2WSC

Improved Model of Plant Photosystem I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.363 
  • R-Value Observed: 0.363 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure Determination and Improved Model of Plant Photosystem I.

Amunts, A.Toporik, H.Borovikova, A.Nelson, N.

(2010) J Biol Chem 285: 3478

  • DOI: 10.1074/jbc.M109.072645
  • Primary Citation of Related Structures:  
    2WSF, 2WSC, 2WSE, 3LW5

  • PubMed Abstract: 
  • Photosystem I functions as a sunlight energy converter, catalyzing one of the initial steps in driving oxygenic photosynthesis in cyanobacteria, algae, and higher plants. Functionally, Photosystem I captures sunlight and transfers the excitation energy through an intricate and precisely organized antenna system, consisting of a pigment network, to the center of the molecule, where it is used in the transmembrane electron transfer reaction ...

    Photosystem I functions as a sunlight energy converter, catalyzing one of the initial steps in driving oxygenic photosynthesis in cyanobacteria, algae, and higher plants. Functionally, Photosystem I captures sunlight and transfers the excitation energy through an intricate and precisely organized antenna system, consisting of a pigment network, to the center of the molecule, where it is used in the transmembrane electron transfer reaction. Our current understanding of the sophisticated mechanisms underlying these processes has profited greatly from elucidation of the crystal structures of the Photosystem I complex. In this report, we describe the developments that ultimately led to enhanced structural information of plant Photosystem I. In addition, we report an improved crystallographic model at 3.3-A resolution, which allows analysis of the structure in more detail. An improved electron density map yielded identification and tracing of subunit PsaK. The location of an additional ten beta-carotenes as well as five chlorophylls and several loop regions, which were previously uninterpretable, are now modeled. This represents the most complete plant Photosystem I structure obtained thus far, revealing the locations of and interactions among 17 protein subunits and 193 non-covalently bound photochemical cofactors. Using the new crystal structure, we examine the network of contacts among the protein subunits from the structural perspective, which provide the basis for elucidating the functional organization of the complex.


    Organizational Affiliation

    Biochemistry Department, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AT3G54890A [auth 1]241Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCA1CAB6At3g54890F28P10.130
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for Q01667 (Arabidopsis thaliana)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM IB [auth 2]269Pisum sativumMutation(s): 0 
Gene Names: lhaB
Find proteins for Q41038 (Pisum sativum)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
LHCA3C [auth 3]276Glycine maxMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTICD [auth 4]251Pisum sativumMutation(s): 0 
Gene Names: lhcA-P4
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for Q9SQL2 (Pisum sativum)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1E [auth A]758Pisum sativumMutation(s): 0 
Gene Names: psaApsaA1
EC: 1.97.1.12
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for P05310 (Pisum sativum)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2F [auth B]734Pisum sativumMutation(s): 0 
Gene Names: psaBpsaA2
EC: 1.97.1.12
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I IRON-SULFUR CENTERG [auth C]81Pisum sativumMutation(s): 0 
Gene Names: psaCfrxA
EC: 1.97.1.12
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for P10793 (Pisum sativum)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT II, CHLOROPLASTICH [auth D]212Spinacia oleraceaMutation(s): 0 
Gene Names: psaD
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for P12353 (Spinacia oleracea)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT IV A, CHLOROPLASTICI [auth E]143Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAE1At4g28750F16A16.140
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for Q9S831 (Arabidopsis thaliana)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT III, CHLOROPLASTICJ [auth F]231Spinacia oleraceaMutation(s): 0 
Gene Names: PSAF
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for P12355 (Spinacia oleracea)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT V, CHLOROPLASTICK [auth G]167Spinacia oleraceaMutation(s): 0 
Gene Names: PSAG
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for P12357 (Spinacia oleracea)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT VI, CHLOROPLASTICL [auth H]144Spinacia oleraceaMutation(s): 0 
Gene Names: PSAH
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for P22179 (Spinacia oleracea)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT VIIIM [auth I]40Pisum sativumMutation(s): 0 
Gene Names: psaI
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for P17227 (Pisum sativum)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT IXN [auth J]44Spinacia oleraceaMutation(s): 0 
Gene Names: psaJ
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for P17230 (Spinacia oleracea)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT PSAK, CHLOROPLASTICO [auth K]131Hordeum vulgareMutation(s): 0 
Gene Names: PSAK
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for P36886 (Hordeum vulgare)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT XI, CHLOROPLASTICP [auth L]216Spinacia oleraceaMutation(s): 0 
Gene Names: PSAL
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for Q41385 (Spinacia oleracea)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I-N SUBUNITQ [auth N]170Phaseolus vulgarisMutation(s): 0 
Gene Names: PSI-NPHAVU_002G269400g
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (Plant)
Find proteins for Q84U30 (Phaseolus vulgaris)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYSTEM I-N SUBUNITR53Pisum sativumMutation(s): 0 
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Oligosaccharides

