4XK8

Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex

Qin, X.Suga, M.Kuang, T.Shen, J.R.

(2015) Science 348: 989-995

  • DOI: 10.1126/science.aab0214
  • Primary Citation of Related Structures:  
    4XK8

  • PubMed Abstract: 
  • Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency ...

    Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency. We report the structure of PSI-LHCI, a 600-kilodalton membrane protein supercomplex, from Pisum sativum (pea) at a resolution of 2.8 angstroms. The structure reveals the detailed arrangement of pigments and other cofactors—especially within LHCI—as well as numerous specific interactions between the PSI core and LHCI. These results provide a firm structural basis for our understanding on the energy transfer and photoprotection mechanisms within the PSI-LHCI supercomplex.


    Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China. Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Tsushima Naka 3-1-1, Okayama 700-8530, Japan. kuangty@ibcas.ac.cn shen@cc.okayama-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A, Q [auth a]742Pisum sativumMutation(s): 0 
Gene Names: psaApsaA1
EC: 1.97.1.12
Find proteins for P05310 (Pisum sativum)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B, R [auth b]733Pisum sativumMutation(s): 0 
Gene Names: psaBpsaA2
EC: 1.97.1.12
Find proteins for P05311 (Pisum sativum)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC, S [auth c]80Pisum sativumMutation(s): 0 
Gene Names: psaCfrxA
EC: 1.97.1.12
Find proteins for P10793 (Pisum sativum)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinD, T [auth d]141Pisum sativumMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinE, U [auth e]64Pisum sativumMutation(s): 0 
Find proteins for E1C9K6 (Pisum sativum)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticF, V [auth f]151Pisum sativumMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticG, W [auth g]95Pisum sativumMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinH, X [auth h]90Pisum sativumMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIII, Y [auth i]30Pisum sativumMutation(s): 0 
Gene Names: psaI
Find proteins for P17227 (Pisum sativum)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXJ, Z [auth j]39Pisum sativumMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaKK, AA [auth k]84Pisum sativumMutation(s): 0 
Find proteins for E1C9L3 (Pisum sativum)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinL, BA [auth l]153Pisum sativumMutation(s): 0 
Find proteins for E1C9L1 (Pisum sativum)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6, chloroplasticM [auth 1], CA [auth 6]195Pisum sativumMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Type II chlorophyll a/b binding protein from photosystem IN [auth 2], DA [auth 7]206Pisum sativumMutation(s): 0 
Gene Names: lhaB
Find proteins for Q41038 (Pisum sativum)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticO [auth 3], EA [auth 8]218Pisum sativumMutation(s): 0 
Gene Names: lhca3
Find proteins for Q32904 (Pisum sativum)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticP [auth 4], FA [auth 9]196Pisum sativumMutation(s): 0 
Gene Names: lhcA-P4
Find proteins for Q9SQL2 (Pisum sativum)
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Small Molecules
Ligands 12 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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HE [auth B], IM [auth b]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CHL
Query on CHL

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AH [auth 3] , AP [auth 8] , BI [auth 4] , CG [auth 2] , DO [auth 7] , GG [auth 2] , HG [auth 2] , HO [auth 7] , 
AH [auth 3],  AP [auth 8],  BI [auth 4],  CG [auth 2],  DO [auth 7],  GG [auth 2],  HG [auth 2],  HO [auth 7],  IG [auth 2],  IO [auth 7],  JF [auth 1],  JO [auth 7],  KN [auth 6],  OF [auth 1],  PG [auth 2],  PN [auth 6],  PP [auth 9],  QO [auth 7],  QP [auth 9],  RH [auth 4],  RP [auth 9],  SH [auth 4],  TH [auth 4],  ZP [auth 9]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
 Ligand Interaction
CLA
Query on CLA

