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- PDB-6k39: Structural analysis of AIMP2-DX2 and HSP70 interaction -

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Basic information

Entry
Database: PDB / ID: 6k39
TitleStructural analysis of AIMP2-DX2 and HSP70 interaction
ComponentsHeat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
KeywordsCHAPERONE / HSP70 / AIMP2-DX2 / substrate binding domain
Function / homology
Function and homology information


type II pneumocyte differentiation / : / Selenoamino acid metabolism / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / death receptor agonist activity / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway ...type II pneumocyte differentiation / : / Selenoamino acid metabolism / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / death receptor agonist activity / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / regulation of mitotic spindle assembly / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / : / regulation of protein ubiquitination / HSF1-dependent transactivation / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Mitochondrial unfolded protein response (UPRmt) / Attenuation phase / chaperone-mediated protein complex assembly / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / transcription regulator inhibitor activity / inclusion body / heat shock protein binding / positive regulation of protein ubiquitination / negative regulation of protein ubiquitination / centriole / protein folding chaperone / Transcriptional and post-translational regulation of MITF-M expression and activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / positive regulation of interleukin-8 production / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / G protein-coupled receptor binding / positive regulation of NF-kappaB transcription factor activity / negative regulation of cell growth / PKR-mediated signaling / histone deacetylase binding / disordered domain specific binding / transcription corepressor activity / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of neuron apoptotic process / cellular response to heat / virus receptor activity / protein refolding / cellular response to oxidative stress / protein-containing complex assembly / blood microparticle / vesicle / molecular adaptor activity / ficolin-1-rich granule lumen / protein ubiquitination / protein stabilization / nuclear speck / cadherin binding / translation / receptor ligand activity / ribonucleoprotein complex / signaling receptor binding / negative regulation of cell population proliferation / focal adhesion / ubiquitin protein ligase binding / apoptotic process / centrosome / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane
Similarity search - Function
AIMP2, lysyl-tRNA synthetase binding domain / AIMP2, thioredoxin-like domain / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / AIMP2 lysyl-tRNA synthetase binding domain / Thioredoxin-like domain / 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. ...AIMP2, lysyl-tRNA synthetase binding domain / AIMP2, thioredoxin-like domain / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / AIMP2 lysyl-tRNA synthetase binding domain / Thioredoxin-like domain / 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 / Glutathione S-transferase, C-terminal domain / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal domain superfamily / ATPase, nucleotide binding domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Heat shock 70 kDa protein 1A / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3981426881 Å
AuthorsCho, H.Y. / Son, S.Y. / Jeon, Y.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2013M3A6A4045160 Korea, Republic Of
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Targeting the interaction of AIMP2-DX2 with HSP70 suppresses cancer development.
Authors: Lim, S. / Cho, H.Y. / Kim, D.G. / Roh, Y. / Son, S.Y. / Mushtaq, A.U. / Kim, M. / Bhattarai, D. / Sivaraman, A. / Lee, Y. / Lee, J. / Yang, W.S. / Kim, H.K. / Kim, M.H. / Lee, K. / Jeon, Y.H. / Kim, S.
History
DepositionMay 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.3Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Nov 22, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
B: Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2


Theoretical massNumber of molelcules
Total (without water)33,4762
Polymers33,4762
Non-polymers00
Water7,819434
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.111, 111.581, 45.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 395 - 545 / Label seq-ID: 2 - 152

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22(chain 'B' and resid 395 through 545)BB

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Components

#1: Protein Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Heat shock 70 kDa protein 1 / HSP70.1 / Multisynthase complex auxiliary component p38 / Protein JTV-1


Mass: 16737.826 Da / Num. of mol.: 2
Fragment: HSP70 substrate binding domain/peptide sequence of DX2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSP72, HSPA1, HSX70, AIMP2, JTV1, PRO0992 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21_CodonPlus(DE3)-RIPL / References: UniProt: P0DMV8, UniProt: Q13155
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG1500, Succinic Acid, Sodium Dihydrogen Phosphate, Glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 2, 2018 / Details: In-vacuum Undulator 20 (IVU 20), 1.8m
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.398→25.632435142 Å / Num. obs: 57251 / % possible obs: 99.48 % / Redundancy: 7.8 % / Biso Wilson estimate: 13.7390102197 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09201 / Rpim(I) all: 0.03537 / Rrim(I) all: 0.09874 / Net I/σ(I): 15.56
Reflection shellResolution: 1.398→1.448 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.7764 / Mean I/σ(I) obs: 4.81 / Num. unique obs: 5431 / CC1/2: 0.849 / Rpim(I) all: 0.3044 / Rrim(I) all: 0.8353 / % possible all: 95.65

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JPV

6jpv


Resolution: 1.3981426881→25.632435142 Å / SU ML: 0.114849978372 / Cross valid method: FREE R-VALUE / σ(F): 1.3552173263 / Phase error: 18.3175273733
RfactorNum. reflection% reflectionSelection details
Rfree0.191814330224 2000 3.49937886025 %Random selection
Rwork0.167303286504 ---
obs0.168173872142 57153 99.5038128069 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.7184850317 Å2
Refinement stepCycle: LAST / Resolution: 1.3981426881→25.632435142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 0 434 2776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006686864201632372
X-RAY DIFFRACTIONf_angle_d0.8967459949773210
X-RAY DIFFRACTIONf_chiral_restr0.0786081960378373
X-RAY DIFFRACTIONf_plane_restr0.00621348773352427
X-RAY DIFFRACTIONf_dihedral_angle_d18.860180485920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3981-1.43310.2391099599781340.2207262901943694X-RAY DIFFRACTION94.1929133858
1.4331-1.47180.213335157661420.1996689578823895X-RAY DIFFRACTION99.4090125585
1.4718-1.51520.2164335866781410.1944262653523888X-RAY DIFFRACTION99.9008182494
1.5152-1.56410.2246902986621410.1871754532283914X-RAY DIFFRACTION100
1.5641-1.61990.176363103991410.1811456129873895X-RAY DIFFRACTION100
1.6199-1.68480.224397528471420.1797637248843923X-RAY DIFFRACTION100
1.6848-1.76150.2033255386481430.1761522628093930X-RAY DIFFRACTION99.9754540992
1.7615-1.85430.2014565138471410.176647720283912X-RAY DIFFRACTION99.9753330044
1.8543-1.97040.2037358946561440.1728035378163934X-RAY DIFFRACTION100
1.9704-2.12250.1835321250951430.1625214070683959X-RAY DIFFRACTION100
2.1225-2.3360.1754581712291440.156490468253976X-RAY DIFFRACTION100
2.336-2.67370.1885065984411460.1610003766924017X-RAY DIFFRACTION99.9759846302
2.6737-3.36740.1952235130511450.1638737170294010X-RAY DIFFRACTION99.951888381
3.3674-25.63670.1759882754761530.1558412142324206X-RAY DIFFRACTION99.6342857143
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)
11.9792896979-3.32400930656-1.583046555837.131288123221.104612016853.24806061606-0.0870556554987-0.3395438572710.4760256229650.1236389689580.236708210476-0.516382305736-0.1245882958020.161398530664-0.09042664617610.126421425224-0.008226721777510.01014439096830.112722560593-0.03046635700540.123747745991158.430990849-12.0060367903192.041299128
25.654387539712.182757210752.321750934784.976098076731.989640219215.71625074557-0.0245975379083-0.04176450085950.1790698396650.1640806365030.0347107522005-0.0725803783741-0.0642529504810.246609012515-0.01886716893370.05754588226560.02563033347590.005110169532740.06386660011490.001203374018820.0472611218338132.24705488718.7206485434202.315850015
35.608467953224.585971027921.128288169723.774370142550.9748825500271.677408760860.110753367377-0.0866566751389-0.1717193737280.08068782412390.024443186815-0.227565600380.07024969094090.431705550775-0.1806404444030.08560715952350.0020780770337-0.01326933373620.180467058656-0.01498804141430.106012975663137.65856152419.61581304201.61325036
41.485036857180.821290835620.9246570810351.613478487640.8474924022791.411900922570.0798275213533-0.0395778772322-0.05373403677360.08591865181450.00517623084568-0.01804715773640.113294041009-0.0600316211214-0.08152748065190.09049647684080.0151352240843-0.004292966067460.08020117697280.0133819536160.105171612832126.58013126315.0248617356195.975050225
56.96086082241-0.1925839146072.794740896690.6100317669710.2397171564664.599658501080.121749069077-0.3301931707140.01156819628130.0468199810344-0.03461484438070.2602365801320.0782250113466-0.611973772342-0.2379356350920.1209658275810.02018105380660.0155101267080.05292333647730.02077984098220.140623705737121.01358283122.1097391275197.477714374
62.675153143822.826735903562.162610872755.231391816783.889152762574.30441023255-0.06795523026330.08528000797240.041094352361-0.2344630628790.146454004515-0.0227353316926-0.1537588822350.112603989003-0.06387289823910.08552324544960.01518248474220.01610125158830.08582446547670.01047541058770.0810762692865128.32473870521.809835528189.106725801
72.163912200771.129791394743.316535097473.455471321022.990281780498.481959951990.08295849464920.08222609248410.0352374259807-0.3406215139740.05011090299980.0522169792215-0.0649980460604-0.0272523197798-0.1325042265710.1320616820260.02496761746380.02215424807270.09771038164290.02365648242650.115373056398124.86249517426.2279033698187.700655355
83.86328516761-3.759406710092.443975852233.98408280052-3.543320441115.520778206940.0298531117483-0.701344196878-0.3861056656180.3533199917910.3239064572050.303075616579-0.0218386229837-0.305553303365-0.354877060590.175295598292-0.0223822327848-0.02162039062740.1964692772040.04098566111690.174573836907133.24504265722.7353557411214.467855438
95.704110855434.278423548064.292697337416.744325102524.886833513784.015490273610.3177607403250.0341545649692-0.5517942226780.9487248244970.053366543206-0.5174863120230.7175516825810.313908175079-0.2837953938960.356900464032-0.00639878851024-0.09717206084210.1689770984460.01804192509180.301366313342133.1405510363.1356743989207.860962673
106.899210429034.20549763328-1.325379788086.640727169141.144310452984.26630113845-0.3237360633930.610685167030.391659367264-0.2504303005090.3616299238310.454385432158-0.078441507083-0.3742990428290.007876708174410.0966656393029-0.011809961493-0.007411210668920.1454773159370.04829032932840.119982831627121.376610525-3.13444884748195.631050129
115.97670095881-4.094057867461.600738600273.56156818952-1.181777148521.774614323470.08869522930480.092052049393-0.0903921016809-0.146891896504-0.03189079968670.07609621692650.0690512410228-0.045170782036-0.06049439947940.0706721593988-0.01647395830950.003904116365240.0709346068575-0.006624479647720.0685906820065146.75569493611.5564608181185.575402106
121.20214325701-0.9435459783310.5108186660362.68977008413-1.035206268941.26702671397-0.007666210964510.0134058196052-0.02034263040370.1154452627690.0402939494359-0.0321091893672-0.0332127861931-0.0261323773166-0.02467712909360.0556980599743-0.01674593117350.009010606372140.07472545510470.0002572093087540.0796766340404155.25126932110.4892058834194.188291109
132.12183161389-0.5317114371822.852610964093.09858244604-2.400472617694.63971405616-0.001108335254230.04741266125980.09364717484890.122322420258-0.005331685280030.01119595232050.002721556750240.0500142357986-0.03413615833910.0839393241033-0.00745990235740.02005098418220.09198363606030.008693096270110.106616507591154.73455775319.8997935835190.083958667
146.605014481614.793512800421.541094807243.759375434840.6132113470822.21532445586-0.3863170640540.484547465913-0.234471675587-0.9309416541570.615519091462-0.5599146024790.03254656368980.232102438933-0.1889759843710.283982250907-0.01369135444940.01148386505850.198795287662-0.05022411959320.164239295283147.47432920110.6097430832170.518544894
154.71692612965-3.056889497373.983246320919.83606778407-4.802964194394.15047219689-0.184927126293-0.153823747688-0.0616473361037-0.2885024919880.100775874138-0.196563191328-0.104231960929-0.6505501336720.1068060760340.1921703505090.0133498529902-0.000820707487870.1607561925380.0004068435073570.179397321781147.255019796-4.33238902543180.122678539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 536 through 545 )
2X-RAY DIFFRACTION2chain 'A' and (resid 395 through 408 )
3X-RAY DIFFRACTION3chain 'A' and (resid 409 through 421 )
4X-RAY DIFFRACTION4chain 'A' and (resid 422 through 453 )
5X-RAY DIFFRACTION5chain 'A' and (resid 454 through 462 )
6X-RAY DIFFRACTION6chain 'A' and (resid 463 through 492 )
7X-RAY DIFFRACTION7chain 'A' and (resid 493 through 503 )
8X-RAY DIFFRACTION8chain 'A' and (resid 504 through 524 )
9X-RAY DIFFRACTION9chain 'A' and (resid 525 through 535 )
10X-RAY DIFFRACTION10chain 'A' and (resid 536 through 545 )
11X-RAY DIFFRACTION11chain 'B' and (resid 395 through 421 )
12X-RAY DIFFRACTION12chain 'B' and (resid 422 through 492 )
13X-RAY DIFFRACTION13chain 'B' and (resid 493 through 511 )
14X-RAY DIFFRACTION14chain 'B' and (resid 512 through 524 )
15X-RAY DIFFRACTION15chain 'B' and (resid 525 through 535 )

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