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- PDB-5bpm: Crystal structure of unhydrolyzed ATP bound human Hsp70 NBD doubl... -

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Basic information

Entry
Database: PDB / ID: 5bpm
TitleCrystal structure of unhydrolyzed ATP bound human Hsp70 NBD double mutant E268Q+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 / 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 / death receptor agonist activity / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation ...positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / 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 / death receptor agonist activity / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation / misfolded protein binding / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein complex assembly / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / inclusion body / ATP metabolic process / protein folding chaperone / 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 / G protein-coupled receptor binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of interleukin-8 production / 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 / cellular response to heat / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / protein refolding / blood microparticle / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / protein stabilization / nuclear speck / cadherin binding / ribonucleoprotein complex / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
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'-TRIPHOSPHATE / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)43,3556
Polymers42,7291
Non-polymers6255
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-48 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.466, 64.278, 144.860
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: 42729.355 Da / Num. of mol.: 1 / Mutation: E268Q, 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) / Variant (production host): RIL / References: UniProt: P0DMV8

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Non-polymers , 5 types, 423 molecules

#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
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: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.83→48.076 Å / Num. all: 38987 / Num. obs: 38938 / % possible obs: 99.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 7.9
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 4 % / Rmerge(I) obs: 1.076 / % possible all: 92.4

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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: 1.83→48.076 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 1998 5.13 %Random selection
Rwork0.1708 ---
obs0.1735 38927 98.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→48.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 35 418 3385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123041
X-RAY DIFFRACTIONf_angle_d1.2794121
X-RAY DIFFRACTIONf_dihedral_angle_d15.1921133
X-RAY DIFFRACTIONf_chiral_restr0.061466
X-RAY DIFFRACTIONf_plane_restr0.007537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8268-1.87250.2948980.25292491X-RAY DIFFRACTION93
1.8725-1.92310.26481540.24112585X-RAY DIFFRACTION99
1.9231-1.97970.27171490.21912617X-RAY DIFFRACTION99
1.9797-2.04360.2661420.20642607X-RAY DIFFRACTION100
2.0436-2.11660.24021370.18452625X-RAY DIFFRACTION99
2.1166-2.20140.25341200.17622657X-RAY DIFFRACTION99
2.2014-2.30160.22861240.17342609X-RAY DIFFRACTION99
2.3016-2.42290.24851480.17132630X-RAY DIFFRACTION100
2.4229-2.57470.26651360.16662679X-RAY DIFFRACTION100
2.5747-2.77350.24091390.17022638X-RAY DIFFRACTION100
2.7735-3.05250.23721110.17432699X-RAY DIFFRACTION99
3.0525-3.49410.24241430.17082656X-RAY DIFFRACTION99
3.4941-4.40180.18991670.14042698X-RAY DIFFRACTION99
4.4018-48.070.17191270.14762843X-RAY DIFFRACTION98
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)
10.2957-0.0962-0.02980.8001-0.01130.8422-0.016-0.0229-0.06730.05910.0140.04410.0086-0.00470.00010.0702-0.0015-00.07280.01030.08531.4298-25.181822.9945
20.30370.05890.20570.29820.20210.21390.2069-0.44470.160.0417-0.2180.0961-0.086-0.24750.03290.1723-0.05980.04970.2409-0.07260.170813.02220.528623.1047
30.3841-0.0635-0.20080.30240.130.23120.02790.0595-0.0499-0.00510.0224-0.0585-0.0519-0.028800.0973-0.0067-0.00370.1034-0.00350.09448.848-17.79715.5164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 229 )
2X-RAY DIFFRACTION2chain 'A' and (resid 230 through 292 )
3X-RAY DIFFRACTION3chain 'A' and (resid 293 through 381 )

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