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- EMDB-54956: Trimeric photosystem I of Acaryochloris marina NIES-2412 -

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Entry
Database: EMDB / ID: EMD-54956
TitleTrimeric photosystem I of Acaryochloris marina NIES-2412
Map data
Sample
  • Complex: Trimeric PSI
    • Protein or peptide: x 4 types
  • Protein or peptide: x 8 types
  • Ligand: x 9 types
KeywordsChlorophyll d / photosystem I / ELECTRON TRANSPORT
Biological speciesAcaryochloris marina (bacteria) / Acaryochloris marina NIES-2412 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsLeong HF / Consoli G
Funding support Netherlands, European Union, United Kingdom, 12 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)714.018.001 Netherlands
European Research Council (ERC)101141764European Union
UK Research and Innovation (UKRI)MR/T017546/1 United Kingdom
UK Research and Innovation (UKRI)MR/T017546/2 United Kingdom
UK Research and Innovation (UKRI)MR/Y011635/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X019284/1 United Kingdom
H2020 Marie Curie Actions of the European Commission955520European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001383/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002015/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00921X United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Z516740/1 United Kingdom
Leverhulme TrustRPG-2022-203 United Kingdom
CitationJournal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionSep 1, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54956.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 600 pix.
= 634.8 Å		1.06 Å/pix.
x 600 pix.
= 634.8 Å		1.06 Å/pix.
x 600 pix.
= 634.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4549089 - 1.4354782
Average (Standard dev.)0.000010587908 (±0.019938467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 634.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54956_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_54956_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 : Trimeric PSI

EntireName: Trimeric PSI
Components
  • Complex: Trimeric PSI
    • Protein or peptide: Photosystem I protein PsaD
    • Protein or peptide: Photosystem I protein PsaE
    • Protein or peptide: Photosystem I protein PsaM
    • Protein or peptide: Photosystem I protein PsaX2
  • Protein or peptide: Photosystem I protein PsaA
  • Protein or peptide: Photosystem I protein PsaB
  • Protein or peptide: Photosystem I protein PsaC
  • Protein or peptide: Photosystem I protein PsaF
  • Protein or peptide: Photosystem I protein PsaI
  • Protein or peptide: Photosystem I protein PsaJ
  • Protein or peptide: Photosystem I protein PsaK
  • Protein or peptide: Photosystem I protein PsaL
  • Ligand: CHLOROPHYLL D ISOMER
  • Ligand: PHEOPHYTIN A
  • Ligand: CHLOROPHYLL D
  • Ligand: PHYLLOQUINONE
  • Ligand: (6'S)-beta,epsilon-carotene
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: water

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Supramolecule #1: Trimeric PSI

SupramoleculeName: Trimeric PSI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4-#5, #11-#12 / Details: trimeric photosystem I from A. marina NIES - 2412
Source (natural)Organism: Acaryochloris marina (bacteria) / Strain: NIES-2412
Molecular weightTheoretical: 922 KDa

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Macromolecule #1: Photosystem I protein PsaA

MacromoleculeName: Photosystem I protein PsaA / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 83.573766 KDa
SequenceString: MTNSPGGPET KGRTAEVDIN PVKASLEVAG KPGHFNKSLS KGPQTTTWIW NLHALAHDFD TQTNDLEEIS RKIFSAHFGH LAIVFVWIS GMIFHAARFS NYYAWLADPL GNKPSAHVVW PIVGQDILNA DVGNGFHGIQ ITSGLFHILR GAGMTAPIEL Y STSIGALV ...String:
MTNSPGGPET KGRTAEVDIN PVKASLEVAG KPGHFNKSLS KGPQTTTWIW NLHALAHDFD TQTNDLEEIS RKIFSAHFGH LAIVFVWIS GMIFHAARFS NYYAWLADPL GNKPSAHVVW PIVGQDILNA DVGNGFHGIQ ITSGLFHILR GAGMTAPIEL Y STSIGALV AAAVTMYAGY FHYHKKAPKL EWFQNAEATI GGHLINLLGL GNLAWTGHLI HVSLPINKML DSGMAPEDIP IP HEYLLDK AFMADLYPSF AQGLAPYFTL NWGVYSDFLT FKGGLDPQTG GLWMTDIAHH HLALAVMYII AGHMYRTNWG IGH HMREIM DAHKGPFTGE GHKGLYDVLT TSWHAQLAIN LACWGSFSIV CAHHMYAMPP YPYLATDYAT QLNLFVHHMW LGGF YIVGG AAHAAIFMVR DYDPAMNQNN VLDRMLRHRD TIIAHLNWVC LFLGFHSFDL YIHNDEMRSL GRPQDMFSDT AIQLQ PIFA QWVQNLQANV AGTIRAPLAE GATSLAWGGD PMFVGGKVAM QHVSLGTADF MIHHIHAFQI HVTVLILLKG VLYARS SRL IPDKASLGFR FPCDGPGRGG TCQSSGWDHV FLGLFWMYNC ISIVNFHFFW KMQSDVWGTA NASGGINYLT AGNWAQS SI TINGWLRDFL WAQSVQVINS YGSALSAYGI LFLGAHFIWA FSLMFLFSGR GYWQELIESI VWAHSKLKIA PAIQPRAM S ITQGRAVGLG HYLLGGIVTS WSFYLARILA LG

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Macromolecule #2: Photosystem I protein PsaB

MacromoleculeName: Photosystem I protein PsaB / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 82.083172 KDa
SequenceString: MATKFPSFSQ DLAQDPTTRR IWYGIATVHD FETHDGMTEE NLYQKIFATH FGHLSIIFLW TAGLLFHVAW QGNFEQWIQD PLTVRPIAH AIWDPHLGDA ATQAFTQAGA SGPVDLCYSG VYHWWYTIGM RTNGDLYSGS IFLMVVAAVM LFAGWLHLQP K FRPSLAWF ...String:
MATKFPSFSQ DLAQDPTTRR IWYGIATVHD FETHDGMTEE NLYQKIFATH FGHLSIIFLW TAGLLFHVAW QGNFEQWIQD PLTVRPIAH AIWDPHLGDA ATQAFTQAGA SGPVDLCYSG VYHWWYTIGM RTNGDLYSGS IFLMVVAAVM LFAGWLHLQP K FRPSLAWF RDAESQMNHH LAVLFGASSL GWTGHLIHVA IPEARGQHVG WDNFLSTMPH PAGLAPFFTG RWAVYAQNPD TT GHIFGTS EGAGTAILTF VGGFHPQTEA LWLTDIAHHH LAIAVLYIVA GHMYRTQFGI GHSMKEIMDA HRDPWYGATL EGL YDTYNE SLHFQLAFHL AALGVITEVV AQHMYSLPSY AFISQDYVTQ AALYTHHQYI GGFLALGAYA HGGIFFVRDY DPER NKGNA LSRLLEHKEA IISHLSWVSM FLGFHTLDLY VHNDVVVAFG TPEKQILPEP IFAEWVQAAH GKLLLGLDSL LSNPQ SIAA TAWPNYGDVW LPGWLDAVNG SSTPFLNIGP GDFLVHHGIA FSIHVTVLIC VKGCLDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DSFYLATFWM LNTIGWVTFY FNWKQLSVWS GNLAQFNNDS TYLMGWLRDY LWGYSAQLIN GYTPFGV NS LSVWAWIFLL GHLCWATGFL FLISWRGYWQ ELIETLVWAH QRTPLANLVM WKDKPVALSI VQGRLVGLVH FAVGYFVT Y GAFVIGATAP LG

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Macromolecule #3: Photosystem I protein PsaC

MacromoleculeName: Photosystem I protein PsaC / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 8.825207 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKAGQIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

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Macromolecule #4: Photosystem I protein PsaD

MacromoleculeName: Photosystem I protein PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 15.12515 KDa
SequenceString:
MAETLTGQTP LFGGSTGGLL SSAETEEKYA ITWTSPKQQV FEMPTGGAAV MNEGENLLYL ARKEQCLALG LRQLRIKKIM DYKIYRVLP DGSNTLLHPK DGVFPEKSNE GRAAVNSVAR SIGENPNPGA IKYTGKQAYD

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Macromolecule #5: Photosystem I protein PsaE

MacromoleculeName: Photosystem I protein PsaE / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 9.350654 KDa
SequenceString:
MVQRGSKVRI LRPESYWFRE IGTVASVDKS GIKYPVIVRF DTCNYNGISG TAAGINTNNF GVHELEEVEA PKAKAKKPAA APKAEG

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Macromolecule #6: Photosystem I protein PsaF

MacromoleculeName: Photosystem I protein PsaF / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 17.691422 KDa
SequenceString:
MRRLFAVLVV LTLWLGVVPP ASADIGGLVP CSESPQFQER AAKARNTTGD PESGRKRFEM YSSALCGADD GLPRIIAGGP WSRAGDFLI PGLLFIYIAG GIGNASRNYQ IANRKKNPKN PAMGEIIIDV PLALSSTIAA LAWPLKALGE VTSGKLTVPD S DVTVSPR

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Macromolecule #7: Photosystem I protein PsaI

MacromoleculeName: Photosystem I protein PsaI / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 3.648337 KDa
SequenceString:
MISDILPAIM TPLVVLIGGG AAMTAFFYYV EREG

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Macromolecule #8: Photosystem I protein PsaJ

MacromoleculeName: Photosystem I protein PsaJ / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 5.457358 KDa
SequenceString:
PPQIDSEKGF MKFFSTAPVI AFVFFTLTAG FLVELNRFFP DILFFPY

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Macromolecule #9: Photosystem I protein PsaK

MacromoleculeName: Photosystem I protein PsaK / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 8.894473 KDa
SequenceString:
MFTPTFLTVA VRAVNWTPTV GVVMIAANIM AIAIAKYSIQ YPNVGPSMPA SSLFGGFSFN AVLGTQVFGH VLGAGAILGL TYLGVL

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Macromolecule #10: Photosystem I protein PsaL

MacromoleculeName: Photosystem I protein PsaL / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 15.588004 KDa
SequenceString:
MTMEMVKHGG DPFVGDLATP VNSSGIVKAW INNLPAYRKG MSANARGLEI GMAHGYYLYG PFATSGPVRG TTMALVSGVL SASCVIIVL TVAMQLYSSL SVPKPRPSVT TADPGSDFGT KEGWSAIGSG FLIGGCGGAV IAGVLSYAIA IFAG

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Macromolecule #11: Photosystem I protein PsaM

MacromoleculeName: Photosystem I protein PsaM / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 3.204925 KDa
SequenceString:
MELSDLQIVI ALVVALLPAL LALNLGTALS K

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Macromolecule #12: Photosystem I protein PsaX2

MacromoleculeName: Photosystem I protein PsaX2 / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina NIES-2412 (bacteria)
Molecular weightTheoretical: 2.973575 KDa
SequenceString:
KNPWPTLPLI WSGIGILAAI WITLQIG

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Macromolecule #13: CHLOROPHYLL D ISOMER

MacromoleculeName: CHLOROPHYLL D ISOMER / type: ligand / ID: 13 / Number of copies: 3 / Formula: G9R
Molecular weightTheoretical: 895.462 Da
Chemical component information

ChemComp-G9R:
CHLOROPHYLL D ISOMER

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Macromolecule #14: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 14 / Number of copies: 6 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #15: CHLOROPHYLL D

MacromoleculeName: CHLOROPHYLL D / type: ligand / ID: 15 / Number of copies: 279 / Formula: CL7
Molecular weightTheoretical: 895.462 Da
Chemical component information

ChemComp-CL7:
CHLOROPHYLL D

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Macromolecule #16: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 16 / Number of copies: 6 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #17: (6'S)-beta,epsilon-carotene

MacromoleculeName: (6'S)-beta,epsilon-carotene / type: ligand / ID: 17 / Number of copies: 57 / Formula: A1JPJ
Molecular weightTheoretical: 536.873 Da

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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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 19 / 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 #20: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 20 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #21: water

MacromoleculeName: water / type: ligand / ID: 21 / Number of copies: 93 / 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

Concentration1 mg/mL
BufferpH: 6.5
Details: 50 mM MES, 1 M betaine monohydrate, 20 mM CaCl2, 5 mM MgCl2 and 10% (v/v) glycerol, pH 6.5 adjusted with NaOH
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 100 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5120 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 151833
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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