8QQD | pdb_00008qqd

CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus

PDB DOI: https://doi.org/10.2210/pdb8QQD/pdb
EM Map EMD-18588: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Thermus thermophilus
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: 2.40 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 2.1 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: 673.23 kDa
Atom Count: 47,025
Modeled Residue Count: 5,625
Deposited Residue Count: 5,625
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PilA	A AA [auth a] B BA [auth b] C A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, U, V, W, X, Y, Z	125	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q72JC0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72JC0 Go to UniProtKB: Q72JC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72JC0
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain AA [auth a] Focus chain B Focus chain BA [auth b] Focus chain C Focus chain CA [auth c] Focus chain D Focus chain DA [auth d] Focus chain E Focus chain EA [auth e] Focus chain F Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth 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
alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	BB [auth 1], BC [auth RA], BD [auth rA], BE [auth HB], DB [auth 3], BB [auth 1], BC [auth RA], BD [auth rA], BE [auth HB], DB [auth 3], DC [auth TA], DD [auth tA], DE [auth JB], FB [auth 5], FC [auth VA], FD [auth vA], HB [auth 7], HC [auth XA], HD [auth xA], JB [auth 9], JC [auth ZA], JD [auth zA], LB [auth BA], LC [auth bA], LD [auth 1A], NB [auth DA], NC [auth dA], ND [auth 3A], PB [auth FA], PC [auth fA], PD [auth 5A], RB [auth HA], RC [auth hA], RD [auth 7A], TA [auth t], TB [auth JA], TC [auth jA], TD [auth 9A], VA [auth v], VB [auth LA], VC [auth lA], VD [auth BB], XA [auth x], XB [auth NA], XC [auth nA], XD [auth DB], ZA [auth z], ZB [auth PA], ZC [auth pA], ZD [auth FB]	3		O-Glycosylation	Interactions Focus chain BB [auth 1] Focus chain BC [auth RA] Focus chain BD [auth rA] Focus chain BE [auth HB] Focus chain DB [auth 3] Focus chain DC [auth TA] Focus chain DD [auth tA] Focus chain DE [auth JB] Focus chain FB [auth 5] Focus chain FC [auth VA] Focus chain FD [auth vA] Focus chain HB [auth 7] Focus chain HC [auth XA] Focus chain HD [auth xA] Focus chain JB [auth 9] Focus chain JC [auth ZA] Focus chain JD [auth zA] Focus chain LB [auth BA] Focus chain LC [auth bA] Focus chain LD [auth 1A] Focus chain NB [auth DA] Focus chain NC [auth dA] Focus chain ND [auth 3A] Focus chain PB [auth FA] Focus chain PC [auth fA] Focus chain PD [auth 5A] Focus chain RB [auth HA] Focus chain RC [auth hA] Focus chain RD [auth 7A] Focus chain TA [auth t] Focus chain TB [auth JA] Focus chain TC [auth jA] Focus chain TD [auth 9A] Focus chain VA [auth v] Focus chain VB [auth LA] Focus chain VC [auth lA] Focus chain VD [auth BB] Focus chain XA [auth x] Focus chain XB [auth NA] Focus chain XC [auth nA] Focus chain XD [auth DB] Focus chain ZA [auth z] Focus chain ZB [auth PA] Focus chain ZC [auth pA] Focus chain ZD [auth FB] Interactions & Density Focus chain BB [auth 1] Focus chain BC [auth RA] Focus chain BD [auth rA] Focus chain BE [auth HB] Focus chain DB [auth 3] Focus chain DC [auth TA] Focus chain DD [auth tA] Focus chain DE [auth JB] Focus chain FB [auth 5] Focus chain FC [auth VA] Focus chain FD [auth vA] Focus chain HB [auth 7] Focus chain HC [auth XA] Focus chain HD [auth xA] Focus chain JB [auth 9] Focus chain JC [auth ZA] Focus chain JD [auth zA] Focus chain LB [auth BA] Focus chain LC [auth bA] Focus chain LD [auth 1A] Focus chain NB [auth DA] Focus chain NC [auth dA] Focus chain ND [auth 3A] Focus chain PB [auth FA] Focus chain PC [auth fA] Focus chain PD [auth 5A] Focus chain RB [auth HA] Focus chain RC [auth hA] Focus chain RD [auth 7A] Focus chain TA [auth t] Focus chain TB [auth JA] Focus chain TC [auth jA] Focus chain TD [auth 9A] Focus chain VA [auth v] Focus chain VB [auth LA] Focus chain VC [auth lA] Focus chain VD [auth BB] Focus chain XA [auth x] Focus chain XB [auth NA] Focus chain XC [auth nA] Focus chain XD [auth DB] Focus chain ZA [auth z] Focus chain ZB [auth PA] Focus chain ZC [auth pA] Focus chain ZD [auth FB]

