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- PDB-9q6m: Crystal Structure of Vibrio cholerae PilU, a PilT-dependent Retra... -

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Basic information

Entry
Database: PDB / ID: 9q6m
TitleCrystal Structure of Vibrio cholerae PilU, a PilT-dependent Retraction ATPase - Crystal Form 1.
ComponentsTwitching motility protein PilT
KeywordsMOTOR PROTEIN / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / PilU / PilT-dependent Retraction ATPase
Function / homology
Function and homology information


DNA endonuclease activity, producing 5'-phosphomonoesters / type IV pilus-dependent motility / ATP hydrolysis activity / ATP binding
Similarity search - Function
Pilus retraction protein PilT/PilU / : / Type II/IV secretion system protein / Type II/IV secretion system protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Twitching motility protein PilT
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMinasov, G. / Shukla, S. / Shuvalova, L. / Brunzelle, J.S. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Protein Sci / Year: 2026
Title: Analysis of the heterogenous structural states of the hexameric ATPase PilU of the type IV pili from Vibrio cholerae.
Authors: Yirui Guo / Shantanu Shukla / George Minasov / Nicole L Inniss / Thomas Klose / Valerie L Tokars / Alfonso Mondragón / Zbyszek Otwinowski / Dominika Borek / Karla J F Satchell /
Abstract: Type IV pili (T4P) mediate surface motility, host interactions, and DNA uptake through cycles of extension and retraction. While the primary retraction ATPase PilT has been extensively characterized, ...Type IV pili (T4P) mediate surface motility, host interactions, and DNA uptake through cycles of extension and retraction. While the primary retraction ATPase PilT has been extensively characterized, its homolog PilU remains less well understood despite being demonstrated as a PilT-dependent retraction ATPase. Here, we determined six PilU structures by cryo-electron microscopy and x-ray crystallography. The structures reveal a homohexameric assembly stabilized by interactions between the C-terminal catalytic domain of one subunit and the N-terminal PAS-like domain of a neighboring subunit. PilU adopts multiple conformational states, exhibiting different combinations of open and closed interfaces even in the absence of nucleotide. Comparison with PilT highlights structural features that likely underlie PilU's weak ATPase activity and its dependence on PilT for function. Together, these findings provide a structural framework for understanding PilU's role within the T4P retraction machinery.
History
DepositionAug 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 3, 2026Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Twitching motility protein PilT
B: Twitching motility protein PilT
C: Twitching motility protein PilT
D: Twitching motility protein PilT
E: Twitching motility protein PilT
F: Twitching motility protein PilT


Theoretical massNumber of molelcules
Total (without water)257,6996
Polymers257,6996
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.311, 133.732, 181.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Twitching motility protein PilT


