[English] 日本語
Yorodumi
- EMDB-60522: 1.8 A resolution structure of the Photosystem I assembly intermed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60522
Title1.8 A resolution structure of the Photosystem I assembly intermediate lacking stromal subunits.
Map data
Sample
  • Complex: Assembly Intermediate of Photosystem I lacking the cytosolic subunits PsaC, PsaD, and PsaE and the transmembrane subunit PsaL.
    • Protein or peptide: x 7 types
  • Ligand: x 12 types
KeywordsPSI / assembly intermediates / photosystem I / biochemistry / cryo-EM / photosystem biogenesis. / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / plasma membrane
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaB / Photosystem I PsaA / 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
Similarity search - Domain/homology
Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesSynechocystis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.83 Å
AuthorsNaschberger A / Komenda J
Funding support Czech Republic, European Union, 2 items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic24-10227S Czech Republic
European Research Council (ERC)854126European Union
CitationJournal: To Be Published
Title: 1.8 A resolution structure of the Photosystem I assembly intermediate lacking stromal subunits
Authors: Charras Q / Gupta S / Tichy M / Al-Amoudi A / Lukes M / Konik P / Sobotka R / Novak P / Komenda J / Naschberger A
History
DepositionJun 12, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_60522.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.729 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.011908391 - 0.046950348
Average (Standard dev.)-0.0001754514 (±0.0013484322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 255.15 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Assembly Intermediate of Photosystem I lacking the cytosolic subu...

EntireName: Assembly Intermediate of Photosystem I lacking the cytosolic subunits PsaC, PsaD, and PsaE and the transmembrane subunit PsaL.
Components
  • Complex: Assembly Intermediate of Photosystem I lacking the cytosolic subunits PsaC, PsaD, and PsaE and the transmembrane subunit PsaL.
    • 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 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: Photosystem I reaction center subunit PsaK 1
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: BETA-CAROTENE
  • Ligand: beta,beta-caroten-4-one
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: CHLORIDE ION
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Zeaxanthin
  • Ligand: water

+
Supramolecule #1: Assembly Intermediate of Photosystem I lacking the cytosolic subu...

SupramoleculeName: Assembly Intermediate of Photosystem I lacking the cytosolic subunits PsaC, PsaD, and PsaE and the transmembrane subunit PsaL.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Synechocystis (bacteria)

+
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: Synechocystis (bacteria)
Molecular weightTheoretical: 83.036398 KDa
SequenceString: MTISPPEREA KAKVSVDNNP VPTSFEKWGK PGHFDRTLAR GPKTTTWIWN LHANAHDFDS QTSDLEDVSR KIFSAHFGHL AVVFVWLSG MYFHGAKFSN YEGWLADPTH IKPSAQVVWP IVGQGILNGD VGGGFHGIQI TSGLFYLWRA SGFTDSYQLY C TAIGGLVM ...String:
MTISPPEREA KAKVSVDNNP VPTSFEKWGK PGHFDRTLAR GPKTTTWIWN LHANAHDFDS QTSDLEDVSR KIFSAHFGHL AVVFVWLSG MYFHGAKFSN YEGWLADPTH IKPSAQVVWP IVGQGILNGD VGGGFHGIQI TSGLFYLWRA SGFTDSYQLY C TAIGGLVM AALMLFAGWF HYHVKAPKLE WFQNVESMMN HHLAGLLGLG SLGWAGHQIH VSMPINKLLD AGVAPKDIPL PH EFILEPS KMAELYPSFA QGLTPFFTLN WGVYSDFLTF KGGLNPVTGG LWLSDTAHHH LAIAVLFIIA GHMYRTNWGI GHS MKEILE AHKGPFTGEG HKGLYEILTT SWHAQLAINL ALLGSLTIIV AQHMYAMPPY PYQAIDYATQ LSLFTHHMWI GGFL IVGAG AHGAIFMVRD YDPAKNVNNL LDRMLRHRDA IISHLNWVCI FLGFHSFGLY IHNDTMRALG RPQDMFSDTA IQLQP IFAQ WVQHLHTLAP GATAPNALAT ASYAFGGETI AVAGKVAMMP ITLGTADFMV HHIHAFTIHV TALILLKGVL YARSSR LVP DKANLGFRFP CDGPGRGGTC QVSGWDHVFL GLFWMYNSLS IVIFHFSWKM QSDVWGTVSP DGSVTHVTLG NFAQSAI TI NGWLRDFLWA QAANVINSYG SALSAYGIMF LAGHFVFAFS LMFLFSGRGY WQELIESIVW AHNKLNVAPA IQPRALSI I QGRAVGVAHY LLGGIVTTWA FFLARSLSIG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

+
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: Synechocystis (bacteria)
Molecular weightTheoretical: 81.369531 KDa
SequenceString: MATKFPKFSQ DLAQDPTTRR IWYGIATAHD FETHDGMTEE NLYQKIFASH FGHIAIIFLW TSGTLFHVAW QGNFEQWIKD PLNIRPIAH AIWDPHFGEG AVNAFTQAGA SNPVNIAYSG VYHWFYTIGM TTNQELYSGA VFLLVLASLF LFAGWLHLQP K FRPSLAWF ...String:
MATKFPKFSQ DLAQDPTTRR IWYGIATAHD FETHDGMTEE NLYQKIFASH FGHIAIIFLW TSGTLFHVAW QGNFEQWIKD PLNIRPIAH AIWDPHFGEG AVNAFTQAGA SNPVNIAYSG VYHWFYTIGM TTNQELYSGA VFLLVLASLF LFAGWLHLQP K FRPSLAWF KNAESRLNHH LAGLFGVSSL AWAGHLVHVA IPEARGQHVG WDNFLSTPPH PAGLMPFFTG NWGVYAADPD TA GHIFGTS EGAGTAILTF LGGFHPQTES LWLTDIAHHH LAIAVIFIIA GHMYRTNWGI GHSIKEILNA HKGPLTGAGH TNL YDTINN SLHFQLGLAL ASLGVITSLV AQHMYSLPSY AFIAQDHTTQ AALYTHHQYI AGFLMVGAFA HGAIFFVRDY DPVA NKDNV LARMLEHKEA LISHLSWVSL FLGFHTLGLY VHNDVVVAFG TPEKQILIEP VFAQWIQATS GKALYGFDVL LSNPD SIAS TTGAAWLPGW LDAINSGTNS LFLTIGPGDF LVHHAIALGL HTTALILIKG ALDARGSKLM PDKKDFGYSF PCDGPG RGG TCDISAWDAF YLAMFWMLNT LGWLTFYWHW KHLGVWSGNV AQFNENSTYL MGWFRDYLWA NSAQLINGYN PYGVNNL SV WAWMFLFGHL VWATGFMFLI SWRGYWQELI ETIVWAHERT PLANLVRWKD KPVALSIVQA RLVGLAHFTV GYVLTYAA F LIASTAGKFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

+
Macromolecule #3: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis (bacteria)
Molecular weightTheoretical: 18.267082 KDa
SequenceString:
MKHLLALLLA FTLWFNFAPS ASADDFANLT PCSENPAYLA KSKNFLNTTN DPNSGKIRAE RYASALCGPE GYPHLIVDGR FTHAGDFLI PSILFLYIAG WIGWVGRSYL IEIRESKNPE MQEVVINVPL AIKKMLGGFL WPLAAVGEYT SGKLVMKDSE I PTSPR

UniProtKB: Photosystem I reaction center subunit III

+
Macromolecule #4: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis (bacteria)
Molecular weightTheoretical: 4.414148 KDa
SequenceString:
MDGSYAASYL PWILIPMVGW LFPAVTMGLL FIHIESEGEG

UniProtKB: Photosystem I reaction center subunit VIII

+
Macromolecule #5: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis (bacteria)
Molecular weightTheoretical: 4.535415 KDa
SequenceString:
MDGLKSFLST APVMIMALLT FTAGILIEFN RFYPDLLFHP

UniProtKB: Photosystem I reaction center subunit IX

+
Macromolecule #6: Photosystem I reaction center subunit PsaK 1

MacromoleculeName: Photosystem I reaction center subunit PsaK 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis (bacteria)
Molecular weightTheoretical: 8.649268 KDa
SequenceString:
MHSFLLATAV PATLSWSPKV AGVMIACNIL AIAFGKLTIK QQNVGTPMPS SNFFGGFGLG AVLGTASFGH ILGAGVILGL ANMGVL

UniProtKB: Photosystem I reaction center subunit PsaK 1

+
Macromolecule #7: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis (bacteria)
Molecular weightTheoretical: 3.382063 KDa
SequenceString:
MALSDTQILA ALVVALLPAF LAFRLSTELY K

UniProtKB: Photosystem I reaction center subunit XII

+
Macromolecule #8: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 8 / Number of copies: 3 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #9: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 9 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

+
Macromolecule #10: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 10 / Number of copies: 92 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
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

+
Macromolecule #12: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 12 / Number of copies: 14 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #13: beta,beta-caroten-4-one

MacromoleculeName: beta,beta-caroten-4-one / type: ligand / ID: 13 / Number of copies: 5 / Formula: ECH
Molecular weightTheoretical: 550.856 Da
Chemical component information

ChemComp-ECH:
beta,beta-caroten-4-one

+
Macromolecule #14: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 14 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #15: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 15 / Number of copies: 26 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

+
Macromolecule #16: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #17: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 17 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #18: Zeaxanthin

MacromoleculeName: Zeaxanthin / type: ligand / ID: 18 / Number of copies: 1 / Formula: 5X6
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-K3I:
Zeaxanthin

+
Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / Number of copies: 355 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 30mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5oy0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 333941
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more