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- PDB-3q5l: Crystal structure of the amino-terminal domain of HSP90 from Leis... -

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Basic information

Entry
Database: PDB / ID: 3q5l
TitleCrystal structure of the amino-terminal domain of HSP90 from Leishmania major, LMJF33.0312:M1-K 213 in the presence of 17-AEP-geldanamycin
ComponentsHeat shock protein 83-1
KeywordsCHAPERONE / SLEEPING SICKNESS / LEISHMANIA / HEAT SHOCK PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding ...ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases ...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-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KX2 / Heat shock protein 83-1
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsWernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / MacKenzie, F. / Fairlamb, A. / Cossar, D. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. ...Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / MacKenzie, F. / Fairlamb, A. / Cossar, D. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Ferguson, M.A.J. / Hui, R. / Pizarro, J.C. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the amino-terminal domain of HSP90 from Leishmania major, LMJF33.0312:M1-K 213 in the presence of 17-AEP-geldanamycin.
Authors: Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / MacKenzie, F. / Fairlamb, A. / Cossar, D. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Authors: Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / MacKenzie, F. / Fairlamb, A. / Cossar, D. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Ferguson, M.A.J. / Hui, R. / Pizarro, J.C. / Hills, T.
History
DepositionDec 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 5, 2012Group: Database references / Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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 83-1
B: Heat shock protein 83-1
C: Heat shock protein 83-1
D: Heat shock protein 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0138
Polymers104,4424
Non-polymers2,5714
Water00
1
A: Heat shock protein 83-1
hetero molecules

B: Heat shock protein 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5064
Polymers52,2212
Non-polymers1,2862
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y,-x-1,z+1/41
Buried area1240 Å2
ΔGint-10 kcal/mol
Surface area20210 Å2
MethodPISA
2
C: Heat shock protein 83-1
hetero molecules

D: Heat shock protein 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5064
Polymers52,2212
Non-polymers1,2862
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-y,x,z-1/41
Buried area1310 Å2
ΔGint-9 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.341, 161.341, 48.142
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 5

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA1 - 15819 - 176
21THRTHRBB1 - 15819 - 176
31THRTHRCC1 - 15819 - 176
41THRTHRDD1 - 15819 - 176
12LEULEUAA165 - 205183 - 223
22LEULEUBB165 - 205183 - 223
32LEULEUCC165 - 205183 - 223
42LEULEUDD165 - 205183 - 223

NCS ensembles :
ID
1
2

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Components

#1: Protein
Heat shock protein 83-1


Mass: 26110.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF33.0312 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Q4I6
#2: Chemical
ChemComp-KX2 / (4E,6Z,8S,9S,10E,12S,13R,14S,16R)-13-hydroxy-8,14-dimethoxy-4,10,12,16-tetramethyl-3,20,22-trioxo-19-{[2-(pyrrolidin-1-yl)ethyl]amino}-2-azabicyclo[16.3.1]docosa-1(21),4,6,10,18-pentaen-9-yl carbamate


Mass: 642.783 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H50N4O8

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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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M disodium tartrate, 1 mM AEP-GA, 4 mM MgCl2, 2 mM TCEP, Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 36754 / Num. obs: 36607 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 72.8 Å2 / Rmerge(I) obs: 0.062 / Χ2: 0.848 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.74.90.60518100.5071100
2.7-2.7450.52417930.523199.9
2.74-2.850.45118270.511199.9
2.8-2.8550.37718370.5511100
2.85-2.9250.28917830.556199.8
2.92-2.9850.24818580.58199.9
2.98-3.064.90.17617920.596199.9
3.06-3.1450.15718280.6081100
3.14-3.2350.13318330.632199.8
3.23-3.3450.10617980.681100
3.34-3.4650.08718370.712199.8
3.46-3.64.90.0718270.772199.9
3.6-3.7650.06118560.84199.9
3.76-3.9650.05518010.88199.9
3.96-4.214.90.0518351.074199.8
4.21-4.534.90.0518351.426199.8
4.53-4.994.90.05318501.869199.8
4.99-5.714.80.04918641.581199.8
5.71-7.194.70.03718751.006199.5
7.19-504.60.03218681.107195.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 61.89 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.65 Å44.75 Å
Translation2.65 Å44.75 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H80

