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 7PNB | pdb_00007pnb

Sulfolobus acidocaldarius 0406 filament.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 7PNB

This is version 1.2 of the entry. See complete history. 

Literature

Electron cryo-microscopy reveals the structure of the archaeal thread filament.

Gaines, M.C., Isupov, M.N., Sivabalasarma, S., Haque, R.U., McLaren, M., Mollat, C.L., Tripp, P., Neuhaus, A., Gold, V.A.M., Albers, S.V., Daum, B.

(2022) Nat Commun 13: 7411-7411

  • DOI: https://doi.org/10.1038/s41467-022-34652-4
  • Primary Citation Related Structures: 
    7PNB

  • PubMed Abstract: 

    Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism.


  • Organizational Affiliation: 
    • Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK.

Macromolecule Content 

  • Total Structure Weight: 248.87 kDa 
  • Atom Count: 15,714 
  • Modeled Residue Count: 1,647 
  • Deposited Residue Count: 1,854 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sulfolobus acidocaldarius 0406 filament.
A, B, C, D, E
A, B, C, D, E, F, G, H, I
206Sulfolobus acidocaldariusMutation(s): 0 
Gene Names: ATZ20_07285
UniProt
Find proteins for Q4JBK8 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore Q4JBK8 
Go to UniProtKB:  Q4JBK8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4JBK8
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-glucopyranose-(1-4)-6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
AA [auth a],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
DA [auth d],
FA [auth f],
GA [auth g],
HA [auth h],
IA [auth i],
J,
KA [auth k],
L,
LA [auth l],
M,
MA [auth m],
N,
NA [auth n],
O,
PA [auth p],
Q,
QA [auth q],
R,
RA [auth r],
S,
SA [auth s],
T,
UA [auth u],
V,
VA [auth v],
W,
WA [auth w],
X,
XA [auth x],
Y,
ZA [auth z]
6N/AN-Glycosylation
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
EA [auth e],
JA [auth j],
K,
OA [auth o],
P,
EA [auth e],
JA [auth j],
K,
OA [auth o],
P,
TA [auth t],
U,
YA [auth y],
Z
4N/AN-Glycosylation

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
MODEL REFINEMENTCCP4 package
RECONSTRUCTIONcryoSPARC3.2.0

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: 2022-09-14
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary