[English] 日本語
Yorodumi
- PDB-1ofi: Asymmetric complex between HslV and I-domain deleted HslU (H. inf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ofi
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 ...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 / cytoplasm
Similarity search - Function
Heat shock protein HslU / ATP-dependent protease, HslV subunit / : / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Helicase, Ruva Protein; domain 3 - #60 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / : / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Helicase, Ruva Protein; domain 3 - #60 / 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 / Nucleophile aminohydrolases, N-terminal / Helicase, Ruva Protein; domain 3 / 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 / Chem-LVS / 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: 3.2 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
G: 4-IODO-3-NITROPHENYL ACETYL-LEUCINYL-LEUCINYL-LEUCINYL-VINYLSULFONE
H: 4-IODO-3-NITROPHENYL ACETYL-LEUCINYL-LEUCINYL-LEUCINYL-VINYLSULFONE
I: 4-IODO-3-NITROPHENYL ACETYL-LEUCINYL-LEUCINYL-LEUCINYL-VINYLSULFONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,82530
Polymers215,7999
Non-polymers4,02621
Water37821
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)439,65160
Polymers431,59918
Non-polymers8,05242
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)439,65160
Polymers431,59918
Non-polymers8,05242
Water1086
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)190.177, 190.177, 114.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

-
Components

-
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
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

-
Non-polymers , 5 types, 42 molecules GHI

#3: Chemical ChemComp-ADP / ADENOSINE-5'-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


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-LVS / 4-IODO-3-NITROPHENYL ACETYL-LEUCINYL-LEUCINYL-LEUCINYL-VINYLSULFONE


Mass: 722.632 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H43IN4O8S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

-
Details

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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 47 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2000 / 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: 3.2→50 Å / Num. obs: 38085 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 4.46 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.6
Reflection shellResolution: 3.2→3.26 Å / Mean I/σ(I) obs: 4.8 / % possible all: 92.7
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 50 Å / Num. measured all: 169771 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 92.7 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 4.8

-
Processing

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

1g3i


Resolution: 3.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.327 3523 10 %RANDOM
Rwork0.232 ---
obs0.232 169771 96.7 %-
Solvent computationSolvent model: DENSITY MODIFICATION
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14798 0 231 21 15050
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.37
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: 3.2→3.26 Å / Total num. of bins used: 20 /
Rfactor% reflection
Rfree0.481 10 %
Rwork0.379 -
obs-92.7 %
Refinement
*PLUS
Num. reflection obs: 31884
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Lowest resolution: 3.22 Å

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more