[English] 日本語
Yorodumi
- PDB-7blz: Red alga C.merolae Photosystem I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7blz
TitleRed alga C.merolae Photosystem I
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 3
  • (Photosystem I iron-sulfur ...) x 2
  • (Photosystem I reaction center subunit ...) x 4
  • Lhcr3
  • PSI-F
  • PSI-K
  • PsaO
  • Similar to chlorophyll a/b-binding protein, CP24
  • Similar to light harvesting protein
KeywordsPHOTOSYNTHESIS / Red alga C.merolae Photosystem I
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane ...thylakoid membrane / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaO / PsaO transmembrane domain / 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 reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI ...Photosystem I PsaO / PsaO transmembrane domain / 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 reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / 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 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit IV / PsaE / : / 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 / 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
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / ERGOSTEROL / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-PGT ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / ERGOSTEROL / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-PGT / PHYLLOQUINONE / PHOSPHATIDYLETHANOLAMINE / (3R)-beta,beta-caroten-3-ol / IRON/SULFUR CLUSTER / Phosphatidylinositol / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Similar to chlorophyll a/b-binding protein, CP24 / Photosystem I subunit O / Similar to light harvesting protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center subunit VII / Photosystem I iron-sulfur center / PSI-K / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNelson, N. / Klaiman, D. / Hippler, M.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
CitationJournal: To Be Published
Title: Red alga C.merolae Photosystem I
Authors: Nelson, N. / Klaiman, D. / Hippler, M.
History
DepositionJan 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12228
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Similar to light harvesting protein
2: Similar to chlorophyll a/b-binding protein, CP24
3: Lhcr3
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I p700 chlorophyll A apoprotein A2
E: Photosystem I iron-sulfur center subunit VII
F: PSI-F
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: PSI-K
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
O: PsaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,161221
Polymers313,23315
Non-polymers160,929206
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 6 types, 6 molecules 123FKO

#1: Protein Similar to light harvesting protein


Mass: 19551.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1VKK5
#2: Protein Similar to chlorophyll a/b-binding protein, CP24


Mass: 19796.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1UU36
#3: Protein Lhcr3


Mass: 19041.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D
#9: Protein PSI-F


Mass: 17997.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: A0A5P9RU83
#12: Protein PSI-K / Photosystem I subunit X


Mass: 5608.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G51
#15: Protein PsaO


Mass: 10485.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1VFJ4

-
Photosystem I P700 chlorophyll a apoprotein ... , 3 types, 3 molecules ABD

#4: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 82215.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY7, photosystem I
#5: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 81976.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY6, photosystem I
#7: Protein Photosystem I p700 chlorophyll A apoprotein A2


Mass: 15567.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY0

-
Photosystem I iron-sulfur ... , 2 types, 2 molecules CE

#6: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8691.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G47, photosystem I
#8: Protein Photosystem I iron-sulfur center subunit VII


Mass: 6985.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FZ1

-
Photosystem I reaction center subunit ... , 4 types, 4 molecules IJLM

#10: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3276.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FQ6
#11: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4410.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: A0A5P9RTH6
#13: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 14690.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FP8
#14: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 2937.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G73

-
Sugars , 2 types, 5 molecules

#24: 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
#31: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 16 types, 450 molecules

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


Mass: 893.489 Da / Num. of mol.: 132 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#17: Chemical
ChemComp-C7Z / (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C40H56O2
#18: Chemical
ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56O
#19: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#20: Chemical ChemComp-ERG / ERGOSTEROL


Mass: 396.648 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H44O
#21: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#22: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#23: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H76O5
#25: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#26: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#27: 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
#28: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#29: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H77O8P
#30: Chemical ChemComp-T7X / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H83O13P
#32: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#33: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Photosystem I / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL
Source (natural)Organism: Cyanidioschyzon merolae strain 10D (eukaryote)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 7220

-
Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7PHENIX1.19-4092-000model fitting
9PHENIX1.19-4092-000model refinement
10RELION3.1.0initial Euler assignment
11RELION3.1.0final Euler assignment
12RELION3.1.0classification
13RELION3.1.03D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1198564
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128943 / Num. of class averages: 8 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 35.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00635406
ELECTRON MICROSCOPYf_angle_d2.03549831
ELECTRON MICROSCOPYf_dihedral_angle_d27.21714753
ELECTRON MICROSCOPYf_chiral_restr0.1174361
ELECTRON MICROSCOPYf_plane_restr0.0098532

+
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