidate how the complex evolved to accommodate the superoxide dismutase, assemble the split PsaA, and integrate antenna proteins in a non-canonical orientation. Based on our data and prior physiological data, we propose that this specialized Photosystem I functions likely as an Mehler machine, redirecting electrons from Photosystem II back to water. This mechanism enables Chromera velia to manage redox imbalance and reduce photorespiration through localized oxygen consumption.


  • Organizational Affiliation
    • King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia.

Macromolecule Content 

  • Total Structure Weight: 826.45 kDa 
  • Atom Count: 46,279 
  • Modeled Residue Count: 4,292 
  • Deposited Residue Count: 5,814 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Fe]A [auth 1]370Chromera veliaMutation(s): 0 
EC: 1.15.1.1
UniProt
Find proteins for A0A0G4HJZ8 (Chromera velia CCMP2878)
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Entity Groups
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UniProt GroupA0A0G4HJZ8
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Fe]B [auth 2]267Chromera veliaMutation(s): 0 
EC: 1.15.1.1
UniProt
Find proteins for A0A0G4FB02 (Chromera velia CCMP2878)
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UniProt GroupA0A0G4FB02
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
photosystem IC [auth A]395Chromera veliaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for D9IXI2 (Chromera velia)
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UniProt GroupD9IXI2
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerD [auth C]80Chromera veliaMutation(s): 0 
EC: 1.97.1.12
UniProt
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UniProt GroupD9IXG0
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIE [auth D]269Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4H942 (Chromera velia CCMP2878)
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UniProt GroupA0A0G4H942
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVF [auth E]133Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4H6U3 (Chromera velia CCMP2878)
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UniProt GroupA0A0G4H6U3
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIG [auth F]326Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4GX86 (Chromera velia CCMP2878)
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UniProt GroupA0A0G4GX86
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I protein (PsaI)H [auth I]211Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4HFQ7 (Chromera velia CCMP2878)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI [auth L]277Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4GX71 (Chromera velia CCMP2878)
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UniProt GroupA0A0G4GX71
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I protein (PsaM)J [auth M]195Chromera veliaMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I protein (PsaR)K [auth R]202Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4FDJ8 (Chromera velia CCMP2878)
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UniProt GroupA0A0G4FDJ8
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Plastid light harvesting proteinL [auth b]293Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4ID45 (Chromera velia CCMP2878)
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UniProt GroupA0A0G4ID45
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Plastid light harvesting proteinM [auth c]237Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4FL36 (Chromera velia CCMP2878)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Plastid light harvesting proteinN [auth d]222Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4HNB1 (Chromera velia CCMP2878)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Plastid light harvesting proteinO [auth e]217Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4HMN0 (Chromera velia CCMP2878)
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UniProt GroupA0A0G4HMN0
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticP [auth f]277Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4I0G6 (Chromera velia CCMP2878)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I protein (PsaV)Q [auth u]424Chromera veliaMutation(s): 0 
UniProt
Find proteins for A0A0G4HRT4 (Chromera velia CCMP2878)
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UniProt GroupA0A0G4HRT4
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1R [auth a]280Chromera veliaMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I protein (PsaB)S [auth B]1,139Chromera veliaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for D9IXI4 (Chromera velia)
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UniProt GroupD9IXI4
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 20
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseT [auth G]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 21
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseU [auth H]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I05
(Subject of Investigation/LOI)

Query on A1I05



Download:Ideal Coordinates CCD File
DJ [auth B][(2~{R})-3-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate
C61 H116 O11
FOFDHSVOXDANPH-DCHOAZFQSA-N
AV0

Query on AV0



Download:Ideal Coordinates CCD File
UB [auth L]Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-VWHTXWAPSA-N
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
BH [auth u]
CB [auth F]
GE [auth c]
OA [auth A]
UC [auth b]
BH [auth u],
CB [auth F],
GE [auth c],
OA [auth A],
UC [auth b],
VC [auth b]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CL0
(Subject of Investigation/LOI)

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 A]
AI [auth B]
BA [auth A]
BI [auth B]
CH [auth a]
AA [auth A],
AI [auth B],
BA [auth A],
BI [auth B],
CH [auth a],
CI [auth B],
DA [auth A],
DI [auth B],
EA [auth A],
EC [auth b],
ED [auth b],
EH [auth a],
EI [auth B],
FA [auth A],
FC [auth b],
FD [auth c],
FG [auth f],
FI [auth B],
GA [auth A],
GC [auth b],
GD [auth c],
GG [auth f],
GH [auth a],
GI [auth B],
HA [auth A],
HC [auth b],
HD [auth c],
HG [auth f],
HH [auth a],
HI [auth B],
IA [auth A],
IC [auth b],
ID [auth c],
IF [auth e],
IG [auth f],
IH [auth a],
II [auth B],
JA [auth A],
JC [auth b],
JD [auth c],
JF [auth e],
JG [auth f],
JH [auth a],
JI [auth B],
KC [auth b],
KD [auth c],
KF [auth e],
KG [auth f],
KI [auth B],
LB [auth L],
LC [auth b],
LD [auth c],
LF [auth e],
LG [auth f],
LI [auth B],
MB [auth L],
MC [auth b],
MD [auth c],
MF [auth e],
MG [auth f],
MH [auth a],
MI [auth B],
NB [auth L],
NC [auth b],
ND [auth c],
NE [auth d],
NF [auth e],
NG [auth f],
NH [auth a],
NI [auth B],
OC [auth b],
OD [auth c],
OE [auth d],
OF [auth e],
OG [auth f],
OH [auth B],
OI [auth B],
PA [auth A],
PD [auth c],
PE [auth d],
PF [auth e],
PG [auth f],
PI [auth B],
QD [auth c],
QE [auth d],
QF [auth e],
QG [auth f],
QI [auth B],
RE [auth d],
RI [auth B],
SA [auth A],
SE [auth d],
SH [auth B],
SI [auth B],
TE [auth d],
TH [auth B],
UE [auth d],
UH [auth B],
VB [auth L],
VH [auth B],
W [auth A],
WA [auth F],
WB [auth R],
WH [auth B],
X [auth A],
XA [auth F],
XB [auth R],
XH [auth B],
Y [auth A],
YA [auth F],
YH [auth B],
Z [auth A],
ZA [auth F],
ZH [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
(Subject of Investigation/LOI)

Query on SQD



Download:Ideal Coordinates CCD File
AF [auth d]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



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DB [auth F]
DD [auth b]
GB [auth F]
NA [auth A]
QB [auth L]
DB [auth F],
DD [auth b],
GB [auth F],
NA [auth A],
QB [auth L],
RA [auth A],
SB [auth L],
WC [auth b],
WG [auth f],
XC [auth b],
ZB [auth R]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
A1L6D
(Subject of Investigation/LOI)

Query on A1L6D



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TF [auth e],
UG [auth f],
WI [auth B],
ZE [auth d]
[(1~{R},5~{S})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{Z})-3,7,12,16-tetramethyl-17-oxidanyl-19-oxidanylidene-19-[(1~{R},4~{S})-1,2,2-trimethyl-4-oxidanyl-cyclopentyl]nonadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate
C42 H58 O6
LUDSIBUOXLKVSG-BDVOIICUSA-N
XAT
(Subject of Investigation/LOI)

Query on XAT



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CC [auth R]
LH [auth a]
MA [auth A]
PC [auth b]
QC [auth b]
CC [auth R],
LH [auth a],
MA [auth A],
PC [auth b],
QC [auth b],
RC [auth b],
RD [auth c],
RF [auth e],
RG [auth f],
SC [auth b],
SD [auth c],
SF [auth e],
SG [auth f],
TD [auth c],
TG [auth f],
UD [auth c],
VE [auth d],
VG [auth f],
WE [auth d],
XE [auth d],
YB [auth R],
YE [auth d]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
BCR
(Subject of Investigation/LOI)

Query on BCR



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DH [auth a]
OB [auth L]
PB [auth L]
PH [auth B]
TC [auth b]
DH [auth a],
OB [auth L],
PB [auth L],
PH [auth B],
TC [auth b],
UI [auth B],
VA [auth F],
VI [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



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AB [auth F]
AC [auth R]
AD [auth b]
AE [auth c]
AG [auth f]
AB [auth F],
AC [auth R],
AD [auth b],
AE [auth c],
AG [auth f],
AH [auth f],
AJ [auth B],
BB [auth F],
BC [auth R],
BD [auth b],
BE [auth c],
BF [auth d],
BG [auth f],
BJ [auth B],
CD [auth b],
CE [auth c],
CF [auth d],
CG [auth f],
CJ [auth B],
DC [auth b],
DE [auth c],
DF [auth d],
DG [auth f],
EB [auth F],
EE [auth c],
EF [auth d],
EG [auth f],
EJ [auth B],
FB [auth F],
FE [auth c],
FF [auth d],
FH [auth a],
FJ [auth B],
GF [auth d],
GJ [auth B],
HB [auth F],
HE [auth c],
HF [auth d],
IB [auth F],
IE [auth c],
JB [auth L],
JE [auth c],
KB [auth L],
KE [auth c],
KH [auth a],
LE [auth c],
ME [auth d],
QA [auth A],
QH [auth B],
RB [auth L],
RH [auth B],
TB [auth L],
UF [auth e],
VD [auth c],
VF [auth e],
WD [auth c],
WF [auth e],
XD [auth c],
XF [auth e],
XG [auth f],
XI [auth B],
YC [auth b],
YD [auth c],
YF [auth e],
YG [auth f],
YI [auth B],
ZC [auth b],
ZD [auth c],
ZF [auth e],
ZG [auth f],
ZI [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
(Subject of Investigation/LOI)

Query on PQN



Download:Ideal Coordinates CCD File
LA [auth A],
TI [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
KA [auth A],
TA [auth C],
UA [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
V [auth 2]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionSynergy Award 854126

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-28
    Type: Initial release
  • Version 1.1: 2026-03-18
    Changes: Data collection, Database references