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AB [auth A] , AD [auth B] , AF [auth K] , AI [auth 4] , AJ [auth a] , AK [auth a] , AL [auth b] , AM [auth b] , 
AB [auth A],  AD [auth B],  AF [auth K],  AI [auth 4],  AJ [auth a],  AK [auth a],  AL [auth b],  AM [auth b],  AN [auth k],  BB [auth A],  BD [auth B],  BH [auth 3],  BJ [auth a],  BL [auth b],  BP [auth 8],  CB [auth A],  CD [auth B],  CH [auth 3],  CJ [auth a],  CL [auth b],  CP [auth 8],  DB [auth A],  DD [auth B],  DF [auth L],  DG [auth 2],  DH [auth 3],  DJ [auth a],  DL [auth b],  DN [auth l],  DP [auth 8],  EB [auth A],  ED [auth B],  EF [auth L],  EG [auth 2],  EH [auth 3],  EJ [auth a],  EL [auth b],  EN [auth l],  EO [auth 7],  EP [auth 8],  FB [auth A],  FD [auth B],  FF [auth L],  FG [auth 2],  FH [auth 3],  FJ [auth a],  FL [auth b],  FN [auth l],  FO [auth 7],  FP [auth 8],  GA [auth A],  GB [auth A],  GD [auth B],  GH [auth 3],  GJ [auth a],  GL [auth b],  GO [auth 7],  GP [auth 8],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth B],  HH [auth 3],  HI [auth a],  HJ [auth a],  HL [auth b],  HP [auth 8],  IA [auth A],  IB [auth A],  ID [auth B],  IH [auth 3],  II [auth a],  IJ [auth a],  IL [auth b],  JA [auth A],  JB [auth A],  JD [auth B],  JG [auth 2],  JI [auth a],  JJ [auth a],  JL [auth b],  KA [auth A],  KB [auth A],  KD [auth B],  KE [auth F],  KF [auth 1],  KG [auth 2],  KI [auth a],  KJ [auth a],  KK [auth a],  KL [auth b],  KO [auth 7],  LA [auth A],  LB [auth A],  LC [auth B],  LD [auth B],  LF [auth 1],  LG [auth 2],  LI [auth a],  LJ [auth a],  LL [auth b],  LN [auth 6],  LO [auth 7],  LP [auth 9],  MA [auth A],  MB [auth A],  MC [auth B],  MD [auth B],  ME [auth F],  MF [auth 1],  MG [auth 2],  MI [auth a],  MJ [auth a],  ML [auth b],  MM [auth f],  MN [auth 6],  MO [auth 7],  MP [auth 9],  NA [auth A],  NB [auth A],  NC [auth B],  ND [auth B],  NE [auth F],  NF [auth 1],  NG [auth 2],  NH [auth 4],  NI [auth a],  NJ [auth a],  NK [auth b],  NL [auth b],  NM [auth f],  NN [auth 6],  NO [auth 7],  NP [auth 9],  OA [auth A],  OB [auth A],  OC [auth B],  OD [auth B],  OG [auth 2],  OH [auth 4],  OI [auth a],  OJ [auth a],  OK [auth b],  OL [auth b],  ON [auth 6],  OO [auth 7],  OP [auth 9],  PA [auth A],  PB [auth A],  PC [auth B],  PD [auth B],  PE [auth G],  PF [auth 1],  PH [auth 4],  PI [auth a],  PJ [auth a],  PK [auth b],  PL [auth b],  PM [auth g],  PO [auth 7],  QA [auth A],  QB [auth A],  QC [auth B],  QD [auth B],  QF [auth 1],  QH [auth 4],  QI [auth a],  QJ [auth a],  QK [auth b],  QL [auth b],  QM [auth g],  QN [auth 6],  RA [auth A],  RB [auth A],  RC [auth B],  RD [auth B],  RE [auth G],  RF [auth 1],  RI [auth a],  RJ [auth a],  RK [auth b],  RL [auth b],  RM [auth g],  RN [auth 6],  SA [auth A],  SB [auth A],  SC [auth B],  SD [auth B],  SE [auth G],  SF [auth 1],  SI [auth a],  SJ [auth a],  SK [auth b],  SL [auth b],  SN [auth 6],  SP [auth 9],  TA [auth A],  TB [auth A],  TC [auth B],  TD [auth B],  TF [auth 1],  TI [auth a],  TJ [auth a],  TK [auth b],  TL [auth b],  TN [auth 6],  TP [auth 9],  UA [auth A],  UB [auth A],  UC [auth B],  UD [auth B],  UF [auth 1],  UG [auth 3],  UH [auth 4],  UI [auth a],  UJ [auth a],  UK [auth b],  UL [auth b],  UN [auth 6],  UP [auth 9],  VA [auth A],  VB [auth A],  VC [auth B],  VD [auth B],  VF [auth 1],  VG [auth 3],  VH [auth 4],  VI [auth a],  VJ [auth a],  VK [auth b],  VL [auth b],  VM [auth j],  VN [auth 6],  VO [auth 8],  VP [auth 9],  WA [auth A],  WB [auth A],  WC [auth B],  WD [auth B],  WE [auth J],  WF [auth 1],  WG [auth 3],  WH [auth 4],  WI [auth a],  WJ [auth a],  WK [auth b],  WL [auth b],  WN [auth 6],  WO [auth 8],  WP [auth 9],  XA [auth A],  XC [auth B],  XD [auth B],  XG [auth 3],  XH [auth 4],  XI [auth a],  XJ [auth a],  XK [auth b],  XL [auth b],  XN [auth 6],  XO [auth 8],  XP [auth 9],  YA [auth A],  YB [auth A],  YC [auth B],  YD [auth B],  YG [auth 3],  YH [auth 4],  YI [auth a],  YJ [auth a],  YK [auth b],  YL [auth b],  YM [auth k],  YO [auth 8],  YP [auth 9],  ZA [auth A],  ZC [auth B],  ZE [auth K],  ZG [auth 3],  ZH [auth 4],  ZI [auth a],  ZK [auth b],  ZL [auth b],  ZM [auth k],  ZO [auth 8]
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
LMG
Query on LMG

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DQ [auth 9], FI [auth 4], GI [auth 4], JN [auth 6], QE [auth G]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
LHG
Query on LHG

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AC [auth A] , AG [auth 1] , BK [auth a] , BO [auth 6] , CK [auth a] , IF [auth 1] , IN [auth 6] , MH [auth 3] , 
AC [auth A],  AG [auth 1],  BK [auth a],  BO [auth 6],  CK [auth a],  IF [auth 1],  IN [auth 6],  MH [auth 3],  TG [auth 2],  UO [auth 7],  ZB [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
XAT
Query on XAT

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BQ [auth 9], DI [auth 4], JP [auth 8], KH [auth 3], RG [auth 2], SO [auth 7], YF [auth 1], ZN [auth 6](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
 Ligand Interaction
LUT
Query on LUT

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AQ [auth 9] , BG [auth 1] , CI [auth 4] , CO [auth 6] , IP [auth 8] , JH [auth 3] , QG [auth 2] , RO [auth 7] , 
AQ [auth 9],  BG [auth 1],  CI [auth 4],  CO [auth 6],  IP [auth 8],  JH [auth 3],  QG [auth 2],  RO [auth 7],  XF [auth 1],  YN [auth 6]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
 Ligand Interaction
BCR
Query on BCR

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AE [auth B] , AO [auth 6] , BC [auth A] , BE [auth B] , BF [auth K] , BN [auth k] , CC [auth A] , CE [auth B] , 
AE [auth B],  AO [auth 6],  BC [auth A],  BE [auth B],  BF [auth K],  BN [auth k],  CC [auth A],  CE [auth B],  CF [auth L],  CM [auth b],  CN [auth l],  CQ [auth 9],  DC [auth A],  DE [auth B],  DK [auth a],  DM [auth b],  EC [auth A],  EE [auth B],  EI [auth 4],  EK [auth a],  EM [auth b],  FC [auth A],  FE [auth B],  FK [auth a],  FM [auth b],  GF [auth L],  GK [auth a],  GM [auth b],  GN [auth l],  HF [auth L],  HK [auth a],  HM [auth b],  HN [auth l],  IK [auth a],  JC [auth A],  KC [auth B],  KP [auth 8],  LH [auth 3],  MK [auth b],  OE [auth F],  OM [auth f],  SG [auth 2],  SM [auth g],  TE [auth G],  TM [auth i],  TO [auth 7],  UE [auth I],  WM [auth j],  XE [auth J],  XM [auth j],  YE [auth K],  ZF [auth 1]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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GE [auth B]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
PQN
Query on PQN

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BM [auth b], XB [auth A], ZD [auth B], ZJ [auth a]PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
SF4
Query on SF4

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GC [auth A], IE [auth C], JE [auth C], JK [auth a], JM [auth c], KM [auth c]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
HTG
Query on HTG

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IC [auth A], LE [auth F], LK [auth a], LM [auth f], UM [auth j], VE [auth J]heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.624α = 90
b = 192.22β = 91.41
c = 175.089γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Derived calculations
  • Version 1.2: 2019-05-01
    Changes: Advisory, Data collection, Derived calculations, Source and taxonomy
  • Version 1.3: 2020-03-04
    Changes: Source and taxonomy, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary