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- PDB-5txv: HslU P21 cell with 4 hexamers -

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Basic information

Entry
Database: PDB / ID: 5txv
TitleHslU P21 cell with 4 hexamers
ComponentsATP-dependent protease ATPase subunit HslU
KeywordsHYDROLASE / AAA+ ATPase
Function / homology
Function and homology information


protein denaturation / HslUV protease complex / proteasome-activating activity / protein unfolding / proteolysis involved in protein catabolic process / cellular response to heat / peptidase activity / response to heat / protein domain specific binding / magnesium ion binding ...protein denaturation / HslUV protease complex / proteasome-activating activity / protein unfolding / proteolysis involved in protein catabolic process / cellular response to heat / peptidase activity / response to heat / protein domain specific binding / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
Heat shock protein HslU / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent protease ATPase subunit HslU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 7.086 Å
AuthorsGrant, R.A. / Chen, J. / Glynn, S.E. / Sauer, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI-16892 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Covalently linked HslU hexamers support a probabilistic mechanism that links ATP hydrolysis to protein unfolding and translocation.
Authors: Baytshtok, V. / Chen, J. / Glynn, S.E. / Nager, A.R. / Grant, R.A. / Baker, T.A. / Sauer, R.T.
History
DepositionNov 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.name
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent protease ATPase subunit HslU
B: ATP-dependent protease ATPase subunit HslU
C: ATP-dependent protease ATPase subunit HslU
D: ATP-dependent protease ATPase subunit HslU
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
G: ATP-dependent protease ATPase subunit HslU
H: ATP-dependent protease ATPase subunit HslU
I: ATP-dependent protease ATPase subunit HslU
J: ATP-dependent protease ATPase subunit HslU
K: ATP-dependent protease ATPase subunit HslU
L: ATP-dependent protease ATPase subunit HslU
M: ATP-dependent protease ATPase subunit HslU
N: ATP-dependent protease ATPase subunit HslU
O: ATP-dependent protease ATPase subunit HslU
P: ATP-dependent protease ATPase subunit HslU
Q: ATP-dependent protease ATPase subunit HslU
R: ATP-dependent protease ATPase subunit HslU
S: ATP-dependent protease ATPase subunit HslU
T: ATP-dependent protease ATPase subunit HslU
U: ATP-dependent protease ATPase subunit HslU
V: ATP-dependent protease ATPase subunit HslU
W: ATP-dependent protease ATPase subunit HslU
X: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,198,93748
Polymers1,188,68424
Non-polymers10,25324
Water0
1
A: ATP-dependent protease ATPase subunit HslU
B: ATP-dependent protease ATPase subunit HslU
C: ATP-dependent protease ATPase subunit HslU
D: ATP-dependent protease ATPase subunit HslU
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,73412
Polymers297,1716
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25380 Å2
ΔGint-85 kcal/mol
Surface area92210 Å2
MethodPISA
2
G: ATP-dependent protease ATPase subunit HslU
H: ATP-dependent protease ATPase subunit HslU
I: ATP-dependent protease ATPase subunit HslU
J: ATP-dependent protease ATPase subunit HslU
K: ATP-dependent protease ATPase subunit HslU
L: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,73412
Polymers297,1716
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26110 Å2
ΔGint-90 kcal/mol
Surface area91630 Å2
MethodPISA
3
M: ATP-dependent protease ATPase subunit HslU
N: ATP-dependent protease ATPase subunit HslU
O: ATP-dependent protease ATPase subunit HslU
P: ATP-dependent protease ATPase subunit HslU
Q: ATP-dependent protease ATPase subunit HslU
R: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,73412
Polymers297,1716
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25750 Å2
ΔGint-95 kcal/mol
Surface area89240 Å2
MethodPISA
4
S: ATP-dependent protease ATPase subunit HslU
T: ATP-dependent protease ATPase subunit HslU
U: ATP-dependent protease ATPase subunit HslU
V: ATP-dependent protease ATPase subunit HslU
W: ATP-dependent protease ATPase subunit HslU
X: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,73412
Polymers297,1716
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24580 Å2
ΔGint-83 kcal/mol
Surface area88070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.497, 420.860, 176.418
Angle α, β, γ (deg.)90.000, 98.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
ATP-dependent protease ATPase subunit HslU / Heat shock protein HslU / Unfoldase HslU


