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- PDB-1ofh: Asymmetric complex between HslV and I-domain deleted HslU (H. inf... -

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Basic information

Entry
Database: PDB / ID: 1ofh
TitleAsymmetric complex between HslV and I-domain deleted HslU (H. influenzae)
Components(ATP-DEPENDENT ...) x 2
KeywordsHYDROLASE / CHAPERONE / ATP-BINDING
Function / homology
Function and homology information


HslU-HslV peptidase / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Heat shock protein HslU / ATP-dependent protease, HslV subunit / 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 ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / ATP-dependent protease subunit HslV / ATP-dependent protease ATPase subunit HslU
Similarity search - Component
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKwon, A.R. / Kessler, B.M. / Overkleeft, H.S. / McKay, D.B.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structure and Reactivity of an Asymmetric Complex between Hslv and I-Domain Deleted Hslu, a Prokaryotic Homolog of the Eukaryotic Proteasome
Authors: Kwon, A.R. / Kessler, B.M. / Overkleeft, H.S. / Mckay, D.B.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Structure of Hsluv Complexed with a Vinyl Sulfone Inhibitor: Corroboration of a Proposed Mechanism of Allosteric Activation of Hslv by Hslu
Authors: Sousa, M.C. / Kessler, B.M. / Overkleeft, H.S. / Mckay, D.B.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal and Solution Structures of an Hsluv Protease-Chaperone Complex
Authors: Sousa, M.C. / Trame, C.B. / Tsuruta, H. / Wilbanks, S.M. / Reddy, V.S. / Mckay, D.B.
History
DepositionApr 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2003Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
B: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
C: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
G: ATP-DEPENDENT PROTEASE HSLV
H: ATP-DEPENDENT PROTEASE HSLV
I: ATP-DEPENDENT PROTEASE HSLV
L: ATP-DEPENDENT PROTEASE HSLV
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,65827
Polymers215,7999
Non-polymers1,85818
Water1,44180
1
A: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
G: ATP-DEPENDENT PROTEASE HSLV
L: ATP-DEPENDENT PROTEASE HSLV
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)435,31554
Polymers431,59918
Non-polymers3,71636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation4_775-x+2,-y+2,z1
MethodPQS
2
B: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
C: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
H: ATP-DEPENDENT PROTEASE HSLV
I: ATP-DEPENDENT PROTEASE HSLV
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

B: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
C: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
H: ATP-DEPENDENT PROTEASE HSLV
I: ATP-DEPENDENT PROTEASE HSLV
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
hetero molecules

B: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
C: ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU
H: ATP-DEPENDENT PROTEASE HSLV
I: ATP-DEPENDENT PROTEASE HSLV
M: ATP-DEPENDENT PROTEASE HSLV
N: ATP-DEPENDENT PROTEASE HSLV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)435,31554
Polymers431,59918
Non-polymers3,71636
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)192.220, 192.220, 115.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

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ATP-DEPENDENT ... , 2 types, 9 molecules ABCGHILMN

#1: Protein ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU


Mass: 34126.020 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-107,244-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Strain: RD / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P43773
#2: Protein
ATP-DEPENDENT PROTEASE HSLV


Mass: 18903.549 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Strain: RD / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P43772, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases

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Non-polymers , 4 types, 98 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsFUNCTION: CHAPERONE SUBUNIT OF A PROTEASOME-LIKE DEGRADATION COMPLEX INTERACTS WITH HSLV.

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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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.5 / Details: PEG-MME 2000, KCL,MG(OAC)2,CITRATE, PH 5.5
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115-20 mg/mlprotein11
210 mMMOPS11pH7.0
31 mMmagnesium acetate11
41 mMATP11
57 %PEG2000MME12
61 M12KCl
710 mMmagnesium acetate12
850 mMcitrate12pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 81671 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 39.8
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 2.3 / % possible all: 74.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 40 Å / Num. measured all: 344637 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 74.9 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G3I

1g3i


Resolution: 2.5→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 4586 6 %RANDOM
Rwork0.224 ---
obs0.224 344637 97 %-
Solvent computationSolvent model: DENSITY MODIFICATION
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15066 0 108 80 15254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.27
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
LS refinement shellResolution: 2.5→2.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 187 6 %
Rwork0.406 3122 -
obs--74.9 %
Refinement
*PLUS
Num. reflection obs: 71454
Solvent computation
*PLUS
Displacement parameters
*PLUS

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