8TUX | pdb_00008tux

Capsid of mature PP7 virion with 3'end region of PP7 genomic RNA

PDB DOI: https://doi.org/10.2210/pdb8TUX/pdb
EM Map EMD-41632: EMDB EMDataResource
NAKB: 8TUX

Classification: VIRAL PROTEIN
Organism(s): Pseudomonas phage PP7
Mutation(s): Yes

Deposited: 2023-08-17 Released: 2024-03-13
Deposition Author(s): Thongchol, J., Zhang, J., Zeng, L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Removal of Pseudomonas type IV pili by a small RNA virus.

Thongchol, J., Yu, Z., Harb, L., Lin, Y., Koch, M., Theodore, M., Narsaria, U., Shaevitz, J., Gitai, Z., Wu, Y., Zhang, J., Zeng, L.

(2024) Science 384: eadl0635-eadl0635

PubMed: 38574145 Search on PubMed
DOI: https://doi.org/10.1126/science.adl0635
Primary Citation of Related Structures:
8TUM, 8TUW, 8TUX

PubMed Abstract:
The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen Pseudomonas aeruginosa . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics.

Organizational Affiliation

Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.

Macromolecule Content

Total Structure Weight: 2,607.4 kDa
Atom Count: 181,475
Modelled Residue Count: 23,597
Deposited Residue Count: 23,597
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Maturation protein A	B [auth m], C [auth M]	448	Pseudomonas phage PP7	Mutation(s): 2
UniProt
Find proteins for Q38061 (Pseudomonas phage PP7) Explore Q38061 Go to UniProtKB: Q38061
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q38061
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	AA [auth x1] AB [auth X1] AC [auth P2] AD [auth p2] AE [auth 2f] AA [auth x1], AB [auth X1], AC [auth P2], AD [auth p2], AE [auth 2f], AF [auth 2F], BA [auth y1], BB [auth Y1], BC [auth Q2], BD [auth q2], BE [auth 2g], BF [auth 2G], CA [auth z1], CB [auth Z1], CC [auth R2], CD [auth r2], CE [auth 2h], CF [auth 2H], D [auth a1], DA [auth A1], DB [auth 01], DC [auth S2], DD [auth s2], DE [auth 2i], DF [auth 2I], E [auth b1], EA [auth B1], EB [auth 11], EC [auth T2], ED [auth t2], EE [auth 2j], EF [auth 2J], F [auth c1], FA [auth C1], FB [auth 21], FC [auth U2], FD [auth u2], FE [auth 2k], FF [auth 2K], G [auth d1], GA [auth D1], GB [auth 31], GC [auth V2], GD [auth v2], GE [auth 2l], GF [auth 2L], H [auth e1], HA [auth E1], HB [auth 41], HC [auth W2], HD [auth w2], HE [auth 2m], HF [auth 2M], I [auth f1], IA [auth F1], IB [auth 51], IC [auth X2], ID [auth x2], IE [auth 2n], IF [auth 2N], J [auth g1], JA [auth G1], JB [auth 61], JC [auth Y2], JD [auth y2], JE [auth 2o], JF [auth 2O], K [auth h1], KA [auth H1], KB [auth 71], KC [auth Z2], KD [auth z2], KE [auth 2p], KF [auth 2P], L [auth i1], LA [auth I1], LB [auth A2], LC [auth a2], LD [auth 02], LE [auth 2q], LF [auth 2Q], M [auth j1], MA [auth J1], MB [auth B2], MC [auth b2], MD [auth 12], ME [auth 2r], MF [auth 2R], N [auth k1], NA [auth K1], NB [auth C2], NC [auth c2], ND [auth 22], NE [auth 2s], NF [auth 2S], O [auth l1], OA [auth L1], OB [auth D2], OC [auth d2], OD [auth 32], OE [auth 2t], OF [auth 2T], P [auth m1], PA [auth M1], PB [auth E2], PC [auth e2], PD [auth 42], PE [auth 2u], PF [auth 2U], Q [auth n1], QA [auth N1], QB [auth F2], QC [auth f2], QD [auth 52], QE [auth 2v], QF [auth 2V], R [auth o1], RA [auth O1], RB [auth G2], RC [auth g2], RD [auth 62], RE [auth 2w], RF [auth 2W], S [auth p1], SA [auth P1], SB [auth H2], SC [auth h2], SD [auth 72], SE [auth 2x], SF [auth 2X], T [auth q1], TA [auth Q1], TB [auth I2], TC [auth i2], TD [auth 82], TE [auth 2y], TF [auth 2Y], U [auth r1], UA [auth R1], UB [auth J2], UC [auth j2], UD [auth 92], UE [auth 2z], UF [auth 2Z], V [auth s1], VA [auth S1], VB [auth K2], VC [auth k2], VD [auth 2a], VE [auth 2A], VF [auth aa], W [auth t1], WA [auth T1], WB [auth L2], WC [auth l2], WD [auth 2b], WE [auth 2B], WF [auth ab], X [auth u1], XA [auth U1], XB [auth M2], XC [auth m2], XD [auth 2c], XE [auth 2C], XF [auth ac], Y [auth v1], YA [auth V1], YB [auth N2], YC [auth n2], YD [auth 2d], YE [auth 2D], YF [auth ad], Z [auth w1], ZA [auth W1], ZB [auth O2], ZC [auth o2], ZD [auth 2e], ZE [auth 2E]	127	Pseudomonas phage PP7	Mutation(s): 0
UniProt
Find proteins for P03630 (Pseudomonas phage PP7) Explore P03630 Go to UniProtKB: P03630
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03630
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 1
Molecule	Chains	Length	Organism	Image
3'end of PP7 genomic RNA	A [auth R]	95	Pseudomonas phage PP7
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Thongchol, J.

Zhang, J.

Zeng, L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21AI156846
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM141659
National Science Foundation (NSF, United States)	United States	MCB-1902392
Other private	United States	Texas A and M University T3
Other private	United States	Texas A and M University X-grants
Other private	United States	Texas A and M University, Center for phage technology grant
National Science Foundation (NSF, United States)	United States	PHY-1734030