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- PDB-4jnf: Allosteric opening of the polypeptide-binding site when an Hsp70 ... -

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Basic information

Entry
Database: PDB / ID: 4jnf
TitleAllosteric opening of the polypeptide-binding site when an Hsp70 binds ATP
ComponentsHsp70 CHAPERONE DnaK
KeywordsCHAPERONE / DnaK / 70kDa heat shock protein (Hsp70) / Substrate Binding Domain (SBD)
Function / homology
Function and homology information


stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone / unfolded protein binding / response to heat / protein-folding chaperone binding / protein refolding / protein-containing complex assembly / DNA replication / ATP hydrolysis activity / protein-containing complex / zinc ion binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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, nucleotide binding domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.621 Å
AuthorsQi, R. / Sarbeng, E.B. / Liu, Q. / Le, K.Q. / Xu, X. / Xu, H. / Yang, J. / Wong, J.L. / Vorvis, C. / Hendrickson, W.A. ...Qi, R. / Sarbeng, E.B. / Liu, Q. / Le, K.Q. / Xu, X. / Xu, H. / Yang, J. / Wong, J.L. / Vorvis, C. / Hendrickson, W.A. / Zhou, L. / Liu, Q.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP.
Authors: Qi, R. / Sarbeng, E.B. / Liu, Q. / Le, K.Q. / Xu, X. / Xu, H. / Yang, J. / Wong, J.L. / Vorvis, C. / Hendrickson, W.A. / Zhou, L. / Liu, Q.
History
DepositionMar 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hsp70 CHAPERONE DnaK


Theoretical massNumber of molelcules
Total (without water)24,0011
Polymers24,0011
Non-polymers00
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.980, 66.980, 128.759
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-984-

HOH

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Components

#1: Protein Hsp70 CHAPERONE DnaK


Mass: 24001.074 Da / Num. of mol.: 1 / Fragment: Substrate binding domain, unp RESIDUES 389-610 / Mutation: N432M,Q433G,S434G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pSMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.47 Å3/Da / Density % sol: 64.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 17, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. all: 42873 / Num. obs: 42873 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.62→1.65 Å / % possible all: 86.8

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Processing

Software
NameClassification
MAR345data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DKX

1dkx


Resolution: 1.621→29.711 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 18.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 1969 4.64 %Random
Rwork0.1913 ---
all0.1924 42464 --
obs0.1924 42464 98.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.621→29.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 0 321 1928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061621
X-RAY DIFFRACTIONf_angle_d0.8442183
X-RAY DIFFRACTIONf_dihedral_angle_d13.864621
X-RAY DIFFRACTIONf_chiral_restr0.055259
X-RAY DIFFRACTIONf_plane_restr0.003289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6206-1.66120.25621290.22992616X-RAY DIFFRACTION91
1.6612-1.70610.26511390.24362813X-RAY DIFFRACTION97
1.7061-1.75630.271360.21522853X-RAY DIFFRACTION98
1.7563-1.81290.19661420.19692880X-RAY DIFFRACTION99
1.8129-1.87770.21321390.18382832X-RAY DIFFRACTION99
1.8777-1.95290.17641410.16752894X-RAY DIFFRACTION99
1.9529-2.04180.18861480.18392914X-RAY DIFFRACTION99
2.0418-2.14940.2111370.17572895X-RAY DIFFRACTION100
2.1494-2.2840.19161390.17742925X-RAY DIFFRACTION100
2.284-2.46030.19091440.18142963X-RAY DIFFRACTION100
2.4603-2.70770.22651380.19292951X-RAY DIFFRACTION100
2.7077-3.09920.22031430.19922964X-RAY DIFFRACTION100
3.0992-3.90320.20711440.18193013X-RAY DIFFRACTION100
3.9032-29.71550.23841500.20272982X-RAY DIFFRACTION95
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)
10.03360.03230.02780.1993-0.02030.1718-0.0688-0.0615-0.03430.0655-0.0203-0.04210.0673-0.0324-0.24480.20350.11580.03180.14730.04780.104919.201122.864619.7264
20.0585-0.0128-0.04870.4132-0.20370.97220.02580.0446-0.09140.05660.00520.17350.0302-0.17920.24220.18510.06970.02480.15640.00560.127910.954326.826811.8997
30.0101-0.00620.00990.0039-0.0060.0087-0.0560.02260.0916-0.0814-0.07490.1583-0.0123-0.302400.18590.014-0.04120.3348-0.02680.4424-3.734825.631113.4005
40.3370.16770.22350.25630.15650.1771-0.0348-0.25930.13780.36980.05460.2309-0.1136-0.25430.04880.26950.09780.0980.20710.05490.23175.068824.993122.0932
50.0299-0.00040.03620.09970.0240.06540.023-0.05970.07550.0014-0.04260.0126-0.0181-0.0536-0.04640.24570.08010.15290.40170.08530.62-5.30627.698822.7046
61.3089-0.5614-0.14930.30250.25480.7202-0.1348-0.0688-0.51880.0358-0.04050.23570.55950.13150.23260.27670.22220.09560.19430.03290.234220.132817.550910.8617
70.70290.3149-0.07020.79290.08610.54480.0487-0.06560.17710.07480.03610.2181-0.12230.0488-0.00280.19780.08260.05440.13270.01770.120210.588742.47667.7344
80.1363-0.0953-0.05640.07360.00170.23680.0054-0.0173-0.0297-0.0032-0.0190.03620.0131-0.0270.02340.35590.22180.12460.35170.03390.6005-12.21856.599510.5129
90.07850.09860.02640.55510.06120.13190.02420.06520.0991-0.01290.01970.3991-0.2907-0.24060.11890.29760.28220.07960.15840.03580.23351.403454.88142.1733
100.24760.08160.08670.02820.02910.0312-0.0078-0.30140.06280.34550.15660.3925-0.3608-0.270.07670.34150.1910.14790.18560.06030.2253.281756.178411.8714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 388:421)
2X-RAY DIFFRACTION2(chain A and resid 422:455)
3X-RAY DIFFRACTION3(chain A and resid 456:464)
4X-RAY DIFFRACTION4(chain A and resid 465:489)
5X-RAY DIFFRACTION5(chain A and resid 490:496)
6X-RAY DIFFRACTION6(chain A and resid 497:520)
7X-RAY DIFFRACTION7(chain A and resid 521:549)
8X-RAY DIFFRACTION8(chain A and resid 550:558)
9X-RAY DIFFRACTION9(chain A and resid 559:579)
10X-RAY DIFFRACTION10(chain A and resid 580:604)

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