[English] 日本語
Yorodumi
- PDB-9zjt: PSI-IsiA Complex from Anabaena 7120 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9zjt
TitlePSI-IsiA Complex from Anabaena 7120
Components
  • (Photosystem I ...) x 12
  • (Photosystem II CP43 protein PsbC ...) x 2
  • Iron stress-induced chlorophyll-binding protein
KeywordsPHOTOSYNTHESIS / Iron Stress Chlorophyll Photosystem I Complex / light harvesting
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosystem I reaction centre subunit VIII ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / 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 / Electron transport accessory-like domain superfamily / 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
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / : ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / : / : / : / : / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XII / Iron stress-induced chlorophyll-binding protein
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsMazor, Y.M. / Maqdisi, R.M. / Gorski, C.G. / Pakrasi, H.P. / Biswas, S.B. / Niedzwiedzki, D.N.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
Citation
Journal: To Be Published
Title: Structure of the PSI-IsiA supercomplex from Anabaena sp. PCC 7120 at 2.2 Angstroms Resolution.
Authors: Mazor, Y.M. / Maqdisi, R.M.
#1: Journal: Nat Commun / Year: 2023
Title: Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120.
Authors: Ryo Nagao / Koji Kato / Tasuku Hamaguchi / Yoshifumi Ueno / Naoki Tsuboshita / Shota Shimizu / Miyu Furutani / Shigeki Ehira / Yoshiki Nakajima / Keisuke Kawakami / Takehiro Suzuki / Naoshi ...Authors: Ryo Nagao / Koji Kato / Tasuku Hamaguchi / Yoshifumi Ueno / Naoki Tsuboshita / Shota Shimizu / Miyu Furutani / Shigeki Ehira / Yoshiki Nakajima / Keisuke Kawakami / Takehiro Suzuki / Naoshi Dohmae / Seiji Akimoto / Koji Yonekura / Jian-Ren Shen /
Abstract: Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property ...Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.
History
DepositionDec 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 4 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Part number: 1 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Part number: 2 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Part number: 3 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Part number: 4 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 2 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 3 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Photosystem I reaction center subunit XI
2: Photosystem II CP43 protein PsbC homolog
3: Photosystem II CP43 protein PsbC homolog
4: Iron stress-induced chlorophyll-binding protein
5: Iron stress-induced chlorophyll-binding protein
6: Iron stress-induced chlorophyll-binding protein
7: Iron stress-induced chlorophyll-binding protein
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2 1
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)740,103292
Polymers518,40118
Non-polymers221,702274
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Photosystem I ... , 12 types, 12 molecules 1ABCDEFIJKMX

#1: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 51717.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: A0A1Z4KKX8
#5: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 83289.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58576, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 1 / PsaB 1


Mass: 83399.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58565, photosystem I
#7: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8825.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P0A410, photosystem I
#8: Protein Photosystem I reaction center subunit II


Mass: 15176.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58573
#9: Protein Photosystem I reaction center subunit IV


Mass: 7897.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58575
#10: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 17850.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58564
#11: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 5066.925 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58560
#12: Protein/peptide Photosystem I reaction center subunit IX


Mass: 5499.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58568
#13: Protein Photosystem I reaction center subunit PsaK


Mass: 8560.202 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: A0ABR6S7R8
#14: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3538.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: Q8YNB0
#15: Protein/peptide Photosystem I 4.8 kDa protein


Mass: 4872.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58566

-
Photosystem II CP43 protein PsbC ... , 2 types, 2 molecules 23

#2: Protein Photosystem II CP43 protein PsbC homolog


Mass: 37540.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: A0A1Z4KKX9
#3: Protein Photosystem II CP43 protein PsbC homolog


Mass: 35161.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: A0A1Z4KKX7

-
Protein , 1 types, 4 molecules 4567

#4: Protein
Iron stress-induced chlorophyll-binding protein / CP43'


Mass: 37501.277 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: Q8YQ35

-
Sugars , 2 types, 6 molecules

#20: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#23: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 9 types, 268 molecules

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


Mass: 893.489 Da / Num. of mol.: 204 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2
#18: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C40H56
#19: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10
#21: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#22: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical ChemComp-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H54O
#26: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Photosystem I monomer with 7 IsiA subunits / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96842 / Symmetry type: POINT
RefinementCross valid method: NONE

+
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