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- PDB-7odd: Crystal structure of bovine Hsc70(aa1-554)E213A/D214A in complex ... -

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Basic information

Entry
Database: PDB / ID: 7odd
TitleCrystal structure of bovine Hsc70(aa1-554)E213A/D214A in complex with tricine
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE
Function / homology
Function and homology information


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 uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy ...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 uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Neutrophil degranulation / non-chaperonin molecular chaperone ATPase / : / Prp19 complex / heat shock protein binding / protein folding chaperone / RNA splicing / spliceosomal complex / ATP-dependent protein folding chaperone / mRNA processing / melanosome / presynapse / protein refolding / protein-macromolecule adaptor activity / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein ...Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Alpha-Beta Complex / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Chem-VLS / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.984 Å
AuthorsZehe, M. / Grimm, C. / Sotriffer, C.
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Combined In-Solution Fragment Screening and Crystallographic Binding-Mode Analysis with a Two-Domain Hsp70 Construct.
Authors: Zehe, M. / Kehrein, J. / Schollmayer, C. / Plank, C. / Kovacs, H. / Merino Asumendi, E. / Holzgrabe, U. / Grimm, C. / Sotriffer, C.
History
DepositionApr 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7518
Polymers60,9791
Non-polymers7727
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint4 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.057, 49.073, 87.271
Angle α, β, γ (deg.)90.000, 99.694, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 60978.867 Da / Num. of mol.: 1 / Mutation: E213A, D214A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: HSPA8, HSC70 / Production host: Escherichia coli (E. coli) / References: UniProt: P19120

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Non-polymers , 5 types, 153 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-VLS / N-[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]glycine


Mass: 179.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5 / Details: PEG 8000, TMAO, HEPES-NaOH, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.98→49 Å / Num. obs: 37852 / % possible obs: 98.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 43.94 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.099 / Net I/σ(I): 8.57
Reflection shellResolution: 1.98→2.1 Å / Mean I/σ(I) obs: 8.57 / Num. unique obs: 5867 / CC1/2: 0.36

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Processing

Software
NameVersionClassification
MxCuBEdata collection
Cootmodel building
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FL9

4fl9


Resolution: 1.984→42.63 Å / SU ML: 0.345 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.5108 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 1891 5 %
Rwork0.2251 35914 -
obs0.2262 37805 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.38 Å2
Refinement stepCycle: LAST / Resolution: 1.984→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 47 146 4354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01224273
X-RAY DIFFRACTIONf_angle_d1.5695764
X-RAY DIFFRACTIONf_chiral_restr0.1071658
X-RAY DIFFRACTIONf_plane_restr0.0053748
X-RAY DIFFRACTIONf_dihedral_angle_d19.77771614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.44311230.42082337X-RAY DIFFRACTION89.95
2.03-2.090.45391340.39012540X-RAY DIFFRACTION98.82
2.09-2.150.34411350.36422576X-RAY DIFFRACTION98.65
2.15-2.220.36251360.33392587X-RAY DIFFRACTION99.16
2.22-2.30.37521350.31672554X-RAY DIFFRACTION98.97
2.3-2.390.31541340.30252546X-RAY DIFFRACTION98.75
2.39-2.50.32171370.28322578X-RAY DIFFRACTION98.51
2.5-2.630.29321350.26622570X-RAY DIFFRACTION98.47
2.63-2.80.2941360.26812600X-RAY DIFFRACTION99.42
2.8-3.010.29121350.25212571X-RAY DIFFRACTION99.01
3.01-3.320.26041360.23572579X-RAY DIFFRACTION98.62
3.32-3.80.23611370.20062596X-RAY DIFFRACTION98.99
3.8-4.780.17641370.16842616X-RAY DIFFRACTION98.5
4.78-42.630.18211410.18062664X-RAY DIFFRACTION98.04
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)
12.13960195202-0.572293598280.6053115167682.03169042806-1.974448556685.168959050890.0672448449885-0.364947542748-0.0839276453496-0.1080446221560.02126863214050.01692482122510.910024331617-0.27079038623-0.03568619632020.446130262685-0.156752108522-0.00792444187010.413601314327-0.01908076035460.358385779178-16.4936554106-16.6258990773-9.17821958128
23.36459289902-0.611878945011-0.5862172078341.27048584726-0.1272926890191.211231034240.0243962677098-0.01947390607460.0800380596984-0.0113218083379-0.0763368947522-0.01055254718430.1767538199660.2005134079090.05367209134840.362334770407-0.1133546296820.002469441455360.2875215785760.004994813523240.252132470789-2.45510325347-9.3875658769-22.770673637
32.43546185332-1.245683987620.1024204595242.63303549736-1.295931720692.788537926920.1551428373950.1415285044550.000785142925590.271944605584-0.21320753231-0.301415390238-0.424977603440.4974328347580.007457315051110.282107285556-0.0863156785583-0.01474576080420.3645943424370.03299679272750.362704045476-45.7717059545-3.7073880287-38.6425577479
43.18243697318-1.152629805040.3039378930952.25857916621-1.033434856482.916201649170.1121710718950.3550462999450.307681597776-0.12216746069-0.227285013-0.0985749232026-0.440627738723-0.06178304916620.06586257412480.3927067706790.02665357254770.03962046464880.3499271238750.04710049275220.434624548934-52.17085879222.29558706887-45.9902391625
51.139898807991.157418861851.377915236931.454506104950.7523686606083.19724502888-0.547483951095-0.2367869768750.6974167172370.337202218017-1.010463137641.08478207329-0.843209139585-0.240174814481.10381389820.771709421699-0.03817559425190.2111548124351.26927373359-0.3737143592270.84988740383-48.4101362113.75395793467-22.2158463493
65.96955346464-2.92494322759-1.573752123242.158322627522.964389848277.542126344690.00262539583282-0.544853848109-0.7132313253591.205741467020.676426433178-0.0423991621450.0440178884718-0.449100538162-0.6941038598310.478425184210.00807075958215-0.02340090759980.5882741167610.01408428426760.660174150779-36.5397715695-7.05441531628-22.1401312426
75.171173868680.5905884339471.98772998656.186269409793.772448680652.821924454630.151604145660.355868198139-0.547848862642-1.908572215820.470326424326-0.566142201806-0.7691772541110.376278340056-0.598663244440.6714406312150.01829729001350.09318346343690.538589156289-0.09544008483980.761132634703-34.6780982655-16.2270241801-36.3408883348
83.37238623102-0.277983805682-1.043014222243.71451233757-0.8280353158075.49543568063-0.1849190885090.270719080856-1.12665537127-0.552401606395-0.348435680893-1.361983677530.8836707280.09196438390610.553120115670.5194074224670.02869060641530.05429596995480.370842811085-0.02241873734030.715929499172-49.3620254069-14.7890558663-42.7838829782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 204 )
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 383 )
3X-RAY DIFFRACTION3chain 'A' and (resid 395 through 461 )
4X-RAY DIFFRACTION4chain 'A' and (resid 462 through 503 )
5X-RAY DIFFRACTION5chain 'A' and (resid 504 through 511 )
6X-RAY DIFFRACTION6chain 'A' and (resid 512 through 524 )
7X-RAY DIFFRACTION7chain 'A' and (resid 525 through 535 )
8X-RAY DIFFRACTION8chain 'A' and (resid 536 through 553 )

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