Mass: 49528.508 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hslU, htpI, b3931, JW3902 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6H5
#2: Chemical...
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris pH 5.8 26% (W/V) PEG3350 260 mM Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 7.086→50 Å / Num. obs: 18657 / % possible obs: 98.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 401.87 Å2 / Rmerge(I) obs: 0.105 / Net I/av σ(I): 15.538 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
7.1-7.224.50.6940.707192.6
7.22-7.354.50.6140.766199.1
7.35-7.494.60.480.848199
7.49-7.654.50.3690.924198.3
7.65-7.814.50.2920.945195.7
7.81-7.994.60.2380.957198.2
7.99-8.194.60.1970.9661100
8.19-8.414.70.1620.981199.9
8.41-8.664.50.1510.983199.8
8.66-8.944.70.1380.985199.9
8.94-9.254.60.1310.986199.8
9.25-9.624.50.1160.991199.7
9.62-10.064.70.1040.991100
10.06-10.584.60.0980.994199.8
10.58-11.244.60.0910.992199.9
11.24-12.094.50.0820.994199.8
12.09-13.294.50.080.994199.5
13.29-15.174.40.0870.993199.7
15.17-18.944.30.0650.994199.8
18.94-5040.0540.995197.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HQY

1hqy


Resolution: 7.086→49.187 Å / SU ML: 1 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 32.76
RfactorNum. reflection% reflection
Rfree0.298 1887 10.15 %
Rwork0.2737 --
obs0.276 18596 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 709.75 Å2 / Biso mean: 414.5644 Å2 / Biso min: 310.28 Å2
Refinement stepCycle: final / Resolution: 7.086→49.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms64241 0 648 0 64889
Biso mean--384.02 --
Num. residues----8177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00365658
X-RAY DIFFRACTIONf_angle_d0.61488682
X-RAY DIFFRACTIONf_chiral_restr0.05710438
X-RAY DIFFRACTIONf_plane_restr0.00311411
X-RAY DIFFRACTIONf_dihedral_angle_d18.76325293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
7.0859-7.27690.34371450.35741215136093
7.2769-7.49030.34041590.34711228138799
7.4903-7.73120.36341390.32471299143898
7.7312-8.00640.34721420.29741276141897
8.0064-8.32550.26011420.273212871429100
8.3255-8.70240.27991480.266713241472100
8.7024-9.15840.27731430.273212851428100
9.1584-9.72810.25791470.252513181465100
9.7281-10.47250.30591440.239812831427100
10.4725-11.51420.28511450.243612991444100
11.5142-13.15240.23521440.2341297144199
13.1524-16.46670.28941480.28451315146399
16.4667-49.18810.36791410.30581283142497
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)
16.59472.7447-4.5473-0.6667-1.48377.9294-0.6232-0.7268-0.93580.7399-0.3869-0.7540.76810.732605.22560.8492-0.00063.7236-0.32114.923528.0503-132.9368-13.5567
2-2.34820.32812.81615.93933.660613.9446-0.22830.12750.40910.89490.1353-0.46212.2509-0.9253-04.8106-0.5805-0.39244.64090.38934.411222.7093-128.584820.9312
31.40994.70750.38295.55282.78253.8404-0.1395-1.2374-0.0913-0.9989-0.89020.09940.2443-0.486803.61770.1432-0.04014.4168-0.48054.336717.1592-97.822832.4407
40.0889-2.27851.26755.9748-1.87177.0151-1.4613-0.62041.094-1.22890.07220.1074-1.7598-0.2954-03.44890.3662-0.34354.7395-0.31755.437510.8821-73.147512.1177
51.0023-0.6749-4.15151.0965-2.49252.9217-0.1544-0.94040.61170.78460.33220.0313-0.73580.6597-05.69910.5155-0.60124.7283-0.19924.559820.4481-76.0826-21.9944
67.669-2.49343.57629.917-0.07363.6326-0.8502-0.00280.4061-0.7068-0.0497-0.16940.65181.281403.62930.54790.03765.062-0.05623.280127.1235-105.7761-33.6014
7-0.0256-0.5303-6.56025.5811-0.937312.14480.37620.5396-0.80731.37710.627-0.57830.5075-0.4863-04.0346-0.0312-0.93234.2182-0.66394.9388-8.9234-68.7138-66.6807
