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- PDB-7ulj: Hsp90b N-terminal domain in complex with 42C -

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Basic information

Entry
Database: PDB / ID: 7ulj
TitleHsp90b N-terminal domain in complex with 42C
ComponentsHeat shock protein HSP 90-beta
KeywordsCHAPERONE / Hsp90 Isoform / molecular chaperone / Hsp90b / and Ligand binding
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
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
N,N-dimethyl-7H-purin-6-amine / Heat shock protein HSP 90-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsStachowski, T.R. / Nithianantham, S. / Vanarotti, M. / Fischer, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM142772 United States
CitationJournal: Protein Sci. / Year: 2023
Title: Pan-HSP90 ligand binding reveals isoform-specific differences in plasticity and water networks.
Authors: Stachowski, T.R. / Nithianantham, S. / Vanarotti, M. / Lopez, K. / Fischer, M.
History
DepositionApr 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
D: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,17316
Polymers98,6794
Non-polymers1,49412
Water10,467581
1
A: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0434
Polymers24,6701
Non-polymers3733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0434
Polymers24,6701
Non-polymers3733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0434
Polymers24,6701
Non-polymers3733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0434
Polymers24,6701
Non-polymers3733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.506, 129.506, 104.454
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 24669.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPCB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P08238
#2: Chemical
ChemComp-42C / N,N-dimethyl-7H-purin-6-amine


Mass: 163.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H9N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 52 % / Description: Rectangular prism
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Sodium cacodylate pH 6.5, 0.1 M Sodium acetate, 5% MPD and 25% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→42.391 Å / Num. obs: 88988 / % possible obs: 99.97 % / Redundancy: 7.7 % / Biso Wilson estimate: 32.05 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.028 / Rrim(I) all: 0.079 / Net I/σ(I): 10.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.82-1.895.51.9488540.3171.1581.81799.95
9.8-42.3917.40.0258610.0080.02198.9

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UCJ

5ucj


Resolution: 1.82→42.391 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 4534 5.1 %
Rwork0.1934 84436 -
obs0.1947 88970 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.45 Å2 / Biso mean: 38.2601 Å2 / Biso min: 18.44 Å2
Refinement stepCycle: final / Resolution: 1.82→42.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 104 581 7335
Biso mean--36.48 41.4 -
Num. residues----853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056862
X-RAY DIFFRACTIONf_angle_d0.8389266
X-RAY DIFFRACTIONf_chiral_restr0.0491051
X-RAY DIFFRACTIONf_plane_restr0.0041180
X-RAY DIFFRACTIONf_dihedral_angle_d14.2942515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.82-1.84070.38121540.36992765
1.8407-1.86230.34541470.332843
1.8623-1.88510.36761710.31132774
1.8851-1.90890.31651730.29522784
1.9089-1.9340.29531670.27842836
1.934-1.96050.30931490.25832761
1.9605-1.98850.2671330.25352807
1.9885-2.01820.27871220.24112858
2.0182-2.04980.26181280.23532812
2.0498-2.08340.26861760.22852822
2.0834-2.11930.26951150.23192828
2.1193-2.15780.26521950.22162770
2.1578-2.19930.26631250.21792812
2.1993-2.24420.25161590.21542776
2.2442-2.2930.25041460.21382821
2.293-2.34630.2291500.21082837
2.3463-2.4050.2561530.21232803
2.405-2.470.2541780.20012783
2.47-2.54270.25461650.2072787
2.5427-2.62480.23511470.19752803
2.6248-2.71860.21551480.19412841
2.7186-2.82740.21631500.19572826
2.8274-2.9560.23631700.20492786
2.956-3.11180.2211280.19112834
3.1118-3.30670.19721580.19192813
3.3067-3.56190.23081440.17582832
3.5619-3.92010.19611440.16212828
3.9201-4.48690.16361480.15042864
4.4869-5.65090.15331440.16322840
5.6509-42.3910.18781470.17462890

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