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


This is version 1.1 of the entry. See complete history


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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UniProt GroupA0A3G1AZM6
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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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UniProt GroupA0A482JYH1
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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

Download Ideal Coordinates CCD File 
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]
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]
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]
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]
(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]
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]
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
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary