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- PDB-1e94: HslV-HslU from E.coli -

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Basic information

Entry
Database: PDB / ID: 1.0E+94
TitleHslV-HslU from E.coli
Components
  • HEAT SHOCK PROTEIN HSLU
  • HEAT SHOCK PROTEIN HSLV
KeywordsCHAPERONE / HSLVU / CLPQY / AAA-ATPASE / ATP-DEPENDENT PROTEOLYSIS / PROTEASOME
Function / homology
Function and homology information


peptidase activity => GO:0008233 / HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity ...peptidase activity => GO:0008233 / HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / 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 / cytoplasm / cytosol
Similarity search - Function
Heat shock protein HslU / ATP-dependent protease, HslV subunit / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 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 / 4-Layer Sandwich / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATP-dependent protease ATPase subunit HslU / ATP-dependent protease subunit HslV / ATP-dependent protease subunit HslV / ATP-dependent protease ATPase subunit HslU
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSong, H.K. / Hartmann, C. / Ravishankar, R. / Bochtler, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Mutational Studies on Hslu and its Docking Mode with Hslv
Authors: Song, H.K. / Hartmann, C. / Ravishankar, R. / Bochtler, M. / Behrendt, R. / Moroder, L. / Huber, R.
#1: Journal: Nature / Year: 2000
Title: The Structures of Hslu and the ATP-Dependent Protease Hslu-Hslv
Authors: Bochtler, M. / Hartmann, C. / Song, H.K. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Crystal Structure of Heat Shock Locus V (Hslv) from Escherichia Coli
Authors: Bochtler, M. / Ditzel, L. / Groll, M. / Huber, R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Hslv-Hslu: A Novel ATP-Dependent Protease Complex in Escherichia Coli Related to the Eukaryotic Proteasome
Authors: Rohrwild, M. / Coux, O. / Huang, H.C. / Moerschell, R.P. / Yoo, S.J. / Seol, J.H. / Chung, C.H. / Goldberg, A.L.
#4: Journal: Gene / Year: 1993
Title: Sequence Analysis of Four New Heat-Shock Genes Constituting the Hslts/Ibpab and Hslvu Operons in Escherichia Coli
Authors: Chuang, S.E. / Burland, V. / Plunkett III, G. / Daniels, D.L. / Blattner, F.R.
History
DepositionOct 7, 2000Deposition site: PDBE / Processing site: PDBE
SupersessionNov 17, 2000ID: 1DOO
Revision 1.0Nov 17, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN HSLV
B: HEAT SHOCK PROTEIN HSLV
C: HEAT SHOCK PROTEIN HSLV
D: HEAT SHOCK PROTEIN HSLV
E: HEAT SHOCK PROTEIN HSLU
F: HEAT SHOCK PROTEIN HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,9508
Polymers176,9386
Non-polymers1,0122
Water5,152286
1
A: HEAT SHOCK PROTEIN HSLV
B: HEAT SHOCK PROTEIN HSLV
x 6


Theoretical massNumber of molelcules
Total (without water)227,84012
Polymers227,84012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation12_565x,x-y+1,-z+1/21
MethodPQS
2
C: HEAT SHOCK PROTEIN HSLV
D: HEAT SHOCK PROTEIN HSLV
x 6


Theoretical massNumber of molelcules
Total (without water)227,84012
Polymers227,84012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation3_465-x+y-1,-x+1,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation12_574x,x-y+2,-z-1/21
MethodPQS
3
E: HEAT SHOCK PROTEIN HSLU
F: HEAT SHOCK PROTEIN HSLU
hetero molecules

E: HEAT SHOCK PROTEIN HSLU
F: HEAT SHOCK PROTEIN HSLU
hetero molecules

E: HEAT SHOCK PROTEIN HSLU
F: HEAT SHOCK PROTEIN HSLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,01012
Polymers302,9736
Non-polymers3,0376
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)172.022, 172.022, 276.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein
HEAT SHOCK PROTEIN HSLV / HSLV


Mass: 18986.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Cellular location: CYTOPLASM / Plasmid: PET12B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31059, UniProt: P0A7B8*PLUS
#2: Protein HEAT SHOCK PROTEIN HSLU / HSLU


