8QQJ | pdb_00008qqj

CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus

PDB DOI: https://doi.org/10.2210/pdb8QQJ/pdb
EM Map EMD-18593: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Thermus thermophilus HB27
Mutation(s): No

Deposited: 2023-10-04 Released: 2024-10-16
Deposition Author(s): Gold, V.A.M., Neuhaus, A., Gaines, M., Isupov, M., McLaren, M.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.63 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

Structural insights into the Thermus thermophilus type IV pilus machinery assembling two distinct pili.

Neuhaus, A., McLaren, M., Isupov, M.N., Gaines, M., Buzzard, E., Sikora, M., Hanus, C., Daum, B., Averhoff, B., Gold, V.A.M.

(2026) Commun Biol 9

PubMed: 41917195 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-026-09762-0
Primary Citation Related Structures:
8QQD, 8QQJ

PubMed Abstract:
Type IV pili are long, filamentous structures that extend from bacterial cell surfaces, enabling cells to respond to changing environments and facilitating genome plasticity. Thermus thermophilus HB27 produces two different type IV pili, each exhibiting distinct structural and functional properties. Here, we combine cryo-electron tomography, mutagenesis, and AlphaFold predictions to generate hypothetical in situ models of the T. thermophilus type IV pilus assembly machinery. Using single-particle cryo-electron microscopy, we determine structures of both filament types, enabling modelling of their surface glycans. Molecular dynamics simulations further reveal the flexibility of these glycans on extrusion. Integration of the filament structures with our hypothetical model of the assembly machinery offers a framework for further dissecting T4P architecture and biogenesis.

Organizational Affiliation

Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK.

Macromolecule Content

Total Structure Weight: 383.41 kDa
Atom Count: 26,815
Modeled Residue Count: 3,441
Deposited Residue Count: 3,441
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type IV narrow pilus major component PilA5	A [auth J] AA [auth a] B [auth A] BA [auth b] C [auth B] A [auth J], AA [auth a], B [auth A], BA [auth b], C [auth B], CA [auth c], D [auth C], DA [auth d], E [auth D], EA [auth e], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	111	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72GL2 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72GL2 Go to UniProtKB: Q72GL2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72GL2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth J] Focus chain AA [auth a] Focus chain B [auth A] Focus chain BA [auth b] Focus chain C [auth B] Focus chain CA [auth c] Focus chain D [auth C] Focus chain DA [auth d] Focus chain E [auth D] Focus chain EA [auth e] Focus chain F [auth E] Focus chain G [auth F] Focus chain H [auth G] Focus chain I [auth H] Focus chain J [auth I] Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
7-Acetamido-5-acetimidoyl-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic aci-(1-4)-alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	AB [auth 0], BB [auth 1], CB [auth 2], DB [auth 3], EB [auth 4], AB [auth 0], BB [auth 1], CB [auth 2], DB [auth 3], EB [auth 4], FA [auth f], FB [auth 5], GA [auth g], GB [auth 6], HA [auth h], HB [auth 7], IA [auth i], IB [auth 8], JA [auth j], JB [auth 9], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], YA [auth y], ZA [auth z]	4	N/A	O-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain BB [auth 1] Focus chain CB [auth 2] Focus chain DB [auth 3] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain FB [auth 5] Focus chain GA [auth g] Focus chain GB [auth 6] Focus chain HA [auth h] Focus chain HB [auth 7] Focus chain IA [auth i] Focus chain IB [auth 8] Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth s] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain VA [auth v] Focus chain WA [auth w] Focus chain XA [auth x] Focus chain YA [auth y] Focus chain ZA [auth z] Interactions & Density Focus chain AB [auth 0] Focus chain BB [auth 1] Focus chain CB [auth 2] Focus chain DB [auth 3] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain FB [auth 5] Focus chain GA [auth g] Focus chain GB [auth 6] Focus chain HA [auth h] Focus chain HB [auth 7] Focus chain IA [auth i] Focus chain IB [auth 8] Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth s] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain VA [auth v] Focus chain WA [auth w] Focus chain XA [auth x] Focus chain YA [auth y] Focus chain ZA [auth z]

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain ZB [auth P] SDF format, chain YB [auth O] SDF format, chain XB [auth N] SDF format, chain WB [auth M] SDF format, chain VB [auth L] SDF format, chain UB [auth K] SDF format, chain TB [auth I] SDF format, chain SB [auth H] SDF format, chain RB [auth G] SDF format, chain QB [auth F] SDF format, chain PB [auth E] SDF format, chain OC [auth e] SDF format, chain OB [auth D] SDF format, chain NC [auth d] SDF format, chain NB [auth C] SDF format, chain MC [auth c] SDF format, chain MB [auth B] SDF format, chain LC [auth b] SDF format, chain LB [auth A] SDF format, chain KC [auth a] SDF format, chain KB [auth J] SDF format, chain JC [auth Z] SDF format, chain IC [auth Y] SDF format, chain HC [auth X] SDF format, chain GC [auth W] SDF format, chain FC [auth V] SDF format, chain EC [auth U] SDF format, chain DC [auth T] SDF format, chain CC [auth S] SDF format, chain BC [auth R] SDF format, chain AC [auth Q] MOL2 format, chain ZB [auth P] MOL2 format, chain YB [auth O] MOL2 format, chain XB [auth N] MOL2 format, chain WB [auth M] MOL2 format, chain VB [auth L] MOL2 format, chain UB [auth K] MOL2 format, chain TB [auth I] MOL2 format, chain SB [auth H] MOL2 format, chain RB [auth G] MOL2 format, chain QB [auth F] MOL2 format, chain PB [auth E] MOL2 format, chain OC [auth e] MOL2 format, chain OB [auth D] MOL2 format, chain NC [auth d] MOL2 format, chain NB [auth C] MOL2 format, chain MC [auth c] MOL2 format, chain MB [auth B] MOL2 format, chain LC [auth b] MOL2 format, chain LB [auth A] MOL2 format, chain KC [auth a] MOL2 format, chain KB [auth J] MOL2 format, chain JC [auth Z] MOL2 format, chain IC [auth Y] MOL2 format, chain HC [auth X] MOL2 format, chain GC [auth W] MOL2 format, chain FC [auth V] MOL2 format, chain EC [auth U] MOL2 format, chain DC [auth T] MOL2 format, chain CC [auth S] MOL2 format, chain BC [auth R] MOL2 format, chain AC [auth Q] mmCIF format, chain ZB [auth P] mmCIF format, chain YB [auth O] mmCIF format, chain XB [auth N] mmCIF format, chain WB [auth M] mmCIF format, chain VB [auth L] mmCIF format, chain UB [auth K] mmCIF format, chain TB [auth I] mmCIF format, chain SB [auth H] mmCIF format, chain RB [auth G] mmCIF format, chain QB [auth F] mmCIF format, chain PB [auth E] mmCIF format, chain OC [auth e] mmCIF format, chain OB [auth D] mmCIF format, chain NC [auth d] mmCIF format, chain NB [auth C] mmCIF format, chain MC [auth c] mmCIF format, chain MB [auth B] mmCIF format, chain LC [auth b] mmCIF format, chain LB [auth A] mmCIF format, chain KC [auth a] mmCIF format, chain KB [auth J] mmCIF format, chain JC [auth Z] mmCIF format, chain IC [auth Y] mmCIF format, chain HC [auth X] mmCIF format, chain GC [auth W] mmCIF format, chain FC [auth V] mmCIF format, chain EC [auth U] mmCIF format, chain DC [auth T] mmCIF format, chain CC [auth S] mmCIF format, chain BC [auth R] mmCIF format, chain AC [auth Q]	AC [auth Q] BC [auth R] CC [auth S] DC [auth T] EC [auth U] AC [auth Q], BC [auth R], CC [auth S], DC [auth T], EC [auth U], FC [auth V], GC [auth W], HC [auth X], IC [auth Y], JC [auth Z], KB [auth J], KC [auth a], LB [auth A], LC [auth b], MB [auth B], MC [auth c], NB [auth C], NC [auth d], OB [auth D], OC [auth e], PB [auth E], QB [auth F], RB [auth G], SB [auth H], TB [auth I], UB [auth K], VB [auth L], WB [auth M], XB [auth N], YB [auth O], ZB [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AC [auth Q] Focus chain BC [auth R] Focus chain CC [auth S] Focus chain DC [auth T] Focus chain EC [auth U] Focus chain FC [auth V] Focus chain GC [auth W] Focus chain HC [auth X] Focus chain IC [auth Y] Focus chain JC [auth Z] Focus chain KB [auth J] Focus chain KC [auth a] Focus chain LB [auth A] Focus chain LC [auth b] Focus chain MB [auth B] Focus chain MC [auth c] Focus chain NB [auth C] Focus chain NC [auth d] Focus chain OB [auth D] Focus chain OC [auth e] Focus chain PB [auth E] Focus chain QB [auth F] Focus chain RB [auth G] Focus chain SB [auth H] Focus chain TB [auth I] Focus chain UB [auth K] Focus chain VB [auth L] Focus chain WB [auth M] Focus chain XB [auth N] Focus chain YB [auth O] Focus chain ZB [auth P] Interactions & Density Focus chain AC [auth Q] Focus chain BC [auth R] Focus chain CC [auth S] Focus chain DC [auth T] Focus chain EC [auth U] Focus chain FC [auth V] Focus chain GC [auth W] Focus chain HC [auth X] Focus chain IC [auth Y] Focus chain JC [auth Z] Focus chain KB [auth J] Focus chain KC [auth a] Focus chain LB [auth A] Focus chain LC [auth b] Focus chain MB [auth B] Focus chain MC [auth c] Focus chain NB [auth C] Focus chain NC [auth d] Focus chain OB [auth D] Focus chain OC [auth e] Focus chain PB [auth E] Focus chain QB [auth F] Focus chain RB [auth G] Focus chain SB [auth H] Focus chain TB [auth I] Focus chain UB [auth K] Focus chain VB [auth L] Focus chain WB [auth M] Focus chain XB [auth N] Focus chain YB [auth O] Focus chain ZB [auth P]