8CMO | pdb_00008cmo

Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.

Fadeeva, M.Klaiman, D.Nelson, N.

To be published.

Macromolecule Content 

  • Total Structure Weight: 732.39 kDa 
  • Atom Count: 50,057 
  • Modeled Residue Count: 4,259 
  • Deposited Residue Count: 4,259 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1 PsaA740CoelastrellaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0AAN0NNU4 (Coelastrella)
Explore A0AAN0NNU4 
Go to UniProtKB:  A0AAN0NNU4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAN0NNU4
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2 PsaB732CoelastrellaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0AAN0NNU5 (Coelastrella)
Explore A0AAN0NNU5 
Go to UniProtKB:  A0AAN0NNU5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAN0NNU5
Sequence Annotations
Expand
Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I subunit VII PsaC80CoelastrellaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0AAN0NNU6 (Coelastrella)
Explore A0AAN0NNU6 
Go to UniProtKB:  A0AAN0NNU6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAN0NNU6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II PsaD142CoelastrellaMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV PsaE61CoelastrellaMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III PsaF165CoelastrellaMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V PsaG93CoelastrellaMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII PsaIH [auth I]41CoelastrellaMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I subunit IX PsaJI [auth J]40CoelastrellaMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaKJ [auth K]89CoelastrellaMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction centre subunit XI PsaLK [auth L]123CoelastrellaMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein of photosystem I Lhca1L [auth 1],
M [auth Z]
194CoelastrellaMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein of photosystem I Lhca3N [auth 3]218CoelastrellaMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein of photosystem I Lhca7O [auth 7]220CoelastrellaMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein of photosystem I Lhca8P [auth 8]214CoelastrellaMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein of photosystem I Lhca4Q [auth 4]207CoelastrellaMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein of photosystem I Lhca5R [auth 5]226CoelastrellaMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein of photosystem I Lhca6S [auth 6]226CoelastrellaMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein of photosystem I Lhca9T [auth 9]184CoelastrellaMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting protein of photosystem I Lhca2 partialU [auth 2]70CoelastrellaMutation(s): 0 

Small Molecules

Ligands 23 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
OG [auth 3],
WF [auth 1],
YD [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL



Download:Ideal Coordinates CCD File
EH [auth 3]
HG [auth Z]
HM [auth 9]
IG [auth Z]
II [auth 8]
EH [auth 3],
HG [auth Z],
HM [auth 9],
IG [auth Z],
II [auth 8],
JM [auth 9],
ML [auth 6],
NK [auth 5],
NL [auth 6],
NM [auth 2],
OJ [auth 4],
OK [auth 5],
PF [auth 1],
PJ [auth 4],
PL [auth 6],
RJ [auth 4],
RL [auth 6],
SK [auth 5],
TI [auth 8],
UJ [auth 4],
WH [auth 7],
WI [auth 8]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AD [auth B]
AF [auth L]
AG [auth Z]
AA [auth A],
AB [auth A],
AD [auth B],
AF [auth L],
AG [auth Z],
AH [auth 3],
AI [auth 7],
AM [auth 9],
BA [auth A],
BB [auth A],
BD [auth B],
BF [auth L],
BG [auth Z],
BH [auth 3],
BM [auth 9],
CA [auth A],
CB [auth A],
CD [auth B],
CE [auth F],
CF [auth L],
CG [auth Z],
CH [auth 3],
CM [auth 9],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth F],
DG [auth Z],
DH [auth 3],
DM [auth 9],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EG [auth Z],
EK [auth 5],
EL [auth 6],
EM [auth 9],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FE [auth F],
FG [auth Z],
FH [auth 3],
FI [auth 7],
FK [auth 5],
FL [auth 6],
FM [auth 9],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GE [auth F],
GG [auth Z],
GH [auth 3],
GI [auth 7],
GJ [auth 4],
GK [auth 5],
GL [auth 6],
GM [auth 9],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth 1],
HH [auth 3],
HI [auth 7],
HJ [auth 4],
HK [auth 5],
HL [auth 6],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IF [auth 1],
IJ [auth 4],
IK [auth 5],
IL [auth 6],
IM [auth 9],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth 1],
JG [auth Z],
JH [auth 3],
JJ [auth 4],
JK [auth 5],
JL [auth 6],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KE [auth G],
KF [auth 1],
KG [auth Z],
KJ [auth 4],
KK [auth 5],
KL [auth 6],
LA [auth A],
LC [auth B],
LD [auth B],
LE [auth G],
LF [auth 1],
LG [auth Z],
LJ [auth 4],
LK [auth 5],
LL [auth 6],
LM [auth 2],
MA [auth A],
MC [auth B],
MD [auth B],
MF [auth 1],
MG [auth Z],
MI [auth 8],
MJ [auth 4],
MK [auth 5],
MM [auth 2],
NA [auth A],
NC [auth B],
ND [auth B],
NF [auth 1],
NH [auth 7],
NI [auth 8],
NJ [auth 4],
OA [auth A],
OC [auth B],
OD [auth B],
OF [auth 1],
OH [auth 7],
OI [auth 8],
OL [auth 6],
OM [auth 2],
PA [auth A],
PC [auth B],
PH [auth 7],
PI [auth 8],
PK [auth 5],
QA [auth A],
QC [auth B],
QF [auth 1],
QH [auth 7],
QI [auth 8],
QJ [auth 4],
QK [auth 5],
QL [auth 6],
RA [auth A],
RC [auth B],
RE [auth J],
RF [auth 1],
RH [auth 7],
RI [auth 8],
RK [auth 5],
SA [auth A],
SC [auth B],
SF [auth 1],
SH [auth 7],
SI [auth 8],
SJ [auth 4],
SL [auth 6],
TA [auth A],
TC [auth B],
TF [auth 1],
TH [auth 7],
TJ [auth 4],
TK [auth 5],
TL [auth 6],
UA [auth A],
UC [auth B],
UH [auth 7],
UI [auth 8],
UK [auth 5],
VA [auth A],
VC [auth B],
VE [auth K],
VG [auth 3],
VH [auth 7],
VI [auth 8],
W [auth A],
WA [auth A],
WB [auth A],
WC [auth B],
WE [auth K],
WG [auth 3],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth B],
XE [auth K],
XG [auth 3],
XH [auth 7],
XI [auth 8],
XK [auth 5],
Y [auth A],
YA [auth A],
YC [auth B],
YE [auth K],
YG [auth 3],
YH [auth 7],
YJ [auth 5],
YK [auth 6],
YL [auth 9],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZF [auth Z],
ZG [auth 3],
ZH [auth 7],
ZK [auth 6],
ZL [auth 9]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0



Download:Ideal Coordinates CCD File
V [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
T7X

Query on T7X



Download:Ideal Coordinates CCD File
QE [auth J]Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
VF [auth 1]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG

Query on LMG



Download:Ideal Coordinates CCD File
JE [auth F],
PE [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
BC [auth B]
BI [auth 7]
IH [auth 3]
KM [auth 9]
NG [auth Z]
BC [auth B],
BI [auth 7],
IH [auth 3],
KM [auth 9],
NG [auth Z],
RB [auth A],
SB [auth A],
UF [auth 1],
UL [auth 6],
VJ [auth 4],
VK [auth 5],
WD [auth B],
WJ [auth 4],
XD [auth B],
YI [auth 8]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH

Query on 3PH



Download:Ideal Coordinates CCD File
BJ [auth 8],
CI [auth 7],
VL [auth 6],
WK [auth 5]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA

Query on DGA



Download:Ideal Coordinates CCD File
UB [auth A]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
LUT

Query on LUT



Download:Ideal Coordinates CCD File
AK [auth 5]
AL [auth 6]
BL [auth 6]
DJ [auth 4]
EJ [auth 4]
AK [auth 5],
AL [auth 6],
BL [auth 6],
DJ [auth 4],
EJ [auth 4],
FF [auth 1],
GF [auth 1],
JI [auth 8],
KH [auth 7],
KI [auth 8],
LH [auth 7],
PG [auth 3],
QG [auth 3],
WL [auth 9],
XF [auth Z],
XL [auth 9],
YF [auth Z],
ZJ [auth 5]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
C7Z

Query on C7Z



Download:Ideal Coordinates CCD File
DK [auth 5],
TE [auth J]
(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
C40 H56 O2
JKQXZKUSFCKOGQ-ANDPMPNWSA-N
RRX

Query on RRX



Download:Ideal Coordinates CCD File
HE [auth F](3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
BK [auth 5]
CK [auth 5]
CL [auth 6]
DF [auth L]
DL [auth 6]
BK [auth 5],
CK [auth 5],
CL [auth 6],
DF [auth L],
DL [auth 6],
EE [auth F],
FJ [auth 4],
LI [auth 8],
MB [auth A],
ME [auth G],
MH [auth 7],
NB [auth A],
OB [auth A],
OE [auth I],
PB [auth A],
QB [auth A],
QD [auth B],
RD [auth B],
RG [auth 3],
SD [auth B],
SE [auth J],
SG [auth 3],
TD [auth B],
TG [auth 3],
UD [auth B],
UG [auth 3],
VD [auth B],
YB [auth A],
ZD [auth B],
ZE [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
CJ [auth 4],
EF [auth 1],
IE [auth F],
NE [auth G],
XJ [auth 4]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LPX

Query on LPX



Download:Ideal Coordinates CCD File
AJ [auth 8](2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
C21 H44 N O7 P
YVYMBNSKXOXSKW-FQEVSTJZSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
LB [auth A],
PD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
NKP

Query on NKP



Download:Ideal Coordinates CCD File
TB [auth A],
ZI [auth 8]
(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
C21 H41 O7 P
WRGQSWVCFNIUNZ-SQUSKLHYSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
AC [auth B],
AE [auth C],
BE [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SPH

Query on SPH



Download:Ideal Coordinates CCD File
DI [auth 7],
EI [auth 7]
SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
DAO

Query on DAO



Download:Ideal Coordinates CCD File
UE [auth K]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
OCA

Query on OCA



Download:Ideal Coordinates CCD File
VB [auth A]OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
CC [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael199/21

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary