8BCW | pdb_00008bcw

Photosystem I assembly intermediate of Avena sativa


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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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.

Macromolecule Content 

  • Total Structure Weight: 341.47 kDa 
  • Atom Count: 22,313 
  • Modeled Residue Count: 2,029 
  • Deposited Residue Count: 2,254 
  • Unique protein chains: 8

Macromolecules

Find similar proteins by:|  3D Structure
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)
Explore A0A3G1AUL2 
Go to UniProtKB:  A0A3G1AUL2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G1AUL2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore A0A3G1AZK6 
Go to UniProtKB:  A0A3G1AZK6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G1AZK6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore A0A3G1ATU7 
Go to UniProtKB:  A0A3G1ATU7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G1ATU7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplastic206Avena sativaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV A, chloroplastic143Avena sativaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplasticF [auth H]94Avena sativaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]33Avena sativaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A3G1AZM6 (Avena sativa)
Explore A0A3G1AZM6 
Go to UniProtKB:  A0A3G1AZM6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G1AZM6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI subunit VH [auth L]213Avena sativaMutation(s): 0 

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
GD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
(Subject of Investigation/LOI)

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
BA [auth A]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
BA [auth A],
BC [auth B],
CA [auth A],
CC [auth B],
DA [auth A],
DC [auth B],
EA [auth A],
EC [auth B],
FA [auth A],
FC [auth B],
GA [auth A],
GC [auth B],
HA [auth A],
HC [auth B],
IA [auth A],
IC [auth B],
J [auth A],
JA [auth A],
JB [auth A],
JC [auth B],
K [auth A],
KA [auth A],
KC [auth B],
L [auth A],
LA [auth A],
LB [auth A],
LC [auth B],
M [auth A],
MA [auth A],
MC [auth B],
N [auth A],
NA [auth A],
NC [auth B],
ND [auth L],
O [auth A],
OA [auth A],
OC [auth B],
OD [auth L],
P [auth A],
PA [auth A],
PB [auth B],
PC [auth B],
PD [auth L],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
Z [auth A],
ZB [auth B],
ZC [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
(Subject of Investigation/LOI)

Query on CL0



Download:Ideal Coordinates CCD File
I [auth A],
KD [auth H]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
(Subject of Investigation/LOI)

Query on LMG



Download:Ideal Coordinates CCD File
NB [auth A]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG



Download:Ideal Coordinates CCD File
BB [auth A],
CB [auth A],
HD [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
(Subject of Investigation/LOI)

Query on BCR



Download:Ideal Coordinates CCD File
CD [auth B]
DB [auth A]
DD [auth B]
EB [auth A]
ED [auth B]
CD [auth B],
DB [auth A],
DD [auth B],
EB [auth A],
ED [auth B],
FB [auth A],
FD [auth B],
GB [auth A],
HB [auth A],
LD [auth I],
MD [auth L],
QD [auth L],
RD [auth L]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU

Query on LMU



Download:Ideal Coordinates CCD File
KB [auth A],
MB [auth A],
OB [auth A]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
(Subject of Investigation/LOI)

Query on PQN



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

Query on SF4



Download:Ideal Coordinates CCD File
IB [auth A],
ID [auth C],
JD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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: 2025-07-09
    Changes: Data collection, Structure summary