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- PDB-3pry: Crystal structure of the middle domain of human HSP90-beta refine... -

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Entry
Database: PDB / ID: 3pry
TitleCrystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution
ComponentsHeat shock protein HSP 90-beta
KeywordsCHAPERONE / Structural Genomics / Structural Genomics Consortium / SGC / heat shock protein / HSP90B
Function / homology
Function and homology information


: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / positive regulation of protein localization to cell surface / ATP-dependent protein binding ...: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / positive regulation of protein localization to cell surface / ATP-dependent protein binding / protein kinase regulator activity / negative regulation of protein metabolic process / positive regulation of tau-protein kinase activity / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / TPR domain binding / positive regulation of transforming growth factor beta receptor signaling pathway / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / positive regulation of phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / HSF1 activation / Attenuation phase / cellular response to interleukin-4 / RHOBTB2 GTPase cycle / Purinergic signaling in leishmaniasis infection / axonal growth cone / DNA polymerase binding / supramolecular fiber organization / : / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nitric-oxide synthase regulator activity / ESR-mediated signaling / positive regulation of cell differentiation / ATP-dependent protein folding chaperone / peptide binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / tau protein binding / placenta development / Regulation of actin dynamics for phagocytic cup formation / kinase binding / histone deacetylase binding / Chaperone Mediated Autophagy / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / double-stranded RNA binding / disordered domain specific binding / unfolded protein binding / melanosome / protein folding / MHC class II protein complex binding / cellular response to heat / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Potential therapeutics for SARS / protein stabilization / protein dimerization activity / regulation of cell cycle / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / virion attachment to host cell / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 ...Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Heat shock protein HSP 90-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsChaikuad, A. / Pilka, E. / Sharpe, T.D. / Cooper, C.D.O. / Phillips, C. / Berridge, G. / Ayinampudi, V. / Fedorov, O. / Keates, T. / Thangaratnarajah, C. ...Chaikuad, A. / Pilka, E. / Sharpe, T.D. / Cooper, C.D.O. / Phillips, C. / Berridge, G. / Ayinampudi, V. / Fedorov, O. / Keates, T. / Thangaratnarajah, C. / Zimmermann, T. / Vollmar, M. / Yue, W.W. / Che, K.H. / Krojer, T. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution
Authors: Chaikuad, A. / Pilka, E. / Sharpe, T.D. / Cooper, C.D.O. / Phillips, C. / Berridge, G. / Ayinampudi, V. / Fedorov, O. / Keates, T. / Thangaratnarajah, C. / Zimmermann, T. / Vollmar, M. / ...Authors: Chaikuad, A. / Pilka, E. / Sharpe, T.D. / Cooper, C.D.O. / Phillips, C. / Berridge, G. / Ayinampudi, V. / Fedorov, O. / Keates, T. / Thangaratnarajah, C. / Zimmermann, T. / Vollmar, M. / Yue, W.W. / Che, K.H. / Krojer, T. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bullock, A. / Structural Genomics Consortium (SGC)
History
DepositionNov 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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 protein HSP 90-beta
B: Heat shock protein HSP 90-beta
C: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,08811
Polymers95,4943
Non-polymers5958
Water3,963220
1
A: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9272
Polymers31,8311
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2687
Polymers31,8311
Non-polymers4366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8932
Polymers31,8311
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.710, 73.710, 149.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12C
22A
32B
13C
23A
33B
14A
24B
34C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROHISHIS4AA287 - 3205 - 38
211PROPROHISHIS4BB287 - 3205 - 38
311PROPROHISHIS4CC287 - 3205 - 38
121PHEPHEPHEPHE6AA321 - 32939 - 47
221PHEPHEPHEPHE6BB321 - 32939 - 47
321PHEPHEPHEPHE6CC321 - 32939 - 47
131ARGARGPROPRO4AA330 - 34048 - 58
231ARGARGPROPRO4BB330 - 34048 - 58
331ARGARGPROPRO4CC330 - 34048 - 58
141ILEILEASPASP2AA353 - 38271 - 100
241ILEILEASPASP2BB353 - 38271 - 100
341ILEILEASPASP2CC353 - 38271 - 100
151ILEILELEULEU3AA400 - 419118 - 137
251ILEILELEULEU3BB400 - 419118 - 137
351ILEILELEULEU3CC400 - 419118 - 137
161ALAALAGLUGLU4AA420 - 465138 - 183
261ALAALAGLUGLU4BB420 - 465138 - 183
361ALAALAGLUGLU4CC420 - 465138 - 183
112METMETILEILE4CC466 - 486184 - 204
212METMETILEILE4AA466 - 486184 - 204
312METMETILEILE4BB466 - 486184 - 204
113THRTHRPHEPHE6CC487 - 508205 - 226
213THRTHRPHEPHE6AA487 - 508205 - 226
313THRTHRPHEPHE6BB487 - 508205 - 226
114GLUGLUGLUGLU4AA509 - 545227 - 263
214GLUGLUGLUGLU4BB509 - 545227 - 263
314GLUGLUGLUGLU4CC509 - 545227 - 263

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Heat shock protein HSP 90-beta / HSP 90 / Heat shock 84 kDa / HSP 84 / HSP84