3h80


Resolution: 2.65→24.54 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2795 / WRfactor Rwork: 0.2239 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8043 / SU B: 25.295 / SU ML: 0.242 / SU R Cruickshank DPI: 0.5494 / SU Rfree: 0.3276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 1822 5 %RANDOM
Rwork0.2267 ---
all0.2292 36598 --
obs0.2292 36452 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 169.71 Å2 / Biso mean: 69.1992 Å2 / Biso min: 36.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.65→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6423 0 184 0 6607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226713
X-RAY DIFFRACTIONr_bond_other_d0.0020.024327
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9929098
X-RAY DIFFRACTIONr_angle_other_deg0.851310597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2885849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37524.909275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.103151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4881531
X-RAY DIFFRACTIONr_chiral_restr0.060.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027533
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021337
X-RAY DIFFRACTIONr_mcbond_it0.2881.54224
X-RAY DIFFRACTIONr_mcbond_other0.061.51745
X-RAY DIFFRACTIONr_mcangle_it0.55426739
X-RAY DIFFRACTIONr_scbond_it0.95532489
X-RAY DIFFRACTIONr_scangle_it1.6664.52359
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A933MEDIUM POSITIONAL0.130.5
12B933MEDIUM POSITIONAL0.170.5
13C933MEDIUM POSITIONAL0.140.5
14D933MEDIUM POSITIONAL0.220.5
11A938LOOSE POSITIONAL0.385
12B938LOOSE POSITIONAL0.495
13C938LOOSE POSITIONAL0.365
14D938LOOSE POSITIONAL0.465
11A933MEDIUM THERMAL0.212
12B933MEDIUM THERMAL0.22
13C933MEDIUM THERMAL0.212
14D933MEDIUM THERMAL0.272
11A938LOOSE THERMAL0.310
12B938LOOSE THERMAL0.3110
13C938LOOSE THERMAL0.3410
14D938LOOSE THERMAL0.3710
21A243MEDIUM POSITIONAL0.130.5
22B243MEDIUM POSITIONAL0.240.5
23C243MEDIUM POSITIONAL0.150.5
24D243MEDIUM POSITIONAL0.150.5
21A231LOOSE POSITIONAL0.275
22B231LOOSE POSITIONAL0.325
23C231LOOSE POSITIONAL0.265
24D231LOOSE POSITIONAL0.255
21A243MEDIUM THERMAL0.172
22B243MEDIUM THERMAL0.172
23C243MEDIUM THERMAL0.182
24D243MEDIUM THERMAL0.222
21A231LOOSE THERMAL0.310
22B231LOOSE THERMAL0.2610
23C231LOOSE THERMAL0.2910
24D231LOOSE THERMAL0.2710
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 139 -
Rwork0.327 2511 -
all-2650 -
obs--99.85 %
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)
13.84170.76280.89044.5432-0.34592.64890.0913-0.2612-0.38890.1127-0.0667-0.0230.4685-0.4713-0.02460.235-0.12060.03460.18640.05650.0758-52.5369-59.7327-16.8389
28.7295-1.16371.10384.6615-1.22731.7804-0.3548-0.38241.46320.32470.15730.357-0.651-0.33520.19750.32830.07760.0160.3502-0.0420.4699-65.2078-29.4627-28.7036
34.2326-0.42620.33553.63550.67471.9207-0.1451-0.2019-0.28970.25460.0951-0.40350.33580.27020.050.14010.04390.0020.18650.03760.0871-21.6086-49.7131-4.1162
44.76250.3401-0.92735.74120.61211.81970.1944-0.56220.46340.6203-0.092-0.1871-0.29420.3146-0.10230.2949-0.0635-0.00490.1719-0.02480.0625-30.3385-17.82648.2146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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