Mass: 42949.852 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_0463 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q9KUQ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 8.2mg/ml, 0.5 Sodium chloride, 0.1M Tris (pH 8.3); Screen: PACT (H5), 0.2M Sodium nitrate, 0.1M Bis Tris propane (pH 8.5), 20% (w/v) PEG 3350; Cryo: 0.2M Sodium nitrate, 0.1M Bis ...Details: Protein: 8.2mg/ml, 0.5 Sodium chloride, 0.1M Tris (pH 8.3); Screen: PACT (H5), 0.2M Sodium nitrate, 0.1M Bis Tris propane (pH 8.5), 20% (w/v) PEG 3350; Cryo: 0.2M Sodium nitrate, 0.1M Bis Tris propane pH 8.5, 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97887 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 56455 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 71.6 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.044 / Rrim(I) all: 0.156 / Rsym value: 0.149 / Χ2: 1.033 / Net I/σ(I): 15.8
Reflection shellResolution: 2.95→3 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2794 / CC1/2: 0.578 / CC star: 0.856 / Rpim(I) all: 0.436 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→29.57 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.907 / SU B: 49.048 / SU ML: 0.397 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26487 2834 5.1 %RANDOM
Rwork0.22303 ---
obs0.22514 53063 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.894 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å2-0 Å20 Å2
2--3.5 Å20 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 2.95→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16537 0 0 86 16623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01216759
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616410
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.84722590
X-RAY DIFFRACTIONr_angle_other_deg0.4871.77337578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.16552101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.6525168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg3.897103101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.22602
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0220059
X-RAY DIFFRACTIONr_gen_planes_other0.0110.023901
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4724.6688422
X-RAY DIFFRACTIONr_mcbond_other2.4724.6688422
X-RAY DIFFRACTIONr_mcangle_it4.098.39110517
X-RAY DIFFRACTIONr_mcangle_other4.098.3910518
X-RAY DIFFRACTIONr_scbond_it3.3515.148337
X-RAY DIFFRACTIONr_scbond_other3.3515.1398338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6649.25512074
X-RAY DIFFRACTIONr_long_range_B_refined8.45343.6518178
X-RAY DIFFRACTIONr_long_range_B_other8.45343.6518178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 198 -
Rwork0.341 3893 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.85910.72891.29622.7906-0.95214.93360.2397-0.0107-0.96310.09030.0091-0.32630.83730.2867-0.24880.40720.1151-0.01080.6018-0.15260.185925.21814.95917.786
22.465-0.36220.56944.0535-0.94683.8833-0.11380.30120.275-0.11830.1134-0.1817-0.5918-0.13070.00040.28230.09930.01080.539-0.03770.049936.96138.64436.981
32.6957-0.5435-3.75347.8496-5.646711.04260.17850.77860.2168-0.6779-0.2221-0.0085-0.0591-0.73720.04360.5705-0.1513-0.11350.46430.22060.36738.5856.79921.416
45.91531.35440.73823.69720.73537.49760.08780.435-0.3388-0.1064-0.0026-0.29950.94260.7484-0.08530.33640.2678-0.0050.3073-0.12460.173943.37814.51650.436
54.92921.10480.0093.01890.04672.31450.10370.0508-0.03070.0199-0.02720.05220.09240.1811-0.07640.13250.1346-0.0330.2043-0.020.01537.55630.26572.865
69.53281.38790.20044.02650.3472.4134-0.55570.64251.5746-0.43310.34150.1242-0.38080.27390.21410.2791-0.0136-0.11080.13390.12230.280141.31748.50368.736
76.6536-0.2314-0.4112.52190.0873.79580.0388-0.7977-0.99730.1473-0.06250.20910.4460.37110.02380.35860.0685-0.05070.17550.18680.483222.15715.56880.45
82.67321.5380.1923.18641.33633.99420.1107-0.08690.04210.1661-0.07860.08530.1405-0.1795-0.03210.14230.00590.06080.10650.02230.07561.23433.75683.446
93.7082-0.92652.05612.6187-0.41386.6551-0.23950.05550.813-0.1575-0.0626-0.2711-0.6170.33940.30210.2284-0.05070.03580.03590.00930.42328.19751.33384.028
106.37810.274-0.59791.9043-0.19163.4306-0.07820.159-0.6437-0.08170.0537-0.0230.4643-0.46410.02440.2994-0.17330.04220.1648-0.04730.1476-12.42618.98773.753
111.8520.54060.65143.74051.48384.5046-0.32460.3050.2047-0.40320.12070.4043-0.4349-0.15630.2040.095-0.0385-0.06570.47190.0780.0601-21.45244.38154.139
1210.53951.3166-0.592811.84033.98259.5567-0.0860.12240.84950.45180.14390.2001-0.1395-0.3924-0.05790.16920.1903-0.08980.2348-0.08450.3139-19.40461.64873.523
135.068-1.43731.04944.02162.00697.20830.0235-0.0144-0.1344-0.2602-0.02650.55630.8867-0.59660.0030.3388-0.3081-0.05610.4493-0.00840.1159-30.51119.26541.277
144.9476-2.1358-0.49453.63730.9482.7530.0960.2245-0.1649-0.1448-0.09850.09190.0302-0.19380.00250.2226-0.1582-0.04980.6496-0.0430.025-23.27932.99718.088
156.5791-2.7368-0.67785.4028-0.02621.6394-0.0122-0.4570.6837-0.05270.1685-0.2394-0.4863-0.064-0.15630.3407-0.0465-0.02560.5406-0.12040.1117-24.5551.07521.709
163.99250.23380.77123.68631.04375.7514-0.09260.121-0.7699-0.28180.0572-0.15910.6201-0.05050.03540.242-0.06650.01740.413-0.11440.1983-10.28415.56112.117
174.6539-2.8615-0.86394.67781.61715.41660.1302-0.05620.9385-0.3915-0.1813-0.4162-0.9503-0.39170.05110.36020.08340.04320.7548-0.15320.244710.74436.6939.514
180.2897-0.1045-0.18266.1678-4.34993.61390.17620.11710.8043-0.827-0.0741-0.7027-0.5451-0.4925-0.1023.42810.93830.29512.054-0.06672.34034.93755.042-0.583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 96
2X-RAY DIFFRACTION2A97 - 300
3X-RAY DIFFRACTION3A301 - 349
4X-RAY DIFFRACTION4B0 - 96
5X-RAY DIFFRACTION5B97 - 198
6X-RAY DIFFRACTION6B199 - 350
7X-RAY DIFFRACTION7C0 - 100
8X-RAY DIFFRACTION8C101 - 198
9X-RAY DIFFRACTION9C199 - 350
10X-RAY DIFFRACTION10D0 - 98
11X-RAY DIFFRACTION11D99 - 314
12X-RAY DIFFRACTION12D315 - 350
13X-RAY DIFFRACTION13E-1 - 97
14X-RAY DIFFRACTION14E98 - 196
15X-RAY DIFFRACTION15E197 - 348
16X-RAY DIFFRACTION16F0 - 94
17X-RAY DIFFRACTION17F95 - 281
18X-RAY DIFFRACTION18F282 - 349

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