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- PDB-6igz: Structure of PSI-LHCI -

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Basic information

Entry
Database: PDB / ID: 6igz
TitleStructure of PSI-LHCI
Components
  • Lhca-a
  • Lhca-b
  • Lhca-c
  • Lhca-d
  • Lhca-g
  • Lhca-h
  • Lhca-i
  • Lhca-j
  • Photosystem I reaction center subunit XII
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaG
  • PsaH
  • PsaI
  • PsaJ
  • PsaK
  • PsaL
KeywordsPLANT PROTEIN / PSI-LHCI
Function / homologyPhotosystem I PsaM, reaction centre / Photosystem I PsaM, reaction centre superfamily / Photosystem I protein M (PsaM) / photosystem I / chloroplast thylakoid membrane / photosynthesis / integral component of membrane / Photosystem I reaction center subunit XII
Function and homology information
Specimen sourceBryopsis corticulans (plant)
Spinacia oleracea (spinach)
Bryopsis plumosa (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.49 Å resolution
AuthorsXiong, P. / Xiaochun, Q.
CitationJournal: Nat Plants / Year: 2019
Title: Structure of a green algal photosystem I in complex with a large number of light-harvesting complex I subunits.
Authors: Xiaochun Qin / Xiong Pi / Wenda Wang / Guangye Han / Lixia Zhu / Mingmei Liu / Linpeng Cheng / Jian-Ren Shen / Tingyun Kuang / Sen-Fang Sui
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 27, 2018 / Release: Feb 13, 2019

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Structure visualization

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Assembly

Deposited unit
A: PsaA
B: PsaB
C: PsaC
D: PsaD
E: PsaE
F: PsaF
G: PsaG
H: PsaH
I: PsaI
J: PsaJ
K: PsaK
L: PsaL
1: Lhca-a
2: Lhca-c
3: Lhca-d
4: Lhca-b
6: Lhca-g
5: Lhca-a
7: Lhca-h
8: Lhca-b
9: Lhca-i
0: Lhca-j
M: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)841,704343
Polyers579,24923
Non-polymers262,455320
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 21 types, 23 molecules ABCDEFGHIJKL1523486790M

#1: Protein/peptide PsaA


Mass: 83412.336 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#2: Protein/peptide PsaB


Mass: 82164.461 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#3: Protein/peptide PsaC


Mass: 8880.307 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#4: Protein/peptide PsaD


Mass: 21733.045 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#5: Protein/peptide PsaE


Mass: 10096.458 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#6: Protein/peptide PsaF


Mass: 25129.158 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#7: Protein/peptide PsaG


Mass: 18226.600 Da / Num. of mol.: 1 / Source: (natural) Spinacia oleracea (spinach)
#8: Protein/peptide PsaH


Mass: 14400.360 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#9: Protein/peptide PsaI


Mass: 3859.615 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#10: Protein/peptide PsaJ


Mass: 4744.679 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#11: Protein/peptide PsaK


Mass: 12487.672 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#12: Protein/peptide PsaL


Mass: 21338.602 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#13: Protein/peptide Lhca-a


Mass: 24458.012 Da / Num. of mol.: 2 / Source: (natural) Bryopsis corticulans (plant)
#14: Protein/peptide Lhca-c


Mass: 27808.264 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#15: Protein/peptide Lhca-d


Mass: 30409.689 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#16: Protein/peptide Lhca-b


Mass: 26575.912 Da / Num. of mol.: 2 / Source: (natural) Bryopsis corticulans (plant)
#17: Protein/peptide Lhca-g


Mass: 29300.680 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#18: Protein/peptide Lhca-h


Mass: 28621.643 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#19: Protein/peptide Lhca-i


Mass: 24152.645 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#20: Protein/peptide Lhca-j


Mass: 26910.092 Da / Num. of mol.: 1 / Source: (natural) Bryopsis corticulans (plant)
#21: Protein/peptide Photosystem I reaction center subunit XII / / PsaM / PSI-M


Mass: 3505.114 Da / Num. of mol.: 1 / Source: (natural) Bryopsis plumosa (plant) / References: UniProt: A0A0D6E2L8

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Non-polymers , 10 types, 320 molecules

#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 218 / Formula: C55H72MgN4O5 / Chlorophyll a
#23: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Formula: C31H46O2 / Phytomenadione
#24: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 11 / Formula: C38H75O10P
#25: Chemical...
ChemComp-8CT / (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene


Mass: 536.873 Da / Num. of mol.: 34 / Formula: C40H56
#26: Chemical ChemComp-HTG / HEPTYL 1-THIOHEXOPYRANOSIDE


Mass: 294.408 Da / Num. of mol.: 2 / Formula: C13H26O5S
#27: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Formula: Fe4S4 / Iron–sulfur cluster
#28: Chemical ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Mass: 949.299 Da / Num. of mol.: 1 / Formula: C51H96O15
#29: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 26 / Formula: C55H70MgN4O6 / Chlorophyll b
#30: Chemical
ChemComp-XAT / (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 / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 20 / Formula: C40H56O4 / Violaxanthin
#31: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Formula: C45H86O10

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSI-LHCI / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21
Source: NATURAL
Source (natural)Organism: Bryopsis corticulans (plant)
Buffer solutionpH: 7.8
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.852 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM softwareName: RELION / Version: 1.4 / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 59525 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00954746
ELECTRON MICROSCOPYf_angle_d1.96678218
ELECTRON MICROSCOPYf_dihedral_angle_d15.14832460
ELECTRON MICROSCOPYf_chiral_restr0.1126449
ELECTRON MICROSCOPYf_plane_restr0.00610222

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