Entity ID: 3
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], AC [auth QA], AD [auth qA], AE [auth GB], CB [auth 2], AB [auth 0], AC [auth QA], AD [auth qA], AE [auth GB], CB [auth 2], CC [auth SA], CD [auth sA], CE [auth IB], EB [auth 4], EC [auth UA], ED [auth uA], EE [auth KB], GB [auth 6], GC [auth WA], GD [auth wA], IB [auth 8], IC [auth YA], ID [auth yA], KB [auth AA], KC [auth aA], KD [auth 0A], MB [auth CA], MC [auth cA], MD [auth 2A], OB [auth EA], OC [auth eA], OD [auth 4A], QB [auth GA], QC [auth gA], QD [auth 6A], SB [auth IA], SC [auth iA], SD [auth 8A], UA [auth u], UB [auth KA], UC [auth kA], UD [auth AB], WA [auth w], WB [auth MA], WC [auth mA], WD [auth CB], YA [auth y], YB [auth OA], YC [auth oA], YD [auth EB]	4	N/A	O-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain AC [auth QA] Focus chain AD [auth qA] Focus chain AE [auth GB] Focus chain CB [auth 2] Focus chain CC [auth SA] Focus chain CD [auth sA] Focus chain CE [auth IB] Focus chain EB [auth 4] Focus chain EC [auth UA] Focus chain ED [auth uA] Focus chain EE [auth KB] Focus chain GB [auth 6] Focus chain GC [auth WA] Focus chain GD [auth wA] Focus chain IB [auth 8] Focus chain IC [auth YA] Focus chain ID [auth yA] Focus chain KB [auth AA] Focus chain KC [auth aA] Focus chain KD [auth 0A] Focus chain MB [auth CA] Focus chain MC [auth cA] Focus chain MD [auth 2A] Focus chain OB [auth EA] Focus chain OC [auth eA] Focus chain OD [auth 4A] Focus chain QB [auth GA] Focus chain QC [auth gA] Focus chain QD [auth 6A] Focus chain SB [auth IA] Focus chain SC [auth iA] Focus chain SD [auth 8A] Focus chain UA [auth u] Focus chain UB [auth KA] Focus chain UC [auth kA] Focus chain UD [auth AB] Focus chain WA [auth w] Focus chain WB [auth MA] Focus chain WC [auth mA] Focus chain WD [auth CB] Focus chain YA [auth y] Focus chain YB [auth OA] Focus chain YC [auth oA] Focus chain YD [auth EB] Interactions & Density Focus chain AB [auth 0] Focus chain AC [auth QA] Focus chain AD [auth qA] Focus chain AE [auth GB] Focus chain CB [auth 2] Focus chain CC [auth SA] Focus chain CD [auth sA] Focus chain CE [auth IB] Focus chain EB [auth 4] Focus chain EC [auth UA] Focus chain ED [auth uA] Focus chain EE [auth KB] Focus chain GB [auth 6] Focus chain GC [auth WA] Focus chain GD [auth wA] Focus chain IB [auth 8] Focus chain IC [auth YA] Focus chain ID [auth yA] Focus chain KB [auth AA] Focus chain KC [auth aA] Focus chain KD [auth 0A] Focus chain MB [auth CA] Focus chain MC [auth cA] Focus chain MD [auth 2A] Focus chain OB [auth EA] Focus chain OC [auth eA] Focus chain OD [auth 4A] Focus chain QB [auth GA] Focus chain QC [auth gA] Focus chain QD [auth 6A] Focus chain SB [auth IA] Focus chain SC [auth iA] Focus chain SD [auth 8A] Focus chain UA [auth u] Focus chain UB [auth KA] Focus chain UC [auth kA] Focus chain UD [auth AB] Focus chain WA [auth w] Focus chain WB [auth MA] Focus chain WC [auth mA] Focus chain WD [auth CB] Focus chain YA [auth y] Focus chain YB [auth OA] Focus chain YC [auth oA] Focus chain YD [auth EB]

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G Query on A2G Download:Ideal Coordinates CCD File SDF format, chain ZE [auth U] SDF format, chain YE [auth T] SDF format, chain XF [auth s] SDF format, chain XE [auth S] SDF format, chain WF [auth r] SDF format, chain WE [auth R] SDF format, chain VF [auth q] SDF format, chain VE [auth Q] SDF format, chain UF [auth p] SDF format, chain UE [auth P] SDF format, chain TF [auth o] SDF format, chain TE [auth O] SDF format, chain SF [auth n] SDF format, chain SE [auth N] SDF format, chain RF [auth m] SDF format, chain RE [auth M] SDF format, chain QF [auth l] SDF format, chain QE [auth L] SDF format, chain PF [auth k] SDF format, chain PE [auth K] SDF format, chain OF [auth j] SDF format, chain OE [auth J] SDF format, chain NF [auth i] SDF format, chain NE [auth I] SDF format, chain MF [auth h] SDF format, chain ME [auth H] SDF format, chain LF [auth g] SDF format, chain LE [auth G] SDF format, chain KF [auth f] SDF format, chain KE [auth F] SDF format, chain JF [auth e] SDF format, chain JE [auth E] SDF format, chain IF [auth d] SDF format, chain IE [auth D] SDF format, chain HF [auth c] SDF format, chain HE [auth C] SDF format, chain GF [auth b] SDF format, chain GE [auth B] SDF format, chain FF [auth a] SDF format, chain FE [auth A] SDF format, chain EF [auth Z] SDF format, chain DF [auth Y] SDF format, chain CF [auth X] SDF format, chain BF [auth W] SDF format, chain AF [auth V] MOL2 format, chain ZE [auth U] MOL2 format, chain YE [auth T] MOL2 format, chain XF [auth s] MOL2 format, chain XE [auth S] MOL2 format, chain WF [auth r] MOL2 format, chain WE [auth R] MOL2 format, chain VF [auth q] MOL2 format, chain VE [auth Q] MOL2 format, chain UF [auth p] MOL2 format, chain UE [auth P] MOL2 format, chain TF [auth o] MOL2 format, chain TE [auth O] MOL2 format, chain SF [auth n] MOL2 format, chain SE [auth N] MOL2 format, chain RF [auth m] MOL2 format, chain RE [auth M] MOL2 format, chain QF [auth l] MOL2 format, chain QE [auth L] MOL2 format, chain PF [auth k] MOL2 format, chain PE [auth K] MOL2 format, chain OF [auth j] MOL2 format, chain OE [auth J] MOL2 format, chain NF [auth i] MOL2 format, chain NE [auth I] MOL2 format, chain MF [auth h] MOL2 format, chain ME [auth H] MOL2 format, chain LF [auth g] MOL2 format, chain LE [auth G] MOL2 format, chain KF [auth f] MOL2 format, chain KE [auth F] MOL2 format, chain JF [auth e] MOL2 format, chain JE [auth E] MOL2 format, chain IF [auth d] MOL2 format, chain IE [auth D] MOL2 format, chain HF [auth c] MOL2 format, chain HE [auth C] MOL2 format, chain GF [auth b] MOL2 format, chain GE [auth B] MOL2 format, chain FF [auth a] MOL2 format, chain FE [auth A] MOL2 format, chain EF [auth Z] MOL2 format, chain DF [auth Y] MOL2 format, chain CF [auth X] MOL2 format, chain BF [auth W] MOL2 format, chain AF [auth V] mmCIF format, chain ZE [auth U] mmCIF format, chain YE [auth T] mmCIF format, chain XF [auth s] mmCIF format, chain XE [auth S] mmCIF format, chain WF [auth r] mmCIF format, chain WE [auth R] mmCIF format, chain VF [auth q] mmCIF format, chain VE [auth Q] mmCIF format, chain UF [auth p] mmCIF format, chain UE [auth P] mmCIF format, chain TF [auth o] mmCIF format, chain TE [auth O] mmCIF format, chain SF [auth n] mmCIF format, chain SE [auth N] mmCIF format, chain RF [auth m] mmCIF format, chain RE [auth M] mmCIF format, chain QF [auth l] mmCIF format, chain QE [auth L] mmCIF format, chain PF [auth k] mmCIF format, chain PE [auth K] mmCIF format, chain OF [auth j] mmCIF format, chain OE [auth J] mmCIF format, chain NF [auth i] mmCIF format, chain NE [auth I] mmCIF format, chain MF [auth h] mmCIF format, chain ME [auth H] mmCIF format, chain LF [auth g] mmCIF format, chain LE [auth G] mmCIF format, chain KF [auth f] mmCIF format, chain KE [auth F] mmCIF format, chain JF [auth e] mmCIF format, chain JE [auth E] mmCIF format, chain IF [auth d] mmCIF format, chain IE [auth D] mmCIF format, chain HF [auth c] mmCIF format, chain HE [auth C] mmCIF format, chain GF [auth b] mmCIF format, chain GE [auth B] mmCIF format, chain FF [auth a] mmCIF format, chain FE [auth A] mmCIF format, chain EF [auth Z] mmCIF format, chain DF [auth Y] mmCIF format, chain CF [auth X] mmCIF format, chain BF [auth W] mmCIF format, chain AF [auth V]	AF [auth V] BF [auth W] CF [auth X] DF [auth Y] EF [auth Z] AF [auth V], BF [auth W], CF [auth X], DF [auth Y], EF [auth Z], FE [auth A], FF [auth a], GE [auth B], GF [auth b], HE [auth C], HF [auth c], IE [auth D], IF [auth d], JE [auth E], JF [auth e], KE [auth F], KF [auth f], LE [auth G], LF [auth g], ME [auth H], MF [auth h], NE [auth I], NF [auth i], OE [auth J], OF [auth j], PE [auth K], PF [auth k], QE [auth L], QF [auth l], RE [auth M], RF [auth m], SE [auth N], SF [auth n], TE [auth O], TF [auth o], UE [auth P], UF [auth p], VE [auth Q], VF [auth q], WE [auth R], WF [auth r], XE [auth S], XF [auth s], YE [auth T], ZE [auth U]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain AF [auth V] Focus chain BF [auth W] Focus chain CF [auth X] Focus chain DF [auth Y] Focus chain EF [auth Z] Focus chain FE [auth A] Focus chain FF [auth a] Focus chain GE [auth B] Focus chain GF [auth b] Focus chain HE [auth C] Focus chain HF [auth c] Focus chain IE [auth D] Focus chain IF [auth d] Focus chain JE [auth E] Focus chain JF [auth e] Focus chain KE [auth F] Focus chain KF [auth f] Focus chain LE [auth G] Focus chain LF [auth g] Focus chain ME [auth H] Focus chain MF [auth h] Focus chain NE [auth I] Focus chain NF [auth i] Focus chain OE [auth J] Focus chain OF [auth j] Focus chain PE [auth K] Focus chain PF [auth k] Focus chain QE [auth L] Focus chain QF [auth l] Focus chain RE [auth M] Focus chain RF [auth m] Focus chain SE [auth N] Focus chain SF [auth n] Focus chain TE [auth O] Focus chain TF [auth o] Focus chain UE [auth P] Focus chain UF [auth p] Focus chain VE [auth Q] Focus chain VF [auth q] Focus chain WE [auth R] Focus chain WF [auth r] Focus chain XE [auth S] Focus chain XF [auth s] Focus chain YE [auth T] Focus chain ZE [auth U] Interactions & Density Focus chain AF [auth V] Focus chain BF [auth W] Focus chain CF [auth X] Focus chain DF [auth Y] Focus chain EF [auth Z] Focus chain FE [auth A] Focus chain FF [auth a] Focus chain GE [auth B] Focus chain GF [auth b] Focus chain HE [auth C] Focus chain HF [auth c] Focus chain IE [auth D] Focus chain IF [auth d] Focus chain JE [auth E] Focus chain JF [auth e] Focus chain KE [auth F] Focus chain KF [auth f] Focus chain LE [auth G] Focus chain LF [auth g] Focus chain ME [auth H] Focus chain MF [auth h] Focus chain NE [auth I] Focus chain NF [auth i] Focus chain OE [auth J] Focus chain OF [auth j] Focus chain PE [auth K] Focus chain PF [auth k] Focus chain QE [auth L] Focus chain QF [auth l] Focus chain RE [auth M] Focus chain RF [auth m] Focus chain SE [auth N] Focus chain SF [auth n] Focus chain TE [auth O] Focus chain TF [auth o] Focus chain UE [auth P] Focus chain UF [auth p] Focus chain VE [auth Q] Focus chain VF [auth q] Focus chain WE [auth R] Focus chain WF [auth r] Focus chain XE [auth S] Focus chain XF [auth s] Focus chain YE [auth T] Focus chain ZE [auth U]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5
RECONSTRUCTION	cryoSPARC	4.4

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R008639/1

Revision History (Full details and data files)

Version 1.0: 2024-10-16
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection
Version 2.0: 2026-04-08
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Structure summary
Version 2.1: 2026-04-22
Changes: Data collection, Database references