[English] 日本語
Yorodumi
- PDB-2qwq: Crystal structure of disulfide-bond-crosslinked complex of bovine... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qwq
TitleCrystal structure of disulfide-bond-crosslinked complex of bovine hsc70 (1-394aa)R171C and bovine Auxilin (810-910aa)D876C in the AMPPNP hydrolyzed form
Components
  • Heat shock cognate 71 kDa protein
  • Putative tyrosine-protein phosphatase auxilin
KeywordsCHAPERONE / chaperone-cochaperone complex / ATP-binding / Nucleotide-binding / Nucleus / Phosphorylation / Stress response / Hydrolase / Protein phosphatase / SH3-binding
Function / homology
Function and homology information


regulation of clathrin coat assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle recycling / synaptic vesicle uncoating ...regulation of clathrin coat assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle recycling / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / clathrin heavy chain binding / late endosomal microautophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / Prp19 complex / presynaptic cytosol / Neutrophil degranulation / postsynaptic cytosol / clathrin-coated vesicle / clathrin binding / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / intracellular transport / autophagosome / dephosphorylation / protein folding chaperone / heat shock protein binding / RNA splicing / protein tyrosine phosphatase activity / ATP-dependent protein folding chaperone / spliceosomal complex / terminal bouton / mRNA processing / SH3 domain binding / melanosome / protein-macromolecule adaptor activity / presynapse / protein refolding / vesicle / postsynaptic density / lysosome / molecular adaptor activity / ribonucleoprotein complex / lysosomal membrane / protein domain specific binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / dendrite / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / DnaJ domain / Defensin A-like - #30 / DnaJ molecular chaperone homology domain / dnaJ domain profile. ...Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / DnaJ domain / Defensin A-like - #30 / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / C2 domain superfamily / Protein-tyrosine phosphatase-like / ATPase, nucleotide binding domain / Helix Hairpins / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Heat shock cognate 71 kDa protein / Auxilin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsJiang, J. / Maes, E.G. / Wang, L. / Taylor, A.B. / Hinck, A.P. / Lafer, E.M. / Sousa, R.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural basis of J cochaperone binding and regulation of Hsp70.
Authors: Jiang, J. / Maes, E.G. / Taylor, A.B. / Wang, L. / Hinck, A.P. / Lafer, E.M. / Sousa, R.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock cognate 71 kDa protein
B: Putative tyrosine-protein phosphatase auxilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8827
Polymers54,1162
Non-polymers7665
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.797, 56.494, 225.878
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Heat shock cognate 71 kDa protein / Heat shock 70 kDa protein 8


Mass: 43368.059 Da / Num. of mol.: 1 / Mutation: R171C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: HSPA8, HSC70 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P19120
#2: Protein Putative tyrosine-protein phosphatase auxilin / DnaJ homolog subfamily C member 6


Mass: 10747.485 Da / Num. of mol.: 1 / Mutation: D876C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: DNAJC6 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q27974, protein-tyrosine-phosphatase

-
Non-polymers , 5 types, 110 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 289 K / Method: microbatch under oil / pH: 8.5
Details: PEG3350, Ammonium Acetate, pH 8.5, microbatch under oil, temperature 289K

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 25924 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Χ2: 1.038 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.283.30.55625611.0671100
2.28-2.373.40.48925071.065199.9
2.37-2.483.40.3825441.0511100
2.48-2.613.40.29625511.0761100
2.61-2.773.40.21425681.0471100
2.77-2.993.40.14725951.0441100
2.99-3.293.40.09525631.032199.9
3.29-3.763.30.05726080.974199.7
3.76-4.743.30.04426310.976199.5
4.74-503.20.03927961.048198.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→31.67 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 22.752 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1310 5.1 %RANDOM
Rwork0.24 ---
obs0.243 25851 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.861 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--0.91 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.21→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3713 0 46 105 3864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223823
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9685167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17424.566173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25415677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1151524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022841
X-RAY DIFFRACTIONr_nbd_refined0.2090.21659
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22618
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2159
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.24
X-RAY DIFFRACTIONr_mcbond_it0.4991.52434
X-RAY DIFFRACTIONr_mcangle_it0.78123800
X-RAY DIFFRACTIONr_scbond_it1.2931578
X-RAY DIFFRACTIONr_scangle_it1.9464.51367
LS refinement shellResolution: 2.21→2.266 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 87 -
Rwork0.356 1773 -
all-1860 -
obs--98.57 %

+
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