[English] 日本語
Yorodumi
- PDB-1do2: TRIGONAL CRYSTAL FORM OF HEAT SHOCK LOCUS U (HSLU) FROM ESCHERICH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1do2
TitleTRIGONAL CRYSTAL FORM OF HEAT SHOCK LOCUS U (HSLU) FROM ESCHERICHIA COLI
ComponentsPROTEIN (HEAT SHOCK LOCUS U)
KeywordsCHAPERONE / HSLU / CLPY / AAA-ATPASE / ATP-DEPENDENT PROTEOLYSIS / PROTEASOME
Function / homology
Function and homology information


protein denaturation / HslUV protease complex / proteasome-activating activity / protein unfolding / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat / 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 / 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
Similarity search - Function
Heat shock protein HslU / : / Ubiquitin-associated (UBA) domain / 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 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) ...Heat shock protein HslU / : / Ubiquitin-associated (UBA) domain / 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 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBochtler, M. / Hartmann, C. / Song, H.K. / Bourenkov, G.P. / Bartunik, H.D.
Citation
Journal: Nature / Year: 2000
Title: The structures of HsIU and the ATP-dependent protease HsIU-HsIV.
Authors: Bochtler, M. / Hartmann, C. / Song, H.K. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R.
#1: 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.
#2: 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.
#3: 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. / Plunket III, G. / Daniels, D.L. / Blattner, F.R.
History
DepositionDec 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (HEAT SHOCK LOCUS U)
B: PROTEIN (HEAT SHOCK LOCUS U)
C: PROTEIN (HEAT SHOCK LOCUS U)
D: PROTEIN (HEAT SHOCK LOCUS U)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,1266
Polymers198,1144
Non-polymers1,0122
Water00
1
A: PROTEIN (HEAT SHOCK LOCUS U)
B: PROTEIN (HEAT SHOCK LOCUS U)
hetero molecules

A: PROTEIN (HEAT SHOCK LOCUS U)
B: PROTEIN (HEAT SHOCK LOCUS U)
hetero molecules

A: PROTEIN (HEAT SHOCK LOCUS U)
B: PROTEIN (HEAT SHOCK LOCUS U)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,6909
Polymers297,1716
Non-polymers1,5193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area25040 Å2
ΔGint-98 kcal/mol
Surface area114790 Å2
MethodPISA, PQS
2
C: PROTEIN (HEAT SHOCK LOCUS U)
D: PROTEIN (HEAT SHOCK LOCUS U)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5633
Polymers99,0572
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24280 Å2
ΔGint-87 kcal/mol
Surface area115080 Å2
MethodPISA
3
C: PROTEIN (HEAT SHOCK LOCUS U)
D: PROTEIN (HEAT SHOCK LOCUS U)
hetero molecules

C: PROTEIN (HEAT SHOCK LOCUS U)
D: PROTEIN (HEAT SHOCK LOCUS U)
hetero molecules

C: PROTEIN (HEAT SHOCK LOCUS U)
D: PROTEIN (HEAT SHOCK LOCUS U)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,6909
Polymers297,1716
Non-polymers1,5193
Water0
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)201.777, 201.777, 171.628
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein
PROTEIN (HEAT SHOCK LOCUS U)


Mass: 49528.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL-1 BLUE / Cellular location: CYTOPLASM / Plasmid: PET12B (T7 PROMOTOR) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6H5
#2: 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
Sequence detailsEDMAN-DEGRADATION HAS SHOWN THAT THE AMINOTERMINAL METHIONINE IS CLEAVED IN THE WILD TYPE. ...EDMAN-DEGRADATION HAS SHOWN THAT THE AMINOTERMINAL METHIONINE IS CLEAVED IN THE WILD TYPE. NEVERTHELESS, THIS METHIONINE RESIDUE HAS BEEN ASSIGNED RESIDUE NUMBER 1. THE FOLLOWING SERINE, THE FIRST RESIDUE OF THE MATURE PROTEIN, HAS BEEN ASSIGNED RESIDUE NUMBER 2 AN ENGINEERED VARIANT OF HSLU WITH THE SEVEN RESIDUE HIS-TAG, MHHHHHH, IN PLACE OF MET1 HAS BEEN USED FOR CRYSTALLIZATION. THIS TAG IS NOT CLEAVED IN THE MUTANT PROTEIN. AS THESE RESIDUES ARE NOT VISIBLE IN THE ELECTRON DENSITY, THEY HAVE BEEN OMITTED FROM THE MODEL.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.09 Å3/Da / Density % sol: 75.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: reservoir: 100 mM sodium cacodylate, 15% glycerol, 10.5% PEG8000, 500 mM (NH4)2(SO4). drop: 0.002 ml reservoir solution, 0.002 ml 16 mg/ml protein in 20 mM Tris/HCl, pH 7.5, 5 mM MgCl2, 1 mM ...Details: reservoir: 100 mM sodium cacodylate, 15% glycerol, 10.5% PEG8000, 500 mM (NH4)2(SO4). drop: 0.002 ml reservoir solution, 0.002 ml 16 mg/ml protein in 20 mM Tris/HCl, pH 7.5, 5 mM MgCl2, 1 mM AMP-PNP, 1 mM NaN3, 0.0005 ml 1.0 M guanidinium chloride, 0.001 ml C12E8 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions in Buffer B
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
116 mg/mlprotein1drop
220 mMTris-HCl1dropBuffer B
31 mMEDTA1dropBuffer B
41 mM1dropBuffer BNaN3
5100 mMsodium cacodylate1reservoir
615 %glycerol1reservoir
710.5 %PEG80001reservoir
8500 mMammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.0712
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 1999 / 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: 4→20 Å / Num. all: 224179 / Num. obs: 32750 / % possible obs: 95.8 % / Redundancy: 6 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 10.5
Reflection shellResolution: 4→4.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.337 / Rsym value: 33.7 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 224179
Reflection shell
*PLUS
% possible obs: 96.5 %

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HSLU FROM HSLU IN HSLVU CRYSTALS

Resolution: 4→15 Å / Rfactor Rfree error: 0.007 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1611 5 %RANDOM
Rwork0.229 ---
obs0.229 32369 95.8 %-
Displacement parametersBiso mean: 50.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.06 Å20.23 Å20 Å2
2---6.06 Å20 Å2
3---12.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12864 0 62 0 12926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.49
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.281.5
X-RAY DIFFRACTIONx_mcangle_it6.672
X-RAY DIFFRACTIONx_scbond_it11.972
X-RAY DIFFRACTIONx_scangle_it15.492.5
LS refinement shellResolution: 4→4.25 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 280 5.2 %
Rwork0.28 5066 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2ANP.PARANP.TOP

+
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