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Entity ID: 19
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
AA [auth W], BA [auth X], CA [auth Y], DA [auth Z], EA [auth a], S [auth M], T [auth O], U [auth P]
AA [auth W], BA [auth X], CA [auth Y], DA [auth Z], EA [auth a], S [auth M], T [auth O], U [auth P], V [auth Q], W [auth S], X [auth T], Y [auth U], Z [auth V]
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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AB [auth 2] , AC [auth 3] , AD [auth A] , AE [auth A] , AF [auth A] , AH [auth B] , AJ [auth K] , BB [auth 2] , 
AB [auth 2],  AC [auth 3],  AD [auth A],  AE [auth A],  AF [auth A],  AH [auth B],  AJ [auth K],  BB [auth 2],  BC [auth 3],  BD [auth A],  BE [auth A],  BF [auth A],  BH [auth B],  BJ [auth K],  CB [auth 2],  CC [auth 3],  CD [auth A],  CE [auth A],  CF [auth A],  CH [auth B],  CJ [auth K],  DB [auth 2],  DC [auth 3],  DD [auth A],  DE [auth A],  DH [auth B],  DJ [auth L],  EB [auth 2],  ED [auth A],  EE [auth A],  EH [auth B],  EJ [auth L],  FA [auth 1],  FB [auth 2],  FC [auth 4],  FD [auth A],  FE [auth A],  FH [auth B],  FJ [auth L],  GA [auth 1],  GB [auth 2],  GC [auth 4],  GD [auth A],  GE [auth A],  GH [auth B],  GI [auth B],  HA [auth 1],  HB [auth 2],  HC [auth 4],  HD [auth A],  HE [auth A],  HH [auth B],  HI [auth B],  IA [auth 1],  IB [auth 2],  IC [auth 4],  ID [auth A],  IE [auth A],  IG [auth B],  IH [auth B],  II [auth B],  JA [auth 1],  JC [auth 4],  JD [auth A],  JE [auth A],  JG [auth B],  JH [auth B],  JJ [auth L],  KA [auth 1],  KB [auth 2],  KC [auth 4],  KD [auth A],  KE [auth A],  KG [auth B],  KH [auth B],  KJ [auth R],  LA [auth 1],  LB [auth 2],  LC [auth 4],  LD [auth A],  LE [auth A],  LG [auth B],  LH [auth B],  LJ [auth R],  MA [auth 1],  MC [auth 4],  MD [auth A],  ME [auth A],  MG [auth B],  MH [auth B],  MI [auth F],  NA [auth 1],  NC [auth 4],  ND [auth A],  NE [auth A],  NG [auth B],  NH [auth B],  NI [auth F],  OA [auth 1],  OB [auth 3],  OC [auth 4],  OD [auth A],  OG [auth B],  OH [auth B],  OI [auth F],  PA [auth 1],  PB [auth 3],  PC [auth 4],  PD [auth A],  PG [auth B],  PH [auth B],  PI [auth G],  QA [auth 1],  QB [auth 3],  QC [auth 4],  QD [auth A],  QG [auth B],  QH [auth B],  QI [auth H],  RA [auth 1],  RB [auth 3],  RC [auth 4],  RD [auth A],  RG [auth B],  RH [auth B],  RI [auth I],  SA [auth 1],  SB [auth 3],  SC [auth 4],  SD [auth A],  SG [auth B],  SH [auth B],  TA [auth 1],  TB [auth 3],  TD [auth A],  TG [auth B],  TH [auth B],  TI [auth I],  UB [auth 3],  UC [auth 4],  UD [auth A],  UG [auth B],  UI [auth J],  VB [auth 3],  VC [auth 4],  VD [auth A],  VG [auth B],  VI [auth J],  WA [auth 2],  WC [auth 4],  WD [auth A],  WG [auth B],  WI [auth J],  XA [auth 2],  XB [auth 3],  XC [auth A],  XD [auth A],  XE [auth A],  XG [auth B],  XI [auth J],  YA [auth 2],  YB [auth 3],  YC [auth A],  YD [auth A],  YE [auth A],  YG [auth B],  YI [auth K],  ZA [auth 2],  ZB [auth 3],  ZC [auth A],  ZD [auth A],  ZE [auth A],  ZG [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
LMG
Query on LMG

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EI [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCR
Query on BCR

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AI [auth B] , BI [auth B] , CI [auth B] , GJ [auth L] , HJ [auth L] , PE [auth A] , QE [auth A] , RE [auth A] , 
AI [auth B],  BI [auth B],  CI [auth B],  GJ [auth L],  HJ [auth L],  PE [auth A],  QE [auth A],  RE [auth A],  SE [auth A],  SI [auth I],  TE [auth A],  UE [auth A],  VH [auth B],  WB [auth 3],  WH [auth B],  XH [auth B],  YH [auth B],  ZH [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMU
Query on LMU

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AG [auth A] , BG [auth A] , CG [auth A] , DF [auth A] , DG [auth A] , DI [auth B] , EC [auth 3] , EF [auth A] , 
AG [auth A],  BG [auth A],  CG [auth A],  DF [auth A],  DG [auth A],  DI [auth B],  EC [auth 3],  EF [auth A],  EG [auth A],  FF [auth A],  FG [auth A],  GF [auth A],  GG [auth A],  HF [auth A],  HG [auth A],  IF [auth A],  IJ [auth L],  JB [auth 2],  JF [auth A],  KF [auth A],  LF [auth A],  MB [auth 2],  MF [auth A],  MJ [auth R],  NB [auth 2],  NF [auth A],  NJ [auth R],  OF [auth A],  PF [auth A],  QF [auth A],  RF [auth A],  SF [auth A],  TC [auth 4],  TF [auth A],  UA [auth 1],  UF [auth A],  VA [auth 1],  VE [auth A],  VF [auth A],  WE [auth A],  WF [auth A],  XF [auth A],  YF [auth A],  ZF [auth A],  ZI [auth K]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
PQN
Query on PQN

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OE [auth A], UH [auth B]PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
SF4
Query on SF4

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FI [auth B], KI [auth C], LI [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
UNL
Query on UNL

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JI [auth B]Unknown ligand
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 19
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
AA [auth M], BA [auth O], CA [auth P], DA [auth Q], EA [auth S], S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]sucroseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.363 
  • R-Value Observed: 0.363 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.655α = 90
b = 189.086β = 91.24
c = 129.388γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2012-08-08
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2018-06-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary