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- PDB-4iyn: Structure of mitochondrial Hsp90 (TRAP1) with ADP-ALF4- -

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Basic information

Entry
Database: PDB / ID: 4iyn
TitleStructure of mitochondrial Hsp90 (TRAP1) with ADP-ALF4-
ComponentsTNF receptor-associated protein 1
KeywordsCHAPERONE / ATP BINDING / ATPase / mitochondria
Function / homology
Function and homology information


nucleic acid metabolic process / 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
Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 ATPase, C-terminal domain ...Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 ATPase, C-terminal domain / Heat Shock Protein 90 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / : / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.312 Å
AuthorsPartridge, J.R. / Lavery, L.A. / Agard, D.A.
CitationJournal: Mol.Cell / Year: 2014
Title: Structural asymmetry in the closed state of mitochondrial Hsp90 (TRAP1) supports a two-step ATP hydrolysis mechanism.
Authors: Lavery, L.A. / Partridge, J.R. / Ramelot, T.A. / Elnatan, D. / Kennedy, M.A. / Agard, D.A.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Apr 3, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: TNF receptor-associated protein 1
B: TNF receptor-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,80612
Polymers164,4612
Non-polymers1,34510
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13240 Å2
ΔGint-106 kcal/mol
Surface area54720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.896, 96.597, 125.901
Angle α, β, γ (deg.)90.00, 134.26, 90.00
Int Tables number5
Space group name H-MC121

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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: 82230.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trap1 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A8WFV1

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Non-polymers , 5 types, 287 molecules

#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18 % (v/v) PEG3350, 0.2 M sodium malonate pH 6.6, 20-36 M hexamine cobalt mixed 1:1 with TRAP1 protein at 1 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2011
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. all: 67376 / Num. obs: 66770 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 50.23 Å2 / Net I/σ(I): 18.6
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.41 / Rsym value: 0.431 / % possible all: 91.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: dev_1214)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: SeMET derivative of TRAP1 with ADP-ALF4

Resolution: 2.312→29.811 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 1994 2.99 %
Rwork0.1912 --
obs0.1924 66710 99.25 %
all-67214 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.312→29.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9690 0 70 277 10037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210013
X-RAY DIFFRACTIONf_angle_d1.14813545
X-RAY DIFFRACTIONf_dihedral_angle_d15.6933805
X-RAY DIFFRACTIONf_chiral_restr0.0761500
X-RAY DIFFRACTIONf_plane_restr0.0051729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3115-2.36930.3681250.28064209X-RAY DIFFRACTION90
2.3693-2.43330.31021350.2454647X-RAY DIFFRACTION100
2.4333-2.50490.28681420.24434620X-RAY DIFFRACTION100
2.5049-2.58570.32271410.23414606X-RAY DIFFRACTION100
2.5857-2.67810.24931400.23044677X-RAY DIFFRACTION100
2.6781-2.78520.28751420.23114604X-RAY DIFFRACTION100
2.7852-2.91190.24221420.22424652X-RAY DIFFRACTION100
2.9119-3.06530.28731420.2154640X-RAY DIFFRACTION100
3.0653-3.25710.24891420.21394642X-RAY DIFFRACTION100
3.2571-3.50820.23791500.20584665X-RAY DIFFRACTION100
3.5082-3.86060.2491450.18084653X-RAY DIFFRACTION100
3.8606-4.41770.20851490.16254676X-RAY DIFFRACTION100
4.4177-5.55990.19161530.16624657X-RAY DIFFRACTION100
5.5599-29.81390.1911460.17074768X-RAY DIFFRACTION100
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)
13.2154-0.1378-0.01832.50480.58951.13990.0613-0.40120.04070.197-0.0705-0.24850.09050.1401-0.00480.3585-0.04620.01310.2952-0.01050.36285.00417.833559.276
21.7378-0.84980.86232.1957-0.76065.64980.01020.15730.0436-0.3209-0.05160.1755-0.09310.02940.04740.4414-0.0501-0.00640.2773-0.04640.5195-4.841530.735332.5387
32.557-1.42231.1553.8512-1.77134.2248-0.4282-0.17690.9558-0.5958-0.06450.7635-0.7039-0.76860.43370.79590.121-0.42150.6243-0.10971.0785-26.237539.943913.1035
43.5812-2.3585-1.65493.01380.40631.507-0.11720.42460.0927-0.1136-0.22820.6891-0.2607-0.54570.35870.7731-0.029-0.3660.7180.05310.7888-33.223920.2293-10.5235
54.63570.61020.19431.75970.28290.74610.1102-0.71430.41810.3792-0.26540.6560.0874-0.21270.11870.4448-0.0940.1960.5131-0.12280.6704-23.158118.501365.3921
61.1772-0.0295-0.05322.26130.91824.64720.11670.02880.26350.0241-0.00820.2424-0.1687-0.0055-0.09920.26140.02010.07240.26910.05020.5095-25.36645.125336.0595
73.9111.01580.27334.21380.99177.5022-0.38620.0435-0.4009-0.20130.27180.32510.520.07050.08030.3566-0.04430.03430.29330.09980.3458-17.4175-5.24449.144
83.3423-1.19480.47122.3841-0.53884.8293-0.03990.41440.0901-0.5009-0.01820.2027-0.04420.22150.06940.6315-0.1592-0.09280.47470.07250.2868-11.04566.1605-13.3956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A and resid 85:310
2X-RAY DIFFRACTION2Chain A and resid 311:472
3X-RAY DIFFRACTION3Chain A and resid 473:566
4X-RAY DIFFRACTION4Chain A and resid 567:718
5X-RAY DIFFRACTION5Chain B and resid 85:310
6X-RAY DIFFRACTION6Chain B and resid 311:472
7X-RAY DIFFRACTION7Chain B and resid 473:566
8X-RAY DIFFRACTION8Chain B and resid 567:717

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