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- PDB-5nro: Structure of full-length DnaK with bound J-domain -

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Basic information

Entry
Database: PDB / ID: 5nro
TitleStructure of full-length DnaK with bound J-domain
Components
  • Chaperone protein DnaJ
  • Chaperone protein DnaK
KeywordsCHAPERONE / DnaK / DnaJ / Hsp70 / Hsp40
Function / homology
Function and homology information


stress response to copper ion / sigma factor antagonist activity / protein disulfide isomerase activity / chaperone cofactor-dependent protein refolding / protein unfolding / protein-disulfide reductase activity / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding ...stress response to copper ion / sigma factor antagonist activity / protein disulfide isomerase activity / chaperone cofactor-dependent protein refolding / protein unfolding / protein-disulfide reductase activity / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / viral process / ADP binding / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / response to heat / protein-folding chaperone binding / protein refolding / protein-containing complex assembly / DNA replication / ATP hydrolysis activity / protein homodimerization activity / protein-containing complex / zinc ion binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / DnaJ domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal ...Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / DnaJ domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Chaperone DnaK / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / Substrate Binding Domain Of DNAk; Chain A, domain 1 / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Helix Hairpins / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Up-down Bundle / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chaperone protein DnaJ / Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsKopp, J. / Kityk, R. / Mayer, M.P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationMA 1278/4-3 Germany
CitationJournal: Mol. Cell / Year: 2018
Title: Molecular Mechanism of J-Domain-Triggered ATP Hydrolysis by Hsp70 Chaperones.
Authors: Kityk, R. / Kopp, J. / Mayer, M.P.
History
DepositionApr 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein DnaK
B: Chaperone protein DnaJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8444
Polymers78,3122
Non-polymers5312
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, DnaK and DnaJ form a hetero dimer; there is no higher oligomerisation state
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-15 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.246, 127.246, 252.885
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Chaperone protein DnaK / / HSP70 / Heat shock 70 kDa protein / Heat shock protein 70


Mass: 66393.922 Da / Num. of mol.: 1 / Mutation: E47C, T199A, F529C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaK, groP, grpF, seg, b0014, JW0013 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8
#2: Protein Chaperone protein DnaJ / / HSP40 / Heat shock protein J


Mass: 11918.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaJ, groP, b0015, JW0014 / Production host: Escherichia coli (E. coli) / References: UniProt: P08622
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 4 Å3/Da / Density % sol: 69.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 9% w/v PEG 8000 0.1M calcium acetate 0.1 M imidazole pH 6.5 protein at 18 mg/ml crystalization drop contained 200 nl protein + 100 nl reservoir solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.872899 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872899 Å / Relative weight: 1
ReflectionResolution: 3.25→46.121 Å / Num. obs: 19859 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.999 / Rpim(I) all: 0.056 / Net I/σ(I): 13.8
Reflection shellResolution: 3.25→3.51 Å / Redundancy: 20.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3983 / CC1/2: 0.515 / Rpim(I) all: 0.608 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B9Q

4b9q


Resolution: 3.25→46.121 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.15
RfactorNum. reflection% reflection
Rfree0.234 974 4.92 %
Rwork0.216 --
obs0.2168 19808 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.25→46.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5097 0 32 4 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095200
X-RAY DIFFRACTIONf_angle_d0.6477016
X-RAY DIFFRACTIONf_dihedral_angle_d11.7033236
X-RAY DIFFRACTIONf_chiral_restr0.043811
X-RAY DIFFRACTIONf_plane_restr0.003924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2501-3.42140.37141190.3562629X-RAY DIFFRACTION100
3.4214-3.63570.33011340.29832632X-RAY DIFFRACTION100
3.6357-3.91630.27781440.25752617X-RAY DIFFRACTION100
3.9163-4.31010.2341360.21192655X-RAY DIFFRACTION100
4.3101-4.93320.23781310.20382695X-RAY DIFFRACTION100
4.9332-6.21290.22821560.21312705X-RAY DIFFRACTION100
6.2129-46.12510.18891540.17632901X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8870.6368-0.81415.58931.15934.880.06950.1635-0.2997-0.19380.0533-0.19960.40160.1665-0.22431.00020.05260.06070.9292-0.07310.979427.874916.1723-29.0949
22.0699-0.58920.59765.7371.32093.41980.2604-0.02060.4546-0.2248-0.1062-0.7791-0.32040.7589-0.22570.9096-0.11860.16911.1066-0.07690.982935.416730.7065-23.9073
34.25222.22950.80343.26190.34551.91880.332-0.1939-0.0397-0.0682-0.11930.05080.29350.0409-0.08411.0436-0.08110.18070.766-0.07090.87598.811822.7915-25.1984
46.26363.05663.02814.94331.53673.51340.0870.20941.27410.06240.09540.2781-0.73780.4820.08551.176-0.11560.20880.8785-0.09721.189118.314641.7727-21.2029
52.5862-0.82460.6145.0206-1.24392.3055-0.191-0.6245-0.17190.90570.1129-0.72390.03210.8781-0.05221.1044-0.0217-0.0011.4956-0.13381.024241.774322.3997-2.6395
62.3876-1.23341.64882.9107-0.32713.2938-0.5602-0.09670.14680.2509-0.1732-0.5476-0.00210.74660.52440.9628-0.00880.16491.1337-0.06251.224236.24889.9581-48.987
73.7911-0.32351.94873.63991.19432.96080.29160.6850.1382-0.3705-0.0485-0.46190.34860.3939-0.23291.27410.02020.15231.0949-0.14181.095832.69923.3938-69.7612
8-0.0064-0.05170.02870.235-0.12380.0518-0.5478-1.07751.41420.78330.1502-0.0818-0.92910.6516-0.10542.0917-0.1384-0.03161.6477-0.04591.813252.717744.21032.6541
90.0101-0.0067-0.0270.00030.0050.10230.24080.24671.5889-0.30430.862-0.0674-0.59730.47790.21042.49590.0353-0.08512.1421-0.33762.193146.78753.79963.4084
100.0027-0.03560.0110.5387-0.58310.53930.80870.90690.68050.0814-0.1374-3.1286-0.23220.89-0.0132.161-0.20320.26321.83370.01742.155146.731744.2769-11.0391
111.4982.92752.84285.8185.55995.4750.20451.07651.07311.21490.4193-1.58-0.92831.7106-1.3182.10630.07680.07012.3102-0.28021.687247.606538.2259-4.4138
120.03410.0298-0.09990.1035-0.02380.24681.5895-0.99211.24730.99160.31870.8871-2.5276-1.0095-0.75253.3099-0.73960.77351.8539-0.41952.295639.9844.90559.0342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 111 )
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 213 )
3X-RAY DIFFRACTION3chain 'A' and (resid 214 through 327 )
4X-RAY DIFFRACTION4chain 'A' and (resid 328 through 369 )
5X-RAY DIFFRACTION5chain 'A' and (resid 370 through 508 )
6X-RAY DIFFRACTION6chain 'A' and (resid 509 through 553 )
7X-RAY DIFFRACTION7chain 'A' and (resid 554 through 604 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 10 )
9X-RAY DIFFRACTION9chain 'B' and (resid 11 through 17 )
10X-RAY DIFFRACTION10chain 'B' and (resid 18 through 40 )
11X-RAY DIFFRACTION11chain 'B' and (resid 41 through 58 )
12X-RAY DIFFRACTION12chain 'B' and (resid 59 through 65 )

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