Mass: 31831.301 Da / Num. of mol.: 3 / Fragment: middle domain (UNP residues 284-543)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPCB / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P08238
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25.5% PEG3350, 0.17 M ammonium sulfate, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2010 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.675
11-H, H+K, -L20.325
ReflectionResolution: 2.28→39.19 Å / Num. all: 41223 / Num. obs: 41218 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.1
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2 / Num. unique all: 6039 / % possible all: 99.9

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1HK7

1hk7


Resolution: 2.28→39.19 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.181 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21716 2023 4.9 %RANDOM
Rwork0.17192 ---
obs0.17417 39156 99.57 %-
all-41218 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.369 Å2
Baniso -1Baniso -2Baniso -3
1-4.93 Å20 Å20 Å2
2--4.93 Å20 Å2
3----9.85 Å2
Refine analyzeLuzzati coordinate error obs: 0.355 Å
Refinement stepCycle: LAST / Resolution: 2.28→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6123 0 36 220 6379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226281
X-RAY DIFFRACTIONr_bond_other_d0.0010.024399
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9728452
X-RAY DIFFRACTIONr_angle_other_deg0.858310678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7265755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46624310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.517151163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9531548
X-RAY DIFFRACTIONr_chiral_restr0.0860.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021302
X-RAY DIFFRACTIONr_mcbond_it2.51333776
X-RAY DIFFRACTIONr_mcbond_other0.95831518
X-RAY DIFFRACTIONr_mcangle_it3.98456087
X-RAY DIFFRACTIONr_scbond_it6.50782505
X-RAY DIFFRACTIONr_scangle_it8.683112362
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A296TIGHT POSITIONAL0.160.05
12B296TIGHT POSITIONAL0.180.05
13C296TIGHT POSITIONAL0.180.05
11A1528MEDIUM POSITIONAL0.590.5
12B1528MEDIUM POSITIONAL0.620.5
13C1528MEDIUM POSITIONAL0.510.5
11A298LOOSE POSITIONAL0.465
12B298LOOSE POSITIONAL0.495
13C298LOOSE POSITIONAL0.615
11A296TIGHT THERMAL1.320.5
12B296TIGHT THERMAL1.190.5
13C296TIGHT THERMAL1.340.5
11A1528MEDIUM THERMAL1.262
12B1528MEDIUM THERMAL1.162
13C1528MEDIUM THERMAL1.22
11A298LOOSE THERMAL1.0910
12B298LOOSE THERMAL1.2410
13C298LOOSE THERMAL1.1110
21C281MEDIUM POSITIONAL0.460.5
22A281MEDIUM POSITIONAL0.550.5
23B281MEDIUM POSITIONAL0.380.5
21C281MEDIUM THERMAL1.242
22A281MEDIUM THERMAL1.082
23B281MEDIUM THERMAL1.172
31C261LOOSE POSITIONAL0.835
32A261LOOSE POSITIONAL1.125
33B261LOOSE POSITIONAL1.015
31C261LOOSE THERMAL4.2110
32A261LOOSE THERMAL4.4710
33B261LOOSE THERMAL2.7710
41A469MEDIUM POSITIONAL0.580.5
42B469MEDIUM POSITIONAL0.520.5
43C469MEDIUM POSITIONAL0.560.5
41A469MEDIUM THERMAL1.362
42B469MEDIUM THERMAL1.362
43C469MEDIUM THERMAL1.182
LS refinement shellResolution: 2.279→2.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 141 -
Rwork0.215 2840 -
obs--98.25 %
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)
11.85280.20510.5580.55750.55591.1925-0.0567-0.0632-0.1028-0.02160.01550.01990.08760.01610.04120.06290.0182-0.0090.0531-0.01080.010711.695834.030538.2921
20.62710.1072-0.20491.0991-0.79132.9485-0.06430.05050.1735-0.09670.032-0.0037-0.16240.01750.03230.0618-0.0296-0.0350.06830.00360.05077.696445.987711.1751
30.64880.4120.85641.8377-0.1491.1385-0.0263-0.0351-0.0749-0.1531-0.0058-0.2191-0.05260.00910.03220.10790.00930.0070.11970.03310.0227-1.408515.61265.9088
40.7296-0.15590.93171.3296-0.57043.2149-0.0586-0.05470.0490.1087-0.0427-0.1384-0.06380.02350.10130.0461-0.0211-0.00680.08260.03330.07314.97144.227431.514
51.81491.442-0.39111.4155-0.78380.4079-0.11680.06560.418-0.12950.13380.3402-0.03-0.0834-0.0170.174-0.0044-0.04840.10410.03330.179340.620736.15034.7728
61.01870.22120.86770.70020.09143.42980.0687-0.12350.0773-0.03960.09610.04090.0235-0.0893-0.16480.0267-0.00510.04040.0849-0.02610.089341.655629.022330.0363
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A284 - 398
2X-RAY DIFFRACTION2A399 - 546
3X-RAY DIFFRACTION3B284 - 388
4X-RAY DIFFRACTION4B389 - 546
5X-RAY DIFFRACTION5C285 - 369
6X-RAY DIFFRACTION6C370 - 545

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