[English] 日本語
Yorodumi
- PDB-8rh5: Oxiplasma meridianum archaellum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rh5
TitleOxiplasma meridianum archaellum
ComponentsOxiplasma meridianum archaellum
KeywordsPROTEIN FIBRIL / cell surface appendage / N-glycosylation
Function / homologybeta-D-galactopyranose
Function and homology information
Biological speciesOxyplasma meridianum (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsIsupov, M.N. / Gaines, M. / Daum, B. / McLaren, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: ISME J / Year: 2025
Title: Unusual cell surfaces, pili, and archaella of Thermoplasmatales archaea.
Authors: Matthew C Gaines / Michail N Isupov / Mathew McLaren / Risat Ul Haque / Alejandra Recalde / Rafael Bargiela / Vicki A M Gold / Sonja-Verena Albers / Peter N Golyshin / Olga V Golyshina / Bertram Daum /
Abstract: Archaea of the order Thermoplasmatales push the boundaries of our current knowledge of prokaryotic life. They show distinct cellular plasticity, heterogenous cell morphologies, and lack a ...Archaea of the order Thermoplasmatales push the boundaries of our current knowledge of prokaryotic life. They show distinct cellular plasticity, heterogenous cell morphologies, and lack a paracrystalline S-layer. As the S-layer has previously been implicated in acting as a stator scaffold for filaments driving cellular propulsion, particularly archaella, we asked whether the absence of an S-layer precludes the formation of functional archaella or pili in Thermoplasmatales. Using cryoEM, we investigated the two Thermoplasmatales species Cuniculiplasma divulgatum and Oxyplasma meridianum. We found that these species indeed generate pili and archaella and that the latter likely function in cellular propulsion. Whereas C. divulgatum produces pili with terminal hooks using a unique assembly machinery, O. meridianum generates unusually wide, "barbed" archaella with a high degree of glycosylation. Our results show that for the generation of functional archaella and pili, a canonical S-layer is not necessary.
History
DepositionDec 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Oct 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Z: Oxiplasma meridianum archaellum
V: Oxiplasma meridianum archaellum
A: Oxiplasma meridianum archaellum
B: Oxiplasma meridianum archaellum
C: Oxiplasma meridianum archaellum
D: Oxiplasma meridianum archaellum
E: Oxiplasma meridianum archaellum
F: Oxiplasma meridianum archaellum
G: Oxiplasma meridianum archaellum
H: Oxiplasma meridianum archaellum
I: Oxiplasma meridianum archaellum
J: Oxiplasma meridianum archaellum
K: Oxiplasma meridianum archaellum
L: Oxiplasma meridianum archaellum
M: Oxiplasma meridianum archaellum
N: Oxiplasma meridianum archaellum
O: Oxiplasma meridianum archaellum
P: Oxiplasma meridianum archaellum
Q: Oxiplasma meridianum archaellum
R: Oxiplasma meridianum archaellum
S: Oxiplasma meridianum archaellum
T: Oxiplasma meridianum archaellum
U: Oxiplasma meridianum archaellum
W: Oxiplasma meridianum archaellum
X: Oxiplasma meridianum archaellum
Y: Oxiplasma meridianum archaellum
a: Oxiplasma meridianum archaellum
b: Oxiplasma meridianum archaellum
c: Oxiplasma meridianum archaellum
d: Oxiplasma meridianum archaellum
e: Oxiplasma meridianum archaellum
f: Oxiplasma meridianum archaellum
g: Oxiplasma meridianum archaellum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)969,892289
Polymers788,29333
Non-polymers181,599256
Water00
1


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

-
Components

#1: Protein ...
Oxiplasma meridianum archaellum


Mass: 23887.668 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Source: (natural) Oxyplasma meridianum (archaea)
#2: Polysaccharide...
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[L-glycero-alpha-D-galacto-heptopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[L-glycero-alpha-D-galacto-heptopyranose-(1-2)]6-deoxy-6-sulfo-beta-D-galacto-heptopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 1084.950 Da / Num. of mol.: 32
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[]{[(4+1)][b-D-Galp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Galp6SH]{[(2+1)][a-D-Galp]{}[(3+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide...
L-glycero-alpha-D-galacto-heptopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]6-deoxy-6-sulfo-beta-D- ...L-glycero-alpha-D-galacto-heptopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]6-deoxy-6-sulfo-beta-D-galacto-heptopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 922.809 Da / Num. of mol.: 96 / Source method: obtained synthetically
DescriptorTypeProgram
[]{[(4+1)][b-D-Galp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Galp6SH]{[(2+1)][a-D-Galp]{}[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide...
alpha-D-mannopyranose-(1-3)-6-deoxy-6-sulfo-beta-D-galacto-heptopyranose-(1-4)-beta-D-glucopyranose- ...alpha-D-mannopyranose-(1-3)-6-deoxy-6-sulfo-beta-D-galacto-heptopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 730.642 Da / Num. of mol.: 64 / Source method: obtained synthetically
DescriptorTypeProgram
[]{[(4+1)][b-D-Galp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Galp6SH]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar...
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: Oxiplasma meridianum archaellum / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Oxyplasma meridianum (archaea)
Buffer solutionpH: 1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Oxiplasma meridianum archaellum
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 51.45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM softwareName: REFMAC / Version: 5.8.0267 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 107.922 ° / Axial rise/subunit: 5.641 Å / Axial symmetry: C1
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1374113 / Symmetry type: HELICAL
RefinementResolution: 2.54→2.54 Å / Cor.coef. Fo:Fc: 0.871 / SU B: 5.93 / SU ML: 0.121 / ESU R: 0.156
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.46595 --
obs0.46595 4090443 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 100.992 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20.01 Å20.02 Å2
2---1.25 Å20.02 Å2
3---2.52 Å2
Refinement stepCycle: 1 / Total: 67118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.01368869
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.161.90696183
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.30757557
ELECTRON MICROSCOPYr_dihedral_angle_2_deg36.82825.7142079
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.611158844
ELECTRON MICROSCOPYr_dihedral_angle_4_deg9.3931599
ELECTRON MICROSCOPYr_chiral_restr0.0590.213439
ELECTRON MICROSCOPYr_gen_planes_refined0.0020.0242563
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.0639.12530327
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it1.9813.68437851
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it1.53810.90638542
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined5.20986770
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.432 302888 -
obs--100 %

+
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