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- PDB-4z1i: Crystal structure of human Trap1 with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4z1i
TitleCrystal structure of human Trap1 with AMPPNP
ComponentsHeat shock protein 75 kDa, mitochondrial
KeywordsCHAPERONE / Mitochondrial Hsp90 / AMPPNP
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
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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsLee, C. / Park, H.K. / Ryu, J.H. / Kang, B.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Development of a Mitochondria-Targeted Hsp90 Inhibitor Based on the Crystal Structures of Human TRAP1
Authors: Lee, C. / Park, H.K. / Jeong, H. / Lim, J. / Lee, A.J. / Cheon, K.Y. / Kim, C.S. / Thomas, A.P. / Bae, B. / Kim, N.D. / Kim, S.H. / Suh, P.G. / Ryu, J.H. / Kang, B.H.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)231,81012
Polymers229,6884
Non-polymers2,1228
Water00
1
A: Heat shock protein 75 kDa, mitochondrial
C: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9056
Polymers114,8442
Non-polymers1,0614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-50 kcal/mol
Surface area37790 Å2
MethodPISA
2
B: Heat shock protein 75 kDa, mitochondrial
D: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9056
Polymers114,8442
Non-polymers1,0614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-63 kcal/mol
Surface area41600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.547, 115.547, 339.936
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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: 57422.090 Da / Num. of mol.: 4 / Fragment: UNP residues 60-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAP1, HSP75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12931
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 23% PEG 4K, 100mM Tris, 0.35M ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 38253 / % possible obs: 99 % / Redundancy: 3.2 % / Net I/σ(I): 2.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data processing
Cootmodel building
PHENIXphasing
RefinementResolution: 3.3→37.822 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2847 1895 4.96 %
Rwork0.2199 --
obs0.2231 38205 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→37.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14117 0 128 0 14245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914545
X-RAY DIFFRACTIONf_angle_d1.67919569
X-RAY DIFFRACTIONf_dihedral_angle_d16.6325451
X-RAY DIFFRACTIONf_chiral_restr0.0662184
X-RAY DIFFRACTIONf_plane_restr0.0082460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2963-3.37870.37051320.29852536X-RAY DIFFRACTION98
3.3787-3.470.36741320.28352525X-RAY DIFFRACTION97
3.47-3.5720.37631380.27162579X-RAY DIFFRACTION98
3.572-3.68720.35941340.25872598X-RAY DIFFRACTION99
3.6872-3.81890.30391370.25092603X-RAY DIFFRACTION100
3.8189-3.97170.33991350.2292615X-RAY DIFFRACTION100
3.9717-4.15220.25871380.21632597X-RAY DIFFRACTION100
4.1522-4.37080.25151400.19262599X-RAY DIFFRACTION100
4.3708-4.64420.24671300.18432611X-RAY DIFFRACTION100
4.6