8RH5 | pdb_00008rh5

Oxiplasma meridianum archaellum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Unusual cell surfaces, pili, and archaella of Thermoplasmatales archaea.

Gaines, M.C.Isupov, M.N.McLaren, M.Haque, R.U.Recalde, A.Bargiela, R.Gold, V.A.M.Albers, S.V.Golyshin, P.N.Golyshina, O.V.Daum, B.

(2025) ISME J 19

  • DOI: https://doi.org/10.1093/ismejo/wraf176
  • Primary Citation of Related Structures:  
    8REY, 8RH5

  • PubMed 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 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 wide, "barbed" archaella with an unusually high degree of glycosylation. Our results show that, for the generation of functional archaella and pili, a canonical S-layer is not necessary.


  • Organizational Affiliation
    • Living Systems Institute, University of Exeter, EX4 4QD, Exeter, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxiplasma meridianum archaellum230Oxyplasma meridianumMutation(s): 0 
UniProt
Find proteins for A0AAX4NFB8 (Oxyplasma meridianum)
Explore A0AAX4NFB8 
Go to UniProtKB:  A0AAX4NFB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAX4NFB8
Glycosylation
Glycosylation Sites: 8
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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
BD [auth 3A],
BG [auth WC],
DC [auth bA],
DF [auth 4B],
FB [auth 9],
BD [auth 3A],
BG [auth WC],
DC [auth bA],
DF [auth 4B],
FB [auth 9],
FE [auth cB],
FH [auth 5C],
HA [auth h],
HD [auth AB],
HG [auth dC],
JC [auth iA],
JF [auth BC],
LB [auth GA],
LE [auth jB],
LH [auth CD],
NA [auth o],
ND [auth HB],
NG [auth kC],
PC [auth pA],
PF [auth IC],
RB [auth NA],
RE [auth qB],
TA [auth v],
TD [auth OB],
TG [auth rC],
VC [auth wA],
VF [auth PC],
XB [auth UA],
XE [auth xB],
ZA [auth 2],
ZD [auth VB],
ZG [auth yC]
6N/AN-Glycosylation
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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
AB [auth 4],
AE [auth XB],
AH [auth 0C],
BB [auth 5],
BC [auth ZA],
AB [auth 4],
AE [auth XB],
AH [auth 0C],
BB [auth 5],
BC [auth ZA],
BE [auth YB],
BF [auth 2B],
BH [auth 1C],
CD [auth 5A],
CG [auth YC],
DB [auth 7],
DD [auth 6A],
DE [auth aB],
DG [auth ZC],
DH [auth 3C],
EC [auth dA],
EF [auth 6B],
FC [auth eA],
FD [auth 8A],
FF [auth 7B],
FG [auth bC],
GB [auth BA],
GE [auth eB],
GH [auth 7C],
HB [auth CA],
HC [auth gA],
HE [auth fB],
HF [auth 9B],
HH [auth 8C],
IA [auth j],
ID [auth CB],
IG [auth fC],
JA [auth k],
JB [auth EA],
JD [auth DB],
JE [auth hB],
JG [auth gC],
JH [auth AD],
KC [auth kA],
KF [auth DC],
LA [auth m],
LC [auth lA],
LD [auth FB],
LF [auth EC],
LG [auth iC],
MB [auth IA],
ME [auth lB],
MH [auth ED],
NB [auth JA],
NC [auth nA],
NE [auth mB],
NF [auth GC],
NH [auth FD],
OA [auth q],
OD [auth JB],
OG [auth mC],
PA [auth r],
PB [auth LA],
PD [auth KB],
PE [auth oB],
PG [auth nC],
PH [auth HD],
QC [auth rA],
