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- PDB-8ssv: Crystal structure of Grp94 N-terminal domain bound to the purine ... -

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Basic information

Entry
Database: PDB / ID: 8ssv
TitleCrystal structure of Grp94 N-terminal domain bound to the purine inhibitor PU-H71.
ComponentsEndoplasmin
KeywordsCHAPERONE / Inhibitor / GRP94
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / unfolded protein binding ...Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / unfolded protein binding / melanosome / protein folding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding
Similarity search - Function
Endoplasmic reticulum targeting sequence. / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase ...Endoplasmic reticulum targeting sequence. / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ACETATE ION / Chem-H71 / DI(HYDROXYETHYL)ETHER / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsQue, N.L.S. / Gewirth, D.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA186866 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA095130 United States
CitationJournal: Proteins / Year: 2025
Title: Selective Inhibition of hsp90 Paralogs: Uncovering the Role of Helix 1 in Grp94-Selective Ligand Binding.
Authors: Que, N.L.S. / Seidler, P.M. / Aw, W.J. / Chiosis, G. / Gewirth, D.T.
History
DepositionMay 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmin
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,30516
Polymers53,0282
Non-polymers2,27714
Water3,549197
1
A: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6496
Polymers26,5141
Non-polymers1,1355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,65510
Polymers26,5141
Non-polymers1,1419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.902, 65.429, 75.376
Angle α, β, γ (deg.)90.000, 95.200, 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, 2 molecules AB

#1: Protein Endoplasmin / 94 kDa glucose-regulated protein / GRP-94 / Heat shock protein 90 kDa beta member 1


Mass: 26514.012 Da / Num. of mol.: 2 / Mutation: Mutated residues 287-327 into GGGG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: HSP90B1, GRP94, TRA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 STAR (DE3) / References: UniProt: P41148

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Non-polymers , 7 types, 211 molecules

#2: Chemical ChemComp-H71 / 8-[(6-IODO-1,3-BENZODIOXOL-5-YL)THIO]-9-[3-(ISOPROPYLAMINO)PROPYL]-9H-PURIN-6-AMINE


Mass: 512.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21IN6O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 400, Calcium acetate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.72→75.07 Å / Num. obs: 23864 / % possible obs: 91.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 21.27 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.051 / Rsym value: 0.106 / Net I/σ(I): 8.9
Reflection shellResolution: 1.72→1.93 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1193 / CC1/2: 0.655 / % possible all: 66.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→75.07 Å / SU ML: 0.2453 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.9439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2516 1192 5 %
Rwork0.2089 22665 -
obs0.2111 23857 44.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.04 Å2
Refinement stepCycle: LAST / Resolution: 1.72→75.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 113 197 3351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643254
X-RAY DIFFRACTIONf_angle_d0.9154407
X-RAY DIFFRACTIONf_chiral_restr0.0535512
X-RAY DIFFRACTIONf_plane_restr0.005556
X-RAY DIFFRACTIONf_dihedral_angle_d10.0564479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.790.4260.309152X-RAY DIFFRACTION2.66
1.79-1.870.305230.272459X-RAY DIFFRACTION8.15
1.87-1.970.2836360.2613905X-RAY DIFFRACTION15.9
1.97-2.090.2827980.25271639X-RAY DIFFRACTION29.19
2.09-2.250.22571120.2412274X-RAY DIFFRACTION39.98
2.25-2.480.28941600.23592806X-RAY DIFFRACTION49.82
2.48-2.830.28721800.22913648X-RAY DIFFRACTION64.1
2.84-3.570.26432770.20235057X-RAY DIFFRACTION88.93
3.57-75.070.22563000.19285725X-RAY DIFFRACTION98.71
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)
10.308940084853-0.017126323054-0.4434374036451.38319462271-0.3138441057431.259332949920.010861007965-0.151284851624-0.1459357352620.226956432043-0.0398941838762-0.1664449884580.2761809083630.3262018123310.04362831536180.1332777356880.05468749679010.006935554566080.005118187126990.03308584119350.05330038547333.49350692489-10.560231125234.4514185081
24.107269856871.235714328682.168977375813.42683677225-0.3061363367843.01049359256-0.3279341254550.261988853011-0.4958771429150.0666497734631-0.0866233299271-0.4165514692380.135285927281-0.0788465030691-0.009613196569650.1474689872030.0698033537723-0.02212275665270.4028945270850.02024988846630.53983304873114.5082476653-17.336231981935.381887483
30.7888326644010.066712624403-0.1053720082371.234573009110.2273780160521.49579966962-0.0616814204411-0.1691901158110.2078372551010.2135770370970.055371575422-0.1090471466630.03338549149680.3220168868350.02172045075060.06754879051010.0134640916475-0.02158245987540.1289984303040.01747304707190.09018693450224.55717323304-3.024499984835.5309617179
41.405237805540.685717146474-0.5183041743143.39767657177-0.4964697662162.816097133470.1622832224070.192791152748-0.202274309956-0.112012356977-0.07742109709360.255433761933-0.0819360107619-0.2113037573740.05107900109720.08532697552270.00140723831515-0.01937823979310.1301742346-0.02433340533340.0716022205053-1.86491059552-9.7436702793818.3785401294
55.104945572711.224237892261.607382285291.075805183160.08167971021770.6238602251160.472068441715-0.468108674401-0.6403650731960.279959998491-0.1847293394770.0874577928301-0.006636664008841.1132301989-0.1951879142870.6655682426990.03270281487040.01212871851010.674936950263-0.07613595775260.43267869048313.0314073914-46.8539470119-11.8944146285
60.527072128081-0.299274521221-0.1216132288721.478869996280.3195417850130.07555262423260.0396265527339-0.0500791794728-0.03719641513910.002530052381460.174728830766-0.941013886475-0.2338248145810.800186867290.1779392899120.277421649332-0.250352471343-0.0438511052250.789977601739-0.04498745258140.66820770909223.5892516225-34.75846699048.93747386921
70.9631578743570.122000620138-0.3445864335372.21831286303-0.4059678077291.29714585473-0.0256871847019-0.1289610621390.09012954721540.0689020616770.0626916737175-0.0377210695817-0.09408181895610.0136168254553-0.02067741541890.1383116078120.00344137105424-0.004232374487650.0685886787872-0.01309810369770.07375924893330.588887972436-32.06191572836.82670378903
80.618333177680.4587422332110.8184785863690.4871048494720.8095903279331.34974107457-0.227240910466-0.1247370076870.3499172574620.353806161606-0.151007381193-0.401429640526-0.5949064311290.662423979905-0.06976575999580.527303246025-0.132683696354-0.1539808102570.279302626769-0.005042600761340.2783237489613.8639302812-30.6547101193-1.04868366298
90.9883017131190.103840020527-0.2832790642081.221446717750.2487810984532.08728144822-0.0369536495444-0.0577124692596-0.1218210544920.08441259935340.0685038648655-0.140803888568-0.05374927234880.2460624890270.03290413729050.0663890501954-0.006620912073530.01532766550520.0967483881956-0.002091654509240.0894454267977.43628817235-41.34460691123.30016329718
102.15747660694-1.035660246981.13544437452.7021232636-1.165019274550.7740630083740.269548702374-0.1300481454220.4168782188830.247281304769-0.211029471777-0.330074169311-0.1384722979150.253445933532-0.0007031505302060.281401225996-0.01757626529740.06837824742650.200094330053-0.01026223918340.1436961127734.24212158354-31.056484077619.9060117406
111.20802900594-1.725946029630.2942809559583.3105430375-0.31462693822.644821523650.118550194745-0.0575900826094-0.0352494490724-0.316010172943-0.0346072181713-0.07155048332960.547848710872-0.60211921007-0.1091412486390.199166793133-0.0432898239491-0.01362020111050.1815049308180.01014027119170.107581494037-6.31395494119-37.1724251118.216043634
124.4803100745-2.76170811295.285124081262.49642990163-3.745316128466.532007080010.4276589037690.700623089773-0.724060203615-0.7824661274430.04106631772590.5697492295650.553987408023-0.26485838819-0.5901726720950.1955555904780.0628476249583-0.1058503740120.423152688494-0.03469451688960.127527036446-4.78307691613-0.099872946968529.3767740313
131.11979192751.260753205110.237222971661.635967178260.2999924664680.196810166673-0.0237148982893-0.140175382680.401727953579-0.0378995095381-0.1874530460820.330902924806-0.0483651397336-0.182874542317-0.02966785594560.19215726203-0.130658675166-0.1477851921620.451643722248-0.01304858697520.15653605548-4.33531519658-42.53714686928.69074007557
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 70 through 161 )AA70 - 1611 - 92
22chain 'A' and (resid 162 through 197 )AA162 - 19793 - 104
33chain 'A' and (resid 198 through 260 )AA198 - 260105 - 167
44chain 'A' and (resid 261 through 337 )AA261 - 337168 - 203
55chain 'B' and (resid 65 through 79 )BF65 - 791 - 15
66chain 'B' and (resid 80 through 97 )BF80 - 9716 - 33
77chain 'B' and (resid 98 through 155 )BF98 - 15534 - 91
88chain 'B' and (resid 156 through 197 )BF156 - 19792 - 110
99chain 'B' and (resid 198 through 260 )BF198 - 260111 - 173
1010chain 'B' and (resid 261 through 277 )BF261 - 277174 - 190
1111chain 'B' and (resid 278 through 337 )BF278 - 337191 - 209
1212chain 'A' and (resid 501 through 801)AC - E501 - 701
1313chain 'B' and (resid 601 through 901)BI - L601 - 901

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