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- EMDB-62693: PSI trimer of Arthrospira platensis NIES-39 -

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Basic information

Entry
Database: EMDB / ID: EMD-62693
TitlePSI trimer of Arthrospira platensis NIES-39
Map data
Sample
  • Complex: PSI-trimer
    • Protein or peptide: x 12 types
  • Ligand: x 10 types
KeywordsPhotosystem I / ELECTRON TRANSPORT / PHOTOSYNTHESIS
Biological speciesArthrospira platensis NIES-39 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsKato K / Nakajima Y / Shen JR / Nagao R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for unique low-energy chlorophylls within photosystem I in Arthrospira platensis
Authors: Kato K / Nakajima Y / Shen JR / Nagao R
History
DepositionDec 12, 2024-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62693.png

Downloads & links

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Map

FileDownload / File: emd_62693.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 296 pix.
= 222.592 Å		0.75 Å/pix.
x 296 pix.
= 222.592 Å		0.75 Å/pix.
x 296 pix.
= 222.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.08989287 - 0.2071208
Average (Standard dev.)0.0007398743 (±0.007454579)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 222.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_62693_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62693_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62693_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PSI-trimer

EntireName: PSI-trimer
Components
  • Complex: PSI-trimer
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Unknown
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem I reaction center subunit psaX
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: UNKNOWN LIGAND
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: PSI-trimer

SupramoleculeName: PSI-trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 1.08 MDa

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 83.347781 KDa
SequenceString: MTISPPEREA KAKVTVDKDP TPTSFERWGK PGHFRRDLAK GPSTTTWIWN LHADAHDFDS HTSDLEDISR KIFSAHFGHL AVIFIWLSG AYFHGAKFSN YEAWLTNPTG IKPSAQVVWP IFGQEILNAD VGGGFQGIQI TSGLFQLWRA SGITNEFQLY C TAIGALVM ...String:
MTISPPEREA KAKVTVDKDP TPTSFERWGK PGHFRRDLAK GPSTTTWIWN LHADAHDFDS HTSDLEDISR KIFSAHFGHL AVIFIWLSG AYFHGAKFSN YEAWLTNPTG IKPSAQVVWP IFGQEILNAD VGGGFQGIQI TSGLFQLWRA SGITNEFQLY C TAIGALVM AGLMLFAGWF HYHKRAPKLE WFQNVESMMN HHLAGLLGLG CLGWTGHQIH VSLPINKLLD AGVAPKDIPL PH EFILNSS LMAELYPSFK QGLTPFFTLN WGVYADFLTF KGGLNPQTGG LWLSDTAHHH LALAVLFIIA GHMYRTNWGI GHS MKELLE AHKGPFTGEG HKGLYEILTT SWHAQLAINL AMLGSLSIIV AHHMYAMPPY PYIATDYPTQ LSLFTHHMWI GAFC IVGAG AHAAIFMVRD YDPAKNVNNL LDRVIRHRDA IISHLNWVCI FLGFHSFGLY VHNDTMRAFG RPQDMFSDTG IQLQP IFAQ WVQNLHTLAP GNTAPNALAS VSPAFGGDVI AVGGKVAMMP IALGTADFMV HHIHAFTIHV TVLILLKGVL YSRSSR LIP DKSELGFRFP CDGPGRGGTC QVSGWDHVFL GLFWMYNSLS IVIFHFSWKM QSDVWGTVAS DGTISHITNG NFAQSAI TI NGWLRDFLWA QASQVINSYG SALSAYGLMF LAAHFVWAFS LMFLFSGRGY WQELIESIVW AHNKLKVAPA IQPRALSI I QGRAVGVAHY LLGGIVTTWA FFLARIISVG

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 83.483039 KDa
SequenceString: MATKFPKFSQ DLAQDPTTRR IWYGIATAHD FETHDGMTEE NLYQKIFASH FGHIAIIFLW TSGSLFHVAW QGNFEQWIKD PLNVRPIAH AIWDPQFGQP AVDAFTQAGA SNPVDIAYSG VYHWWYTIGM RTNGDLYQGS IFLLLLAAVF LFAGWLHLQP K YRPSLSWF ...String:
MATKFPKFSQ DLAQDPTTRR IWYGIATAHD FETHDGMTEE NLYQKIFASH FGHIAIIFLW TSGSLFHVAW QGNFEQWIKD PLNVRPIAH AIWDPQFGQP AVDAFTQAGA SNPVDIAYSG VYHWWYTIGM RTNGDLYQGS IFLLLLAAVF LFAGWLHLQP K YRPSLSWF KNAESRLNHH LAGLFGVSSL AWTGHLVHVA IPESRGQHVG WDNFLSTLPH PAGLAPFFTG NWGVYAQNPD TV RHVFGTS EGSGTAILTF LGGFHPQTES LWLTDMAHHH LAIAVIFIIA GHMYRTNFGI GHSIKEMCDA KDFFGRRLEG PFN MPHQGI YETYNNSLHF QLGWHLACLG VITSLVAQHM YSIPPYAFIA KDYTTMAALY THHQYIAGFL MVGAFAHGAI FLVR DYDPE QNKGNVLARV LDHKEAIISH LSWVSLFLGF HTLGIYVHND VVVAFGTPEK QILIEPVFAQ FIQAAHGKAV YAMDV LLSN PESIATTAWP NYGNVWLPGW LDAINSGTNS LFLTIGPGDF LVHHAIALGL HTTTLILVKG ALDARGSKLM PDKKDF GYA FPCDGPGRGG TCDISAWDSF YLAMFWMLNT LGWLTFYWHW KHLGIWQGNV AQFNESSTYL MGWFRDYLWL NSSQLIN GY NPFGTNNLSV WAWMFLFGHL VWATGFMFLI SWRGYWQELI ETIVWAHERT PLANLVRWKD KPVALSIVQA RVVGLAHF T VGYILTYAAF LIASTAGKFG

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 8.823235 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKAGQIA SSPRTEDCIG CKRCETACPT DFLSVRVYLG AETTRSMGLA Y

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 15.863099 KDa
SequenceString:
MVETLTGKAP KFGGSTGGLL TKAQVEEKYA ITWTSTKEQV FEMPTGGAAI MNEGENLLYL ARKEQCLALG TQLRTKFKPK IEDFKIYRI FPNGEMEYLH PKDGVFPEKV NEGREFNGKI DRKIGDNPNP ASVKFSGKAT YES

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 8.621794 KDa
SequenceString:
MVQRGSKVRI LRQESYWFQE VGTVVSVDKS GIRYPVIVRF DKVNYNAYCG VDGGVNTNNF AEAELIEVEA PAKAAKK

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 17.740369 KDa
SequenceString:
MRRLLALVLA LGLWFGGSAA AEAYNLTPCS DSAAFQQRAQ TSIARSANPD QAKARFERYS QELCGEDGLP HLIVDGSLSH AGDFLIPSV LFLYIAGWIG WVGRSYLQYA GKDKKATEKE IIIDVPKAVQ LMLGGFLWPL AALKEMTTGE MFAKDNEITV S PR

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Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 4.236111 KDa
SequenceString:
MTGDYAASFL PWILIPVVCW LMPAVLMGLL FIHIESDA

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 4.765721 KDa
SequenceString:
MQNFLKYLST VPVLAAVWLL ITAGILIEFN RFFPDLLFHP L

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Macromolecule #9: Unknown

MacromoleculeName: Unknown / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 6.996616 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 17.018334 KDa
SequenceString:
MPQATDQGLI QAYNGDPFVG HLSTPISDSA FTRTFIGNLP AYRPGLSPLL RGLEIGMAHG YFIGGPWVKF GTQRGTEFAN LNGLICGLA MLLIATACLA AYGLVTFQGD KSEEGDSLQS AAGWSQFAGG FFIGGMGSAF LAFFLLENFA VVDAIFRGLV N N

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Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 3.426116 KDa
SequenceString:
MSLTDTQVFV ALVIALIPGI LAFRLSTELY K

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Macromolecule #12: Photosystem I reaction center subunit psaX

MacromoleculeName: Photosystem I reaction center subunit psaX / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Molecular weightTheoretical: 4.107841 KDa
SequenceString:
MANKSGGFPY PFRTFWAIVL LGINLVVAGY YFHIIQ

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Macromolecule #13: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 13 / Number of copies: 3 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #14: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 14 / Number of copies: 273 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #15: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 15 / Number of copies: 6 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #16: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 16 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #17: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 17 / Number of copies: 60 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #18: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 18 / Number of copies: 6 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #19: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 19 / Number of copies: 15 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #20: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 20 / Number of copies: 3 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Macromolecule #21: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 21 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #22: water

MacromoleculeName: water / type: ligand / ID: 22 / Number of copies: 351 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMMES-NaOHMES
0.03 %DDMDDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 60000

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Image processing

Particle selectionNumber selected: 4493216
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1jb0

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 121244
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: ModelAngelo
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-9l0a:
PSI trimer of Arthrospira platensis NIES-39

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