8BCV

Photosystem I assembly intermediate of Avena sativa


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Photosystem I assembly intermediate of Avena sativa

Naschberger, A.Amunts, A.Nelson, N.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1750Avena sativaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A3G1AUL2 (Avena sativa)
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UniProt GroupA0A3G1AUL2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2734Avena sativaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A3G1AZK6 (Avena sativa)
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UniProt GroupA0A3G1AZK6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Avena sativaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A3G1ATU7 (Avena sativa)
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UniProt GroupA0A3G1ATU7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II206Avena sativaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV143Avena sativaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIF [auth H]94Avena sativaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]36Avena sativaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A3G1AZM6 (Avena sativa)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIH [auth L]213Avena sativaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIII [auth F]178Avena sativaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VJ [auth G]144Avena sativaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXK [auth J]52Avena sativaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A3G1AZP2 (Avena sativa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XL [auth K]130Avena sativaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 1, chloroplasticM [auth 1]242Avena sativaMutation(s): 0 
UniProt
Find proteins for A0A482JYH1 (Avena sativa)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 2, chloroplasticN [auth 2]207Avena sativaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticO [auth 3]269Avena sativaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 4, chloroplasticP [auth 4]256Avena sativaMutation(s): 0 
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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DI [auth 4],
PD [auth B],
ZE [auth J]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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FG [auth 2]
GF [auth 1]
GG [auth 2]
HG [auth 2]
LF [auth 1]
FG [auth 2],
GF [auth 1],
GG [auth 2],
HG [auth 2],
LF [auth 1],
MH [auth 4],
NH [auth 4],
OG [auth 2],
OH [auth 4],
TG [auth 3],
WH [auth 4],
YG [auth 3]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-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]
AE [auth L]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth L],
AF [auth K],
AH [auth 3],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth L],
BG [auth 2],
BH [auth 3],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth L],
CF [auth K],
CG [auth 2],
CH [auth 3],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DF [auth K],
DG [auth 2],
DH [auth 3],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EG [auth 2],
EH [auth 3],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GE [auth F],
HA [auth A],
HC [auth B],
HD [auth B],
HF [auth 1],
IA [auth A],
IB [auth A],
IC [auth B],
IE [auth F],
IF [auth 1],
IG [auth 2],
IH [auth 4],
JA [auth A],
JC [auth B],
JD [auth B],
JE [auth F],
JF [auth 1],
JG [auth 2],
JH [auth 4],
KA [auth A],
KC [auth B],
KF [auth 1],
KG [auth 2],
KH [auth 4],
LA [auth A],
LC [auth B],
LG [auth 2],
LH [auth 4],
MA [auth A],
MC [auth B],
MF [auth 1],
MG [auth 2],
NA [auth A],
NC [auth B],
NF [auth 1],
NG [auth 2],
OA [auth A],
OC [auth B],
OF [auth 1],
PA [auth A],
PC [auth B],
PE [auth G],
PF [auth 1],
PH [auth 4],
QA [auth A],
QC [auth B],
QF [auth 1],
QH [auth 4],
R [auth A],
RA [auth A],
RB [auth A],
RC [auth B],
RF [auth 1],
RH [auth 4],
S [auth A],
SA [auth A],
SB [auth A],
SC [auth B],
SE [auth G],
SF [auth 1],
SH [auth 4],
T [auth A],
TA [auth A],
TB [auth A],
TC [auth B],
TE [auth G],
TF [auth 1],
TH [auth 4],
U [auth A],
UA [auth A],
UC [auth B],
UG [auth 3],
UH [auth 4],
V [auth A],
VA [auth A],
VC [auth B],
VG [auth 3],
VH [auth 4],
W [auth A],
WA [auth A],
WC [auth B],
WG [auth 3],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XE [auth J],
XG [auth 3],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZG [auth 3]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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Q [auth A],
WD [auth H]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

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AI [auth 4],
BI [auth 4],
OE [auth F],
UB [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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JB [auth A]
KB [auth A]
QD [auth B]
RD [auth B]
RG [auth 2]
JB [auth A],
KB [auth A],
QD [auth B],
RD [auth B],
RG [auth 2],
XF [auth 1]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT (Subject of Investigation/LOI)
Query on XAT

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QG [auth 2],
VF [auth 1]
(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
QDL (Subject of Investigation/LOI)
Query on QDL

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YH [auth 4]Antheraxanthin
C40 H56 O3
OFNSUWBAQRCHAV-OYQUVCAXSA-N
C7Z (Subject of Investigation/LOI)
Query on C7Z

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AG [auth 1](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
LUT (Subject of Investigation/LOI)
Query on LUT

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GH [auth 3]
HH [auth 3]
PG [auth 2]
UF [auth 1]
WE [auth J]
GH [auth 3],
HH [auth 3],
PG [auth 2],
UF [auth 1],
WE [auth J],
WF [auth 1],
XH [auth 4]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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BF [auth K]
DE [auth L]
EE [auth L]
EF [auth K]
FE [auth F]
BF [auth K],
DE [auth L],
EE [auth L],
EF [auth K],
FE [auth F],
FH [auth 3],
KD [auth B],
KE [auth F],
LB [auth A],
LD [auth B],
MB [auth A],
MD [auth B],
NB [auth A],
ND [auth B],
OB [auth A],
OD [auth B],
PB [auth A],
QE [auth G],
UE [auth G],
XD [auth I],
YE [auth J],
ZD [auth L],
ZH [auth 4]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU (Subject of Investigation/LOI)
Query on LMU

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CI [auth 4]
EI [auth 4]
FF [auth 1]
FI [auth 4]
HE [auth F]
CI [auth 4],
EI [auth 4],
FF [auth 1],
FI [auth 4],
HE [auth F],
LE [auth F],
ME [auth F],
NE [auth F],
RE [auth G],
SD [auth B],
SG [auth 2],
VB [auth A],
VD [auth H],
VE [auth G],
WB [auth A],
YD [auth L],
YF [auth 1],
ZF [auth 1]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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HB [auth A],
ID [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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QB [auth A],
TD [auth C],
UD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Swedish Foundation for Strategic ResearchSwedenARC19-0051
Knut and Alice Wallenberg FoundationSweden2018.0080
Israel Science FoundationIsrael569/17

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release