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- EMDB-15970: Photosystem I assembly intermediate of Avena sativa -

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Basic information

Entry
Database: EMDB / ID: EMD-15970
TitlePhotosystem I assembly intermediate of Avena sativa
Map data
Sample
  • Complex: Assembly Intermediate of PSI from Avena sativa
    • Protein or peptide: x 8 types
  • Ligand: x 10 types
KeywordsPSI structure / assembly intermediate / Monocotyledons / etiolation / PHOTOSYNTHESIS
Function / homology
Function and homology information


thylakoid membrane / chloroplast thylakoid / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...thylakoid membrane / chloroplast thylakoid / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB ...Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesAvena sativa (oats)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.11 Å
AuthorsNaschberger A / Amunts A / Nelson N
Funding support Sweden, Israel, 3 items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchARC19-0051 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
Israel Science Foundation569/17 Israel
CitationJournal: To Be Published
Title: Photosystem I assembly intermediate of Avena sativa
Authors: Naschberger A / Amunts A / Nelson N
History
DepositionOct 17, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15970.png

Downloads & links

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Map

FileDownload / File: emd_15970.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.053
Minimum - Maximum-0.1587909 - 0.47037214
Average (Standard dev.)-0.000074220974 (±0.0050321287)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15970_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15970_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15970_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 : Assembly Intermediate of PSI from Avena sativa

EntireName: Assembly Intermediate of PSI from Avena sativa
Components
  • Complex: Assembly Intermediate of PSI from Avena sativa
    • 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, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit IV A, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit VI, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: PSI subunit V
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: water

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Supramolecule #1: Assembly Intermediate of PSI from Avena sativa

SupramoleculeName: Assembly Intermediate of PSI from Avena sativa / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Avena sativa (oats)

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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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Avena sativa (oats)
Molecular weightTheoretical: 83.263305 KDa
SequenceString: MIIRSPEPEV KIVVDRDPVK TSFEEWARPG HFSRTLAKGP DTTTWIWNLH ADAHDFDSHT GDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQLWRASG ITSELQLYCT A IGALIFAA ...String:
MIIRSPEPEV KIVVDRDPVK TSFEEWARPG HFSRTLAKGP DTTTWIWNLH ADAHDFDSHT GDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQLWRASG ITSELQLYCT A IGALIFAA LMLFAGWFHY HKAAPKLAWF QDVESMLNHH LAGLLGLGSL SWAGHQIHVS LPINQFLDAG VDPKEIPLPH EF ILNRDLL AQLYPSFAEG ATPFFTLNWS KYAEFLTFRG GLDPVTGGLW LTDIAHHHLA IAILFLIAGH MYRTNWGIGH GLK DILEAH KGPFTGQGHK GLYEILTTSW HAQLSLNLAM LGSTTIVVAH HMYSMPPYPY LATDYGTQLS LFTHHMWIGG FLIV GAAAH AAIFMVRDYD PTTRYNDLLD RVLRHRDAII SHLNWVCIFL GFHSFGLYIH NDTMSALGRP QDMFSDTAIQ LQPIF AQWV QNIHATAPGV TAPGATTSTS LTWGGGELVA VGGKVALLPI PLGTADFLVH HIHAFTIHVT VLILLKGVLF ARSSRL IPD KANLGFRFPC DGPGRGGTCQ VSAWDHVFLG LFWMYNAISV VIFHFSWKMQ SDVWGTISDQ GMVTHITGGN FAQSSIT IN GWLRDFLWAQ ASQVIQSYGS SLSAYGLFFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAPAT QPRALSII Q GRAVGVTHYL LGGIATTWAF FLARIIAVG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Avena sativa (oats)
Molecular weightTheoretical: 82.605781 KDa
SequenceString: MELRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFESWIQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA AGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSTLS LVAGWLHLQP K WKPSLSWF ...String:
MELRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFESWIQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA AGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSTLS LVAGWLHLQP K WKPSLSWF KNAESRLNHH LSGLFGVSSL AWTGHLVHVA IPASRGEYVR WNNFLDVLPY PQGLGPLLTG QWNLYAQNPD SS NHLFGTA QGAGTAILTL LGGFHPQTQS LWLTDIAHHH LAIAFIFLIA GHMYRTNFGI GHSIKDLLEA HTPPGGRLGR GHK GLYDTI NNSIHFQLGL ALASLGVITS LVAQHMYSLP AYAFIAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNED NVLARMLDHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPIFAQWIQS AHGKTTYGFD ILLSS TNGP AFNAGRSLWL PGWLNAVNEN SNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLAVFWM LNTIGWVTFY WHWKHITLWQ GNVSQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWMFLF GHLVWATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLIR WRDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG KFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Avena sativa (oats)
Molecular weightTheoretical: 8.909345 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPTDVLEMIP WDGCKAKQIA SAPRTEDCVG CKRCESACPT DFLSVRVYLG PETTRSMALS Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I reaction center subunit II, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II, chloroplastic
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Avena sativa (oats)
Molecular weightTheoretical: 22.081225 KDa
SequenceString: MAMATQASAA TRHLITAAWS PSSKPRAVSL ALPSTRGPAP LCAAASDSPA PATKEPEAAP APAGFVPPQL DPSTPSPIFG GSTGGLLRK AQVEEFYVIT WTSPKEQVFE MPTGGAAIMR EGPNLLKLAR KEQCLALGNR LRSKYKIAYQ FYRVFPNGEV Q YLHPKDGV ...String:
MAMATQASAA TRHLITAAWS PSSKPRAVSL ALPSTRGPAP LCAAASDSPA PATKEPEAAP APAGFVPPQL DPSTPSPIFG GSTGGLLRK AQVEEFYVIT WTSPKEQVFE MPTGGAAIMR EGPNLLKLAR KEQCLALGNR LRSKYKIAYQ FYRVFPNGEV Q YLHPKDGV YPEKVNAGRQ GVGQNFRSIG KNVSPIEVKF TGKNTFDV

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Macromolecule #5: Photosystem I reaction center subunit IV A, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit IV A, chloroplastic
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Avena sativa (oats)
Molecular weightTheoretical: 15.298426 KDa
SequenceString:
MASTNMASAT SRFMLAAGMP ARGSSSNRVS FVSSNRLGRR LVVRAEEEPA APPAPTPAVT ETAEGAVATK APAKVKPPPI GPKRGTKVK ILRRESYWYN GTGSVVTVDQ DPNTRYPVVV RFAKVNYAGV STNNYALDEI KEVV

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Macromolecule #6: Photosystem I reaction center subunit VI, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit VI, chloroplastic
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Avena sativa (oats)
Molecular weightTheoretical: 10.088463 KDa
SequenceString:
YGEKSVYFDL EDIGNTTGQW DLYGSDAPSP YNGLQSKFFN TFAAPFTKRG LLLKFLLLGG GSLLAYVSAS ASPDLLPIKK GPQLPPTPG PRGKI

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Avena sativa (oats)
Molecular weightTheoretical: 3.648486 KDa
SequenceString:
LNLPSIFVPL VGLVFPAIAM TSLFLYVQKN KIV

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #8: PSI subunit V

MacromoleculeName: PSI subunit V / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Avena sativa (oats)
Molecular weightTheoretical: 22.575064 KDa
SequenceString: MATAYAPPMA SQLLKSSNSS LVCSKPRGLS GASLTTRRPR FVVKAIKADK PNYQVVQPIN GDPFIGSLET PVTSSPLVAW YLSNLPAYR TAVSPLLRGI EVGLAHGYLL VGPFALTGPL RNTPVHGQAG ALGAIGLVTI LSVVLTMYGV ASFEDGAPST A PSLTLTGR ...String:
MATAYAPPMA SQLLKSSNSS LVCSKPRGLS GASLTTRRPR FVVKAIKADK PNYQVVQPIN GDPFIGSLET PVTSSPLVAW YLSNLPAYR TAVSPLLRGI EVGLAHGYLL VGPFALTGPL RNTPVHGQAG ALGAIGLVTI LSVVLTMYGV ASFEDGAPST A PSLTLTGR KKEADKLQTA EGWAQFTGGF FFGGVSGAIW AYFLLYVLDL PYFFK

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Macromolecule #9: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 9 / Number of copies: 2 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #10: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 10 / Number of copies: 86 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #11: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 11 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #12: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 12 / Number of copies: 3 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #13: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 13 / Number of copies: 13 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #14: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 14 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #15: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 15 / Number of copies: 3 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMU:
DODECYL-ALPHA-D-MALTOSIDE / detergent*YM

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Macromolecule #16: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 16 / Number of copies: 1 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #17: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 17 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #18: water

MacromoleculeName: water / type: ligand / ID: 18 / Number of copies: 517 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.346 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 169213
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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