9WLS | pdb_00009wls

PSI complex of A.thaliana isolated using DOC based Clear-Native-PAGE method


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9WLS

This is version 1.0 of the entry. See complete history

Literature

A novel method for cryo-EM protein sample preparation based on Clear-Native-PAGE

Yang, Z.Kameo, S.Seki, S.Kurisu, G.Tanaka, R.Kawamoto, A.Takabayashi, A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 586.32 kDa 
  • Atom Count: 36,141 
  • Modeled Residue Count: 3,267 
  • Deposited Residue Count: 4,061 
  • Unique protein chains: 17

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6, chloroplasticA [auth 1]241Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q01667 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 2, chloroplasticB [auth 2]257Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SYW8 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 3-1, chloroplasticC [auth 3]273Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SY97 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 4, chloroplasticD [auth 4]251Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P27521 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]750Arabidopsis thalianaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P56766 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]734Arabidopsis thalianaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P56767 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]81Arabidopsis thalianaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P62090 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II-2, chloroplasticH [auth D]204Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SA56 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV A, chloroplasticI [auth E]143Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9S831 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticJ [auth F]221Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SHE8 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticK [auth G]160Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9S7N7 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI-2, chloroplasticL [auth H]145Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SUI6 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]37Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56768 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]44Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56769 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplasticO [auth K]130Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SUI5 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplasticP [auth L]219Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SUI4 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit N, chloroplasticQ [auth N]171Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P49107 (Arabidopsis thaliana)
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Reference Sequence

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



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

Query on CHL



Download:Ideal Coordinates CCD File
AB [auth 2]
EB [auth 3]
FC [auth 4]
LC [auth 4]
QB [auth 3]
AB [auth 2],
EB [auth 3],
FC [auth 4],
LC [auth 4],
QB [auth 3],
R [auth 1],
W [auth 1],
XA [auth 2],
ZA [auth 2]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0
(Subject of Investigation/LOI)

Query on CL0



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

Query on CLA



Download:Ideal Coordinates CCD File
AD [auth A]
AG [auth B]
BD [auth A]
BE [auth A]
BG [auth B]
AD [auth A],
AG [auth B],
BD [auth A],
BE [auth A],
BG [auth B],
CA [auth 1],
CB [auth 3],
CD [auth A],
CE [auth A],
CG [auth B],
DB [auth 3],
DC [auth 4],
DD [auth A],
DE [auth A],
DF [auth B],
DG [auth B],
ED [auth A],
EF [auth B],
EG [auth B],
EH [auth K],
FB [auth 3],
FD [auth A],
FE [auth A],
FF [auth B],
FG [auth B],
FH [auth K],
GC [auth 4],
GD [auth A],
GF [auth B],
GG [auth B],
HB [auth 3],
HD [auth A],
HE [auth A],
HF [auth B],
HG [auth B],
IB [auth 3],
ID [auth A],
IE [auth A],
IF [auth B],
JB [auth 3],
JC [auth 4],
JD [auth A],
JE [auth A],
JF [auth B],
JH [auth L],
KC [auth 4],
KD [auth A],
KE [auth A],
KF [auth B],
KH [auth L],
LA [auth 2],
LD [auth A],
LF [auth B],
LH [auth L],
MC [auth A],
MD [auth A],
ME [auth B],
MF [auth B],
MG [auth F],
NB [auth 3],
NC [auth A],
ND [auth A],
NE [auth B],
NF [auth B],
OD [auth A],
OE [auth B],
OF [auth B],
PB [auth 3],
PE [auth B],
PF [auth B],
PG [auth F],
QC [auth A],
QD [auth A],
QE [auth B],
QF [auth B],
RC [auth A],
RD [auth A],
RE [auth B],
RF [auth B],
RG [auth G],
S [auth 1],
SC [auth A],
SD [auth A],
SE [auth B],
SF [auth B],
SG [auth G],
T [auth 1],
TC [auth A],
TD [auth A],
TE [auth B],
TF [auth B],
UA [auth 2],
UC [auth A],
UE [auth B],
UF [auth B],
V [auth 1],
VA [auth 2],
VC [auth A],
VD [auth A],
VE [auth B],
VF [auth B],
WA [auth 2],
WC [auth A],
WD [auth A],
WF [auth B],
WG [auth H],
X [auth 1],
XC [auth A],
XF [auth B],
Y [auth 1],
YC [auth A],
YF [auth B],
YG [auth J],
ZB [auth 4],
ZC [auth A],
ZD [auth A],
ZF [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
(Subject of Investigation/LOI)

Query on LMG



Download:Ideal Coordinates CCD File
AH [auth J]
KG [auth F]
NH [auth N]
OG [auth F]
VG [auth G]
AH [auth J],
KG [auth F],
NH [auth N],
OG [auth F],
VG [auth G],
WB [auth 4]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG



Download:Ideal Coordinates CCD File
HA [auth 1],
KA [auth 1],
MA [auth 2],
UD [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
(Subject of Investigation/LOI)

Query on XAT



Download:Ideal Coordinates CCD File
FA [auth 1],
IA [auth 1],
QA [auth 2]
(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
A1LXP
(Subject of Investigation/LOI)

Query on A1LXP



Download:Ideal Coordinates CCD File
GA [auth 1]
GB [auth 3]
JA [auth 1]
LB [auth 3]
TA [auth 2]
GA [auth 1],
GB [auth 3],
JA [auth 1],
LB [auth 3],
TA [auth 2],
VB [auth 4],
YB [auth 4],
ZG [auth J]
Lutein
C40 H56 O2
KBPHJBAIARWVSC-RGZFRNHPSA-N
BCR
(Subject of Investigation/LOI)

Query on BCR



Download:Ideal Coordinates CCD File
AC [auth 4]
AE [auth A]
AF [auth B]
BF [auth B]
CH [auth J]
AC [auth 4],
AE [auth A],
AF [auth B],
BF [auth B],
CH [auth J],
DH [auth K],
EE [auth A],
GE [auth A],
HH [auth L],
IH [auth L],
LE [auth A],
LG [auth F],
MH [auth L],
NG [auth F],
PC [auth A],
QG [auth G],
RB [auth 3],
UG [auth G],
XD [auth A],
XE [auth B],
XG [auth I],
YE [auth B],
ZE [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
(Subject of Investigation/LOI)

Query on PQN



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

Query on SF4



Download:Ideal Coordinates CCD File
IG [auth C],
JG [auth C],
OC [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UNL(
Subject of Investigation/LOI)

Query on UNL



Download:Ideal Coordinates CCD File
AA [auth 1]
BA [auth 1]
BB [auth 2]
BC [auth 4]
BH [auth J]
AA [auth 1],
BA [auth 1],
BB [auth 2],
BC [auth 4],
BH [auth J],
CC [auth 4],
DA [auth 1],
EA [auth 1],
EC [auth 4],
GH [auth K],
HC [auth 4],
IC [auth 4],
KB [auth 3],
MB [auth 3],
NA [auth 2],
OA [auth 2],
OB [auth 3],
OH [auth N],
PA [auth 2],
RA [auth 2],
SA [auth 2],
SB [auth 3],
TB [auth 4],
TG [auth G],
U [auth 1],
UB [auth 4],
XB [auth 4],
YA [auth 2],
Z [auth 1]
Unknown ligand
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0.2
MODEL REFINEMENTServalcat0.4.115

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23H04958
Japan Society for the Promotion of Science (JSPS)Japan23H04960

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-17
    Type: Initial release