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- PDB-7exp: Crystal structure of zebrafish TRAP1 with AMPPNP and MitoQ -

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Basic information

Entry
Database: PDB / ID: 7exp
TitleCrystal structure of zebrafish TRAP1 with AMPPNP and MitoQ
ComponentsTNF receptor-associated protein 1
KeywordsCHAPERONE / TRAP1 / HSP90 / Mitoquinone / MitoQ
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / mitochondrial inner membrane / calcium ion binding / protein kinase binding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding
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
Chem-05M / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å
AuthorsLee, H. / Yoon, N.G. / Kang, B.H. / Lee, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Mitoquinone Inactivates Mitochondrial Chaperone TRAP1 by Blocking the Client Binding Site.
Authors: Yoon, N.G. / Lee, H. / Kim, S.Y. / Hu, S. / Kim, D. / Yang, S. / Hong, K.B. / Lee, J.H. / Kang, S. / Kim, B.G. / Myung, K. / Lee, C. / Kang, B.H.
History
DepositionMay 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TNF receptor-associated protein 1
B: TNF receptor-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,89111
Polymers148,0102
Non-polymers1,8819
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-103 kcal/mol
Surface area52360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.339, 96.522, 125.615
Angle α, β, γ (deg.)90.000, 134.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-964-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1HISHISchain A and segidAA85 - 71913 - 647
2GLUGLUchain B and segidBB85 - 71713 - 645

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TNF receptor-associated protein 1 / Trap1 protein


Mass: 74004.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trap1 / Production host: Escherichia coli (E. coli) / References: UniProt: A8WFV1

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Non-polymers , 5 types, 235 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-05M / 2,3-dimethoxy-5-methyl-6-[10-(triphenyl-$l^{5}-phosphanyl)decyl]cyclohexa-2,5-diene-1,4-dione


Mass: 584.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H45O4P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG3350, 0.2M Sodium malonate pH 6.5, 30uM hexaaminecobalt(III) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.297→50 Å / Num. obs: 67378 / % possible obs: 99 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 21
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.424 / Num. unique obs: 3161

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IPE

4ipe


Resolution: 2.297→31.205 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2412 2011 2.99 %
Rwork0.1953 65357 -
obs0.1967 67368 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 292.78 Å2 / Biso mean: 64.859 Å2 / Biso min: 20.21 Å2
Refinement stepCycle: final / Resolution: 2.297→31.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9441 0 104 226 9771
Biso mean--69.11 53.58 -
Num. residues----1173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089745
X-RAY DIFFRACTIONf_angle_d1.40413120
X-RAY DIFFRACTIONf_chiral_restr0.0571462
X-RAY DIFFRACTIONf_plane_restr0.0071671
X-RAY DIFFRACTIONf_dihedral_angle_d15.7353655
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4817X-RAY DIFFRACTION9.539TORSIONAL
12B4817X-RAY DIFFRACTION9.539TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2973-2.35480.35651190.339429491
2.3548-2.41840.35741410.3198461698
2.4184-2.48960.32011390.2954462798
2.4896-2.56990.33521390.2776462599
2.5699-2.66170.30981450.2554469799
2.6617-2.76820.28161520.2364467599
2.7682-2.89410.28741370.2232467299
2.8941-3.04650.25761480.2152466699
3.0465-3.23720.27241480.21164701100
3.2372-3.48690.24021500.18614713100
3.4869-3.83720.23271460.17394718100
3.8372-4.39120.19731480.15684765100
4.3912-5.52740.20771460.15524743100
5.5274-31.2050.19431530.16654845100
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)
11.5469-0.2321-0.08130.3958-0.35430.8821-0.0486-1.1051-0.10890.3749-0.13490.60280.1409-0.12560.09830.4971-0.1560.11880.8547-0.22310.5905-109.142-25.1907159.1062
22.7452-0.27040.85443.6086-0.3543.05910.1737-0.14020.0707-0.0163-0.1451-0.44340.03990.1095-0.03450.1981-0.0236-0.00050.2368-0.0010.2777-77.2667-27.5894146.0147
33.6594-1.55040.54711.4626-1.69913.37360.0660.8073-0.0373-0.192-0.211-0.41420.44070.78230.2580.46870.064-0.05130.5629-0.01910.3551-82.2992-15.3427118.9479
41.8883-0.80832.14661.9803-1.28954.9573-0.06810.21760.1008-0.3598-0.1630.3427-0.2276-0.16430.15850.45960.0303-0.10040.3568-0.0720.4391-97.668-11.9739119.5134
50.2734-0.26280.26310.6305-0.78240.9793-0.10490.03840.3915-0.3811-0.08470.7674-0.9871-0.38170.53171.22010.3174-0.98290.6213-0.33240.8428-114.6483-3.006296.4404
61.52720.53170.41240.47840.95113.0819-0.25690.01720.3152-0.4943-0.49430.5022-0.6284-0.89230.81230.92060.2653-0.37230.7606-0.23541.032-120.6767-13.645490.8784
72.4275-0.7375-0.71651.28410.08572.0096-0.44680.35820.0721-0.49-0.31530.9077-0.3662-0.90230.55850.6212-0.0083-0.31260.7197-0.12280.682-118.4088-27.049178.7961
83.53080.29260.17781.16080.14180.62420.1345-0.73180.49820.2916-0.18060.33710.0397-0.17410.03080.3627-0.09610.12020.5125-0.11760.4299-110.9444-26.2739154.8085
90.7440.2851-0.8460.42990.013.5218-0.1680.0791-0.0638-0.13910.04780.06670.05250.04050.1140.33550.01260.00550.30340.05940.4083-106.5314-42.8091101.9755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 85 through 123 )A85 - 123
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 312 )A124 - 312
3X-RAY DIFFRACTION3chain 'A' and (resid 313 through 348 )A313 - 348
4X-RAY DIFFRACTION4chain 'A' and (resid 349 through 497 )A349 - 497
5X-RAY DIFFRACTION5chain 'A' and (resid 498 through 538 )A498 - 538
6X-RAY DIFFRACTION6chain 'A' and (resid 539 through 622 )A539 - 622
7X-RAY DIFFRACTION7chain 'A' and (resid 623 through 719 )A623 - 719
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 312 )B85 - 312
9X-RAY DIFFRACTION9chain 'B' and (resid 313 through 717 )B313 - 717

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