Mass: 50495.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Cellular location: CYTOPLASM / Plasmid: PET12B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32168, UniProt: P0A6H5*PLUS
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEDMAN-DEGRADATION HAS SHOWN THAT THE AMINO-TERMINAL METHIONINE IS CLEAVED IN HSLV TO EXPOSE A ...EDMAN-DEGRADATION HAS SHOWN THAT THE AMINO-TERMINAL METHIONINE IS CLEAVED IN HSLV TO EXPOSE A THREONINE RESIDUE THAT ACTS AS THE NUCLEOPHILE IN PROTEOLYSIS. FOR CONSISTENCY WITH THE PROTEASOME NUMBERING SCHEME, THIS THREONINE RESIDUE IS ASSIGNED SEQUENCE NUMBER 1. THE FOLLOWING RESIDUES ARE NUMBERED CONSECUTIVELY, UNLIKE IN ENTRY 1NED FOR HSLV WHERE THE NUMBERING SCHEME HAS BEEN CHOSEN TO EMPHASIZE THE SIMILARITY OF HSLV WITH THE BETA-SUBUNITS OF 20S PROTEASOMES. AN ENGINEERED VARIANT OF HSLV WITH THE CARBOXY-TERMINAL TAG EFHHHHHH WAS USED FOR CRYSTALLIZATION. AS THE TAG RESIDUES AND THE LAST TWO RESIDUES OF THE WILD TYPE SEQUENCE ARE NOT VISIBLE IN THE ELECTRON DENSITY, THEY HAVE BEEN OMITTED FROM THE MODEL.

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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: 3.34 Å3/Da / Density % sol: 63.15 %
Crystal growpH: 6.3
Details: 20 MG/ML SOLUTION OF HSLU SUPPLEMENTED WITH 1 MM AMP-PNP IN BUFFER (20 MM TRIS/HCL, PH 7.5, 1 MM EDTA, 1 MM NAN3) MIXED IN 2:1 VOLUME RATIO WITH 16 MG/ML HSLV IN 300 MM NACL, 20 MM TRIS/HCL, ...Details: 20 MG/ML SOLUTION OF HSLU SUPPLEMENTED WITH 1 MM AMP-PNP IN BUFFER (20 MM TRIS/HCL, PH 7.5, 1 MM EDTA, 1 MM NAN3) MIXED IN 2:1 VOLUME RATIO WITH 16 MG/ML HSLV IN 300 MM NACL, 20 MM TRIS/HCL, PH 7.5, 1 MM EDTA, 1 MM NAN3. 0.002 ML RESERVOIR PLUS 0.002 ML PROTEIN SOLUTION EQUILIBRATED AGAINST 0.5 ML RESERVOIR SOLUTION. RESERVOIR CONTAINED 100 MM MES, PH 6.3 AND 2.0 M SODIUM ACETATE 0.4 MG/ML RESORUFIN-LABELLED CASEIN
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Details: A:B=2:1 ratio, Bochtler, M., (2000) Nature, 403, 800.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlHslU1dropsolutionA
220 mMTris-HCl1dropsolutionA
31 mMEDTA1dropsolutionA
41 mM1dropsolutionANaN3
51 mMAMP-PNP1dropsolutionA
616 mg/mlhistidine-tagged HslV1dropsolutionB
7300 mM1dropsolutionBNaCl
820 mMTris-HCl1dropsolutionB
91 mMEDTA1dropsolutionB
101 mM1dropsolutionBNaN3
11100 mMMES1reservoir
122.0 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.0712
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2000 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0712 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 59863 / % possible obs: 99.8 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12
Reflection shellResolution: 2.8→2.87 Å / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 25 Å / Num. measured all: 706383 / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DOO

1doo
PDB Unreleased entry


Resolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: ZERO OCCUPANCY COORDINATES IN I- DOMAIN ARE TAKEN FROM THOSE OF TRIGONAL HSLU MODEL (1DO2) THE ELECTRON DENSITY OF RESIDUES FROM 175 - 209 IN HSLU MODEL (CHAIN E AND F) IS COMPLETELY ...Details: ZERO OCCUPANCY COORDINATES IN I- DOMAIN ARE TAKEN FROM THOSE OF TRIGONAL HSLU MODEL (1DO2) THE ELECTRON DENSITY OF RESIDUES FROM 175 - 209 IN HSLU MODEL (CHAIN E AND F) IS COMPLETELY DISORDERED THE ELECTRON DENSITY OF CORE REGION (RESIDUE FROM 89 - 92) IN HSLU (CHAIN E AND F) WAS NOT CLEAR AND MANY ATOMS IN THIS REGION HAVE ZERO OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.3044 -10 %RANDOM
Rwork0.2543 ---
obs0.2543 54988 92.3 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.411 Å2-7.504 Å20 Å2
2--12.411 Å20 Å2
3----24.821 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11679 0 62 286 12027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0142
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.649
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2ANP.PARANP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.3044
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0142

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