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- PDB-5bn9: Crystal structure of ADP bound human Hsp70 NBD mutant R272K. -

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Basic information

Entry
Database: PDB / ID: 5bn9
TitleCrystal structure of ADP bound human Hsp70 NBD mutant R272K.
ComponentsHeat shock 70 kDa protein 1A
KeywordsHYDROLASE / ATP hydrolysis activity
Function / homology
Function and homology information


positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity ...positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / protein folding chaperone / inclusion body / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of interleukin-8 production / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / protein stabilization / blood microparticle / nuclear speck / ribonucleoprotein complex / cadherin binding / negative regulation of cell population proliferation / focal adhesion / signaling receptor binding / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Defensin A-like - #30 / 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 ...Defensin A-like - #30 / 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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.689 Å
AuthorsNarayanan, D. / Engh, R.A.
Funding support Norway, 1items
OrganizationGrant numberCountry
FRINAT191303 Norway
CitationJournal: To Be Published
Title: Nucleotide binding to variants of the HSP70-NBD.
Authors: Narayanan, D. / Pflug, A. / Christopeit, T. / Kyomuhendo, P. / Engh, R.A.
History
DepositionMay 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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: Heat shock 70 kDa protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5496
Polymers42,7301
Non-polymers8195
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-19 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.933, 63.210, 143.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Heat shock 70 kDa protein 1A / Heat shock 70 kDa protein 1 / HSP70.1


Mass: 42730.340 Da / Num. of mol.: 1 / Mutation: R272K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSPA1, HSX70 / Plasmid: pET28b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DMV8

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Non-polymers , 6 types, 250 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25 % PEG-3350 W/V, 0.1 M HEPES / PH range: 7.0 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.689→47.48 Å / Num. obs: 46875 / % possible obs: 97.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.05569 / Net I/σ(I): 16.89
Reflection shellResolution: 1.689→1.75 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.5899 / Mean I/σ(I) obs: 1.94 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Coot0.7.1model building
MOLREP11phasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ATV

3atv


Resolution: 1.689→47.48 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2000 4.46 %Random selection
Rwork0.179 ---
obs0.18 46836 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.689→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 49 245 3226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063074
X-RAY DIFFRACTIONf_angle_d1.0664165
X-RAY DIFFRACTIONf_dihedral_angle_d14.4741151
X-RAY DIFFRACTIONf_chiral_restr0.041467
X-RAY DIFFRACTIONf_plane_restr0.006542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.689-1.73170.27511250.25572788X-RAY DIFFRACTION87
1.7317-1.77850.22361390.21953143X-RAY DIFFRACTION97
1.7785-1.83090.24341430.20613209X-RAY DIFFRACTION100
1.8309-1.890.26511440.19573209X-RAY DIFFRACTION100
1.89-1.95750.20231430.18713205X-RAY DIFFRACTION99
1.9575-2.03590.23511440.18453225X-RAY DIFFRACTION100
2.0359-2.12860.22781430.18213214X-RAY DIFFRACTION99
2.1286-2.24080.19771440.17333227X-RAY DIFFRACTION99
2.2408-2.38120.21551440.18423229X-RAY DIFFRACTION99
2.3812-2.5650.20841440.18913231X-RAY DIFFRACTION99
2.565-2.82310.23491440.18783228X-RAY DIFFRACTION99
2.8231-3.23150.20371460.19393267X-RAY DIFFRACTION99
3.2315-4.07080.1771470.16473280X-RAY DIFFRACTION98
4.0708-47.480.15491500.14973380X-RAY DIFFRACTION96
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)
10.91430.05510.3371.93850.07811.5075-0.00730.0158-0.046-0.08590.08050.2704-0.001-0.3662-0.04990.1084-0.0064-0.00710.20710.03320.156336.952772.167516.2542
20.6639-0.37230.73661.22180.31512.09230.0032-0.07090.11240.2427-0.0040.153-0.2904-0.2235-0.01340.23920.0240.0530.14440.00540.155842.910781.507629.8612
31.6404-0.2707-0.12882.0933-0.62551.73350.0155-0.13210.02520.3181-0.0219-0.1948-0.06560.26940.00840.166-0.0059-0.04140.16310.00520.153857.294971.69134.5313
40.70960.043-0.10031.5674-0.11451.7325-0.0356-0.06610.00980.19630.05710.1096-0.0621-0.1756-0.00430.13660.02050.02670.14740.02880.133741.652669.220328.2012
50.3299-0.1334-0.05270.5187-0.25931.1916-0.07590.0195-0.1252-0.08550.09530.04460.2934-0.0601-0.01740.1684-0.01610.01990.11590.01430.163844.410961.680820.5545
61.6906-0.15490.38841.61440.121.51760.11840.0108-0.2788-0.006-0.0177-0.00670.2864-0.0627-0.07220.1681-0.0194-0.00570.13840.0060.165551.922765.25715.3951
71.60610.33520.85731.9270.64342.41050.1155-0.30340.27270.0907-0.10670.0873-0.4383-0.1349-0.01450.2368-0.02970.05770.2138-0.06850.204958.959295.250921.1961
81.32450.7579-0.07851.69920.58251.36590.008-0.0039-0.1679-0.06710.0265-0.20680.0640.0846-0.02980.13370.00930.01080.14640.00390.161159.255472.72083.4919
91.33140.1698-0.71880.36-0.55271.0052-0.0720.2213-0.0033-0.07270.1185-0.00140.0956-0.1283-0.04630.1272-0.018-0.00210.1517-0.00080.124347.47574.13834.7228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 4 THROUGH 28 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 29 THROUGH 58 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 59 THROUGH 109 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 110 THROUGH 151 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 152 THROUGH 182 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 183 THROUGH 229 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 230 THROUGH 306 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 307 THROUGH 343 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 344 THROUGH 382 )

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