QF [auth KC],
RA [auth t],
RC [auth sA],
RD [auth MB],
RF [auth LC],
RG [auth pC],
SB [auth PA],
SE [auth sB],
TB [auth QA],
TC [auth uA],
TE [auth tB],
TF [auth NC],
UA [auth x],
UD [auth QB],
UG [auth tC],
VA [auth y],
VB [auth SA],
VD [auth RB],
VE [auth vB],
VG [auth uC],
WC [auth yA],
WF [auth RC],
XA [auth 0],
XC [auth zA],
XD [auth TB],
XF [auth SC],
XG [auth wC],
YB [auth WA],
YE [auth zB],
ZB [auth XA],
ZC [auth 1A],
ZE [auth 0B],
ZF [auth UC]
5N/AN-Glycosylation
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-6-deoxy-6-sulfo-beta-D-galacto-heptopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose
AC [auth YA],
AD [auth 2A],
AF [auth 1B],
AG [auth VC],
CB [auth 6],
AC [auth YA],
AD [auth 2A],
AF [auth 1B],
AG [auth VC],
CB [auth 6],
CC [auth aA],
CE [auth ZB],
CF [auth 3B],
CH [auth 2C],
EB [auth 8],
ED [auth 7A],
EE [auth bB],
EG [auth aC],
EH [auth 4C],
GC [auth fA],
GD [auth 9A],
GF [auth 8B],
GG [auth cC],
IB [auth DA],
IC [auth hA],
IE [auth gB],
IF [auth AC],
IH [auth 9C],
KA [auth l],
KB [auth FA],
KD [auth EB],
KE [auth iB],
KG [auth hC],
KH [auth BD],
MA [auth n],
MC [auth mA],
MD [auth GB],
MF [auth FC],
MG [auth jC],
OB [auth KA],
OC [auth oA],
OE [auth nB],
OF [auth HC],
OH [auth GD],
QA [auth s],
QB [auth MA],
QD [auth LB],
QE [auth pB],
QG [auth oC],
QH [auth ID],
SA [auth u],
SC [auth tA],
SD [auth NB],
SF [auth MC],
SG [auth qC],
UB [auth RA],
UC [auth vA],
UE [auth uB],
UF [auth OC],
WA [auth z],
WB [auth TA],
WD [auth SB],
WE [auth wB],
WG [auth vC],
YA [auth 1],
YC [auth 0A],
YD [auth UB],
YF [auth TC],
YG [auth xC]
4N/AN-Glycosylation
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download Ideal Coordinates CCD File 
AI [auth D]
AJ [auth Q]
AK [auth f]
BI [auth E]
BJ [auth R]
AI [auth D],
AJ [auth Q],
AK [auth f],
BI [auth E],
BJ [auth R],
BK [auth g],
CI [auth E],
CJ [auth R],
CK [auth g],
DI [auth F],
DJ [auth S],
EI [auth F],
EJ [auth S],
FI [auth G],
FJ [auth T],
GI [auth G],
GJ [auth T],
HI [auth H],
HJ [auth U],
II [auth H],
IJ [auth U],
JI [auth I],
JJ [auth W],
KI [auth I],
KJ [auth W],
LI [auth J],
LJ [auth X],
MI [auth J],
MJ [auth X],
NI [auth K],
NJ [auth Y],
OI [auth K],
OJ [auth Y],
PI [auth L],
PJ [auth a],
QI [auth L],
QJ [auth a],
RH [auth V],
RI [auth M],
RJ [auth b],
SH [auth V],
SI [auth M],
SJ [auth b],
TH [auth A],
TI [auth N],
TJ [auth c],
UH [auth A],
UI [auth N],
UJ [auth c],
VH [auth B],
VI [auth O],
VJ [auth d],
WH [auth B],
WI [auth O],
WJ [auth d],
XH [auth C],
XI [auth P],
XJ [auth e],
YH [auth C],
YI [auth P],
YJ [auth e],
ZH [auth D],
ZI [auth Q],
ZJ [auth f]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0267

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union109784

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Data collection, Database references
  • Version 1.2: 2025-10-01
    Changes: Data collection, Database references