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- PDB-6pxi: The crystal structure of a singly capped HslUV complex with an ax... -

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Basic information

Entry
Database: PDB / ID: 6pxi
TitleThe crystal structure of a singly capped HslUV complex with an axial pore plug and a HslU E257Q mutation
Components
  • ATP-dependent protease ATPase subunit HslU
  • ATP-dependent protease subunit HslV
KeywordsHYDROLASE / AAA+ ATPase / peptidase
Function / homology
Function and homology information


HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / : / peptidase activity / cellular response to heat ...HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / : / peptidase activity / cellular response to heat / response to heat / protein domain specific binding / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Heat shock protein HslU / ATP-dependent protease, HslV subunit / : / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Proteasome B-type subunit / Proteasome beta-type subunit profile. ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / : / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Helicase, Ruva Protein; domain 3 / Nucleophile aminohydrolases, N-terminal / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent protease ATPase subunit HslU / ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.447 Å
AuthorsBaytshtok, V. / Grant, R.A. / Sauer, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Cell Rep / Year: 2021
Title: Heat activates the AAA+ HslUV protease by melting an axial autoinhibitory plug.
Authors: Baytshtok, V. / Fei, X. / Shih, T.T. / Grant, R.A. / Santos, J.C. / Baker, T.A. / Sauer, R.T.
History
DepositionJul 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
Revision 1.3Jun 19, 2024Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code ..._entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,51811
Polymers176,3756
Non-polymers1,1435
Water181
1
A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules

A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules

A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)532,55333
Polymers529,12518
Non-polymers3,42815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)168.604, 168.604, 162.886
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11C-201-

SO4

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Components

#1: Protein
ATP-dependent protease subunit HslV / Heat shock protein HslV


Mass: 18915.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hslV, htpO, yiiC, b3932, JW3903 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7B8, HslU-HslV peptidase
#2: Protein ATP-dependent protease ATPase subunit HslU / Heat shock protein HslU / Unfoldase HslU


Mass: 50356.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hslU, htpI, b3931, JW3902 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6H5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.85 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 6, 2016 / Details: Varimax-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.45
ReflectionResolution: 3.447→100 Å / Num. obs: 29212 / % possible obs: 81.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.081 / Rrim(I) all: 0.141 / Χ2: 0.983 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.45-3.511.50.66610210.5830.5840.890.68259.3
3.51-3.571.50.58710660.6520.510.7810.61559.8
3.57-3.641.50.51410960.5720.4390.6790.6762.2
3.64-3.721.50.67611480.5460.5890.9010.83764.6
3.72-3.81.50.49711770.7090.4310.6610.67867.1
3.8-3.891.50.51412810.7870.4410.680.78572.7
3.89-3.981.50.52213700.7980.4440.6890.84576.2
3.98-4.091.60.41214040.8980.3440.540.85780
4.09-4.211.70.35115120.8920.2860.4560.8984.9
4.21-4.351.90.25315410.9160.190.3191.0487
4.35-4.52.20.18515970.9480.1310.2291.17790.7
4.5-4.682.30.17916190.9670.1250.2210.99190.9
4.68-4.92.60.16316510.9680.1080.1980.95792.6
4.9-5.152.70.17616720.9660.1160.2130.91494.1
5.15-5.482.80.15817180.9740.1030.190.83694.9
5.48-5.92.80.16216880.9660.1080.1970.84695.3
5.9-6.492.80.12717190.970.0830.1530.87694.4
6.49-7.432.80.08416890.9910.0530.11.00993.2
7.43-9.362.80.05417060.9930.0340.0641.41392.7
9.36-1002.70.04415370.9950.030.0541.31280.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G4A

1g4a


Resolution: 3.447→48.672 Å / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.52
RfactorNum. reflection% reflection
Rfree0.2852 2225 7.69 %
Rwork0.2573 --
obs0.2606 28950 80.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 193.94 Å2 / Biso mean: 111.2388 Å2 / Biso min: 62.77 Å2
Refinement stepCycle: final / Resolution: 3.447→48.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11093 0 69 1 11163
Biso mean--92.23 67.08 -
Num. residues----1437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211304
X-RAY DIFFRACTIONf_angle_d0.4415273
X-RAY DIFFRACTIONf_chiral_restr0.0511797
X-RAY DIFFRACTIONf_plane_restr0.0021969
X-RAY DIFFRACTIONf_dihedral_angle_d18.634230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4485-3.53440.35171060.33311373147956
3.5344-3.62960.34071060.30221430153657
3.6296-3.73590.27721060.30731494160060
3.7359-3.85590.3081180.28781640175865
3.8559-3.99290.38351310.30981757188870
3.9929-4.15180.34681360.32521895203176
4.1518-4.33940.30451510.29342017216879
4.3394-4.56630.29961510.28622116226783
4.5663-4.84960.36841550.2712118227384
4.8496-5.21950.30881560.27392187234386
5.2195-5.73650.29791640.27532223238788
5.7365-6.54790.34241700.26582250242088
6.5479-8.18010.22251640.20422232239686
8.1801-22.1710.20281700.19012197236782
Refinement TLS params.Method: refined / Origin x: -60.0585 Å / Origin y: 62.3341 Å / Origin z: 57.3627 Å
111213212223313233
T0.6917 Å2-0.1439 Å2-0.0316 Å2-0.8679 Å2-0.0055 Å2--0.8303 Å2
L0.2303 °20.0686 °20.0182 °2-0.1442 °2-0.0905 °2--0.4176 °2
S-0.0102 Å °-0.0346 Å °0.0152 Å °0.0154 Å °0.0046 Å °-0.0146 Å °-0.0822 Å °0.0283 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 174
2X-RAY DIFFRACTION1allB1 - 174
3X-RAY DIFFRACTION1allC1 - 174
4X-RAY DIFFRACTION1allD1 - 174
5X-RAY DIFFRACTION1allE2 - 450
6X-RAY DIFFRACTION1allF2 - 450
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allH1 - 3

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