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- PDB-7ulk: Human TRAP1 NM in complex with 42C -

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Basic information

Entry
Database: PDB / ID: 7ulk
TitleHuman TRAP1 NM in complex with 42C
ComponentsHeat shock protein 75 kDa, mitochondrial
KeywordsCHAPERONE / Trap1 / Hsp90 Isoform / Heat shock protein 75 kDa / molecular chaperone / and Isoform-specific properties
Function / homology
Function and homology information


translational attenuation / negative regulation of cellular respiration / Citric acid cycle (TCA cycle) / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of reactive oxygen species biosynthetic process / : / cell periphery / ATP-dependent protein folding chaperone ...translational attenuation / negative regulation of cellular respiration / Citric acid cycle (TCA cycle) / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of reactive oxygen species biosynthetic process / : / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space / unfolded protein binding / protein folding / mitochondrial inner membrane / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane
Similarity search - Function
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 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein 75 kDa, mitochondrial
B: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3656
Polymers114,9582
Non-polymers4074
Water1,40578
1
A: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6823
Polymers57,4791
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6823
Polymers57,4791
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.624, 89.399, 95.599
Angle α, β, γ (deg.)90.000, 111.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heat shock protein 75 kDa, mitochondrial / HSP 75 / TNFR-associated protein 1 / Tumor necrosis factor type 1 receptor-associated protein / TRAP-1


Mass: 57479.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAP1, HSP75 / Plasmid: pET-15b / Details (production host): Cleavable 6His-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12931
#2: Chemical ChemComp-42C / N,N-dimethyl-7H-purin-6-amine


Mass: 163.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.9 % / Description: Thin plate
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium cacodylate pH 6.5, 0.2 M CaCl2, and 18% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 9, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→45.213 Å / Num. obs: 43292 / % possible obs: 85.54 % / Redundancy: 3.7 % / Biso Wilson estimate: 48.95 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.066 / Rrim(I) all: 0.128 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.34-2.423.71.49933070.391.0261.3473.36
9.06-45.2133.60.0448020.9580.0290.05295.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y3O

5y3o


Resolution: 2.34→45.213 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 1819 4.61 %
Rwork0.2225 37610 -
obs0.2246 39429 85.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.51 Å2 / Biso mean: 73 Å2 / Biso min: 26.25 Å2
Refinement stepCycle: final / Resolution: 2.34→45.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6839 0 44 78 6961
Biso mean--90.3 60.79 -
Num. residues----867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027151
X-RAY DIFFRACTIONf_angle_d0.5229684
X-RAY DIFFRACTIONf_chiral_restr0.0381080
X-RAY DIFFRACTIONf_plane_restr0.0031245
X-RAY DIFFRACTIONf_dihedral_angle_d13.2984342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.34-2.40330.33981120.3398245973
2.4033-2.4740.35171310.3206250475
2.474-2.55390.29481210.2902259978
2.5539-2.64510.30321280.2994266479
2.6451-2.7510.37311290.2813256777
2.751-2.87620.30811360.2646285484
2.8762-3.02780.30241450.2667308191
3.0278-3.21750.29311470.2503313993
3.2175-3.46580.30551570.229317094
3.4658-3.81440.25531530.2071309491
3.8144-4.3660.22371470.1875303289
4.366-5.49920.22711580.18329497
5.4992-45.2130.26951550.2168315391
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)
11.96520.5231-0.53331.2460.15862.97490.0104-0.5658-0.11130.3555-0.2229-0.31780.00790.52310.04860.552-0.0144-0.09660.74610.07730.55191.4555-19.832657.4419
23.32820.1876-0.14512.4553-0.63392.4310.0163-0.2166-0.0080.2022-0.1295-0.0535-0.06540.12420.03110.25870.0371-0.03530.33240.04240.3045-5.529-18.128853.2262
32.1016-1.5314-1.83620.80711.24042.8640.12740.00790.2123-0.06330.0436-0.1599-0.1397-0.35510.0320.4444-0.00250.05260.49520.03980.4482-31.2691-10.314257.1742
41.56680.2514-1.40880.7002-0.16942.4556-0.16620.54730.06630.48530.1312-0.35350.7104-0.06260.04970.68520.1509-0.04940.5901-0.04630.5656-33.7895-16.125569.6967
51.3913-0.0945-1.3220.14390.0522.1324-0.3174-0.2691-0.0525-0.11370.2894-0.31940.10490.53210.08140.54340.0530.05250.7151-0.0910.4281-28.2115-10.470671.9917
60.9633-0.7573-0.14732.90490.50843.7134-0.0769-0.10150.23540.51110.25720.4785-0.5276-0.62160.03890.71010.17010.14890.6056-0.00330.5219-48.80781.240582.4322
74.53270.7103-0.1542.4048-0.39932.1693-0.03930.0103-0.2095-0.2582-0.0601-0.06570.09550.25130.01950.3335-0.01890.02360.33130.00590.3289-6.3072-8.0449121.7306
81.5645-0.23761.54281.8325-0.32414.88260.2393-0.1194-0.179-0.41760.02970.14640.4102-0.6090.05870.5312-0.0906-0.06380.3982-0.0140.3722-42.7763-21.118100.2191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 109 )A69 - 109
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 277 )A110 - 277
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 346 )A278 - 346
4X-RAY DIFFRACTION4chain 'A' and (resid 347 through 373 )A347 - 373
5X-RAY DIFFRACTION5chain 'A' and (resid 374 through 411 )A374 - 411
6X-RAY DIFFRACTION6chain 'A' and (resid 412 through 551 )A412 - 551
7X-RAY DIFFRACTION7chain 'B' and (resid 69 through 297 )B69 - 297
8X-RAY DIFFRACTION8chain 'B' and (resid 298 through 550 )B298 - 550

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