[English] 日本語
Yorodumi
- PDB-9fq8: Perkinsus marinus Respiratory complex CIV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fq8
TitlePerkinsus marinus Respiratory complex CIV
Components
  • (Cytochrome c oxidase ...) x 18
  • Amino acid transporter transmembrane domain-containing protein
  • Cg8 protein
  • Cytochrome Coxidase subunit, putative
  • Cytochrome oxidase subunit II copper A binding domain-containing protein
  • GINS subunit domain-containing protein
  • Merozoite surface protein, putative
  • Peptidase M14 carboxypeptidase A domain-containing protein
  • Ubiquitin, putative
KeywordsMEMBRANE PROTEIN / Respiratory complex / CIV
Function / homology
Function and homology information


L-amino acid transmembrane transporter activity / DNA strand elongation involved in mitotic DNA replication / GINS complex / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / metallocarboxypeptidase activity / copper ion binding / proteolysis / extracellular space / zinc ion binding / membrane
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / GINS complex, subunit Psf1 / GINS, helical bundle-like domain superfamily / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) ...Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / GINS complex, subunit Psf1 / GINS, helical bundle-like domain superfamily / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxin / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / : / Chem-LPP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PEROXIDE ION / Ubiquitin, putative ...CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / : / Chem-LPP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PEROXIDE ION / Ubiquitin, putative / Peptidase M14 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Merozoite surface protein, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / GINS subunit domain-containing protein / Amino acid transporter transmembrane domain-containing protein / Cytochrome c oxidase polypeptide II / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesPerkinsus marinus (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWu, F. / Amunts, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2018-StG-805230European Union
CitationJournal: To Be Published
Title: Perkinsus marinus Respiratory complex CIV
Authors: Wu, F. / Amunts, A.
History
DepositionJun 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
4A: Cytochrome c oxidase subunit 6B
4B: Peptidase M14 carboxypeptidase A domain-containing protein
4C: Cytochrome c oxidase subunit 40
4D: Cytochrome c oxidase subunit 34
4E: Merozoite surface protein, putative
4F: Ubiquitin, putative
4G: Cytochrome c oxidase subunit 33
4H: Cytochrome c oxidase subunit 30
4I: Cytochrome c oxidase subunit 6C
4J: Cytochrome c oxidase subunit 24
4K: Cytochrome c oxidase subunit 37
4L: Cytochrome c oxidase subunit 7A
4M: Cytochrome c oxidase subunit 35
4N: Cytochrome c oxidase polypeptide II
4O: GINS subunit domain-containing protein
4P: Cytochrome oxidase subunit II copper A binding domain-containing protein
4Q: Cytochrome c oxidase subunit 1
4R: Cytochrome c oxidase subunit 32
4S: Cytochrome c oxidase subunit 7C
4T: Cytochrome c oxidase 13
4U: Amino acid transporter transmembrane domain-containing protein
4V: Cg8 protein
4W: Cytochrome c oxidase subunit 19
4X: Cytochrome Coxidase subunit, putative
4Y: Cytochrome c oxidase subunit 18
4Z: Cytochrome c oxidase subunit 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)451,67763
Polymers419,46526
Non-polymers32,21337
Water181
1


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

-
Components

-
Cytochrome c oxidase ... , 18 types, 18 molecules 4A4C4D4G4H4I4J4K4L4M4N4Q4R4S4T4W4Y4Z

#1: Protein Cytochrome c oxidase subunit 6B


Mass: 12040.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#3: Protein Cytochrome c oxidase subunit 40 / COX40


Mass: 8828.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L7H1
#4: Protein Cytochrome c oxidase subunit 34 / COX34


Mass: 11072.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#7: Protein Cytochrome c oxidase subunit 33 / COX33


Mass: 12070.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KJE7
#8: Protein Cytochrome c oxidase subunit 30 / COX30


Mass: 15972.974 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#9: Protein Cytochrome c oxidase subunit 6C / COX6C


Mass: 23967.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LPW2
#10: Protein Cytochrome c oxidase subunit 24 / COX24


Mass: 21376.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#11: Protein Cytochrome c oxidase subunit 37 / COX37


Mass: 10228.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KST9
#12: Protein Cytochrome c oxidase subunit 7A / COX7A


Mass: 15282.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KPD1
#13: Protein Cytochrome c oxidase subunit 35 / COX35


Mass: 11003.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#14: Protein Cytochrome c oxidase polypeptide II


Mass: 14594.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LND1
#17: Protein Cytochrome c oxidase subunit 1


Mass: 52063.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: cytochrome-c oxidase
#18: Protein Cytochrome c oxidase subunit 32 / COX32


Mass: 12904.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KSX3
#19: Protein Cytochrome c oxidase subunit 7C / COX7C


Mass: 7711.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LPK3
#20: Protein Cytochrome c oxidase 13 / COX13


Mass: 14001.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#23: Protein Cytochrome c oxidase subunit 19 / COX19


Mass: 16881.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L0W2
#25: Protein Cytochrome c oxidase subunit 18 / COX18


Mass: 12898.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L2M0
#26: Protein Cytochrome c oxidase subunit 31 / COX31


Mass: 22296.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)

-
Protein , 7 types, 7 molecules 4B4E4F4P4U4V4X

#2: Protein Peptidase M14 carboxypeptidase A domain-containing protein


Mass: 10475.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KED7
#5: Protein Merozoite surface protein, putative


Mass: 18761.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5L0U1
#6: Protein Ubiquitin, putative


Mass: 9423.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5KBY9
#16: Protein Cytochrome oxidase subunit II copper A binding domain-containing protein


Mass: 21273.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#21: Protein Amino acid transporter transmembrane domain-containing protein


Mass: 10665.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LG64
#22: Protein Cg8 protein


Mass: 21719.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)
#24: Protein Cytochrome Coxidase subunit, putative


Mass: 26522.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote)

-
Protein/peptide , 1 types, 1 molecules 4O

#15: Protein/peptide GINS subunit domain-containing protein


Mass: 5427.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perkinsus marinus (eukaryote) / References: UniProt: C5LG07

-
Non-polymers , 12 types, 38 molecules

#27: Chemical ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#28: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#29: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#30: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#31: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
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: Perkinsus marinus Respiratory complex CIV / Type: COMPLEX / Entity ID: #1-#26 / Source: NATURAL
Source (natural)Organism: Perkinsus marinus (eukaryote)
Buffer solutionpH: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 296890 / Symmetry type: POINT

+
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