80.64081.24594.05180.66213.10226.5660.3745-0.07970.61030.14720.2195-0.70440.5185-0.2749-04.01830.1060.16524.1987-0.5215.0361-5.3747-66.3387-102.4861
93.424-0.22191.2114.7159-1.39970.3329-0.32531.69230.253-2.06230.17820.1597-0.75620.011505.2812-0.19530.24464.8919-0.18154.1005-9.0219-38.4555-117.8038
102.8421-1.99522.0338.58144.20317.1992-0.79220.1110.7298-0.94330.16380.76720.3682-0.053304.52960.01450.69274.15870.12454.8483-13.1979-9.6278-100.2253
110.63234.8697-1.93235.68150.464312.306-0.3598-0.9749-0.30840.25780.9976-0.5405-1.6527-0.517803.33280.50710.12123.5062-0.37115.4273-22.9288-11.5702-68.9803
121.50752.6417-0.17942.67781.36993.91791.0823-0.19830.29510.2925-1.23070.53480.6511-0.848404.03810.2263-0.22884.094-0.23934.6017-20.522-43.0795-51.2088
130.64051.04211.56175.8262-0.3831.2461-0.18130.90780.5974-0.5901-0.30610.0018-0.65750.208505.4445-0.18670.6935.07450.48784.657-16.9241-125.9936-110.9881
14-0.4338-4.92341.0839-0.4762-1.17323.8406-1.1418-0.28760.13561.75410.10340.8729-1.1429-1.5969-06.7838-0.54610.4744.9953-0.74315.9655-22.9101-114.2127-81.3615
15-0.86260.6132-2.01572.2691-1.91258.66220.64-0.2556-0.5012-0.5953-0.50070.3427-1.24581.005304.5577-0.527-0.36163.9112-0.2325.1692-20.4754-134.064-52.2445
163.3283-1.81982.811912.15210.26932.8251-0.4649-0.7632-0.6134-2.04310.33250.6374-0.20410.165304.1698-0.4094-0.34564.07850.39434.8585-11.8384-165.993-55.5398
178.45810.2460.22034.39481.26764.6937-0.37631.5308-0.9036-1.7987-0.36580.00710.54270.36804.78460.056-0.33124.22560.31474.1279-12.1868-180.2239-88.713
186.3178-2.2663-0.25941.5072-1.36574.68420.27191.9375-0.06770.4621-0.45710.6530.157-0.0082-07.04580.58570.16773.9687-0.16354.3008-13.2592-160.4524-114.7622
195.4814-0.6835-1.56379.3523-4.54053.9195-1.3804-0.4091-0.5515-1.07410.8743-1.47011.24370.3094-06.47390.1823-0.05254.9541-1.18714.934925.7598-29.2463-1.1794
205.0669-5.4814-2.283411.89613.15128.2803-0.17471.3391-0.81570.68070.33140.06261.79510.663404.4652-0.7835-0.20284.9462-0.36484.891420.8567-9.096527.6237
210.9633-1.38190.166312.2875-1.70882.44690.1336-0.16530.5312-0.615-0.1557-0.20651.03790.0281-04.50330.41480.05234.6175-0.20973.842714.777122.664923.4263
224.0479-0.422-1.08637.45255.66888.9817-0.259-0.23041.5126-1.09930.9309-1.02710.8767-0.834505.1246-0.09060.38784.97060.14224.224513.888937.2417-9.4623
231.4955-0.46541.0362.54371.5827-1.63460.20551.2434-0.517-0.5745-0.1246-1.5443-0.3477-0.3002-04.955-0.58980.11867.7092-0.87624.143519.181318.8938-35.4231
242.7931-0.5884-1.76024.202-1.24872.6628-0.47510.8439-0.3429-0.29020.0601-0.4710.3288-0.8973-03.9498-0.486-0.03745.416-0.87224.542528.5885-15.5208-30.361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 450
2X-RAY DIFFRACTION2chain BB4 - 450
3X-RAY DIFFRACTION3chain CC3 - 450
4X-RAY DIFFRACTION4chain DD2 - 450
5X-RAY DIFFRACTION5chain EE4 - 450
6X-RAY DIFFRACTION6chain FF2 - 450
7X-RAY DIFFRACTION7chain GG2 - 450
8X-RAY DIFFRACTION8chain HH2 - 450
9X-RAY DIFFRACTION9chain II2 - 450
10X-RAY DIFFRACTION10chain JJ3 - 450
11X-RAY DIFFRACTION11chain KK2 - 450
12X-RAY DIFFRACTION12chain LL2 - 450
13X-RAY DIFFRACTION13chain MM5 - 450
14X-RAY DIFFRACTION14chain NN3 - 450
15X-RAY DIFFRACTION15chain OO2 - 450
16X-RAY DIFFRACTION16chain PP2 - 450
17X-RAY DIFFRACTION17chain QQ3 - 450
18X-RAY DIFFRACTION18chain RR3 - 450
19X-RAY DIFFRACTION19chain SS2 - 450
20X-RAY DIFFRACTION20chain TT2 - 450
21X-RAY DIFFRACTION21chain UU2 - 450
22X-RAY DIFFRACTION22chain VV2 - 450
23X-RAY DIFFRACTION23chain WW2 - 450
24X-RAY DIFFRACTION24chain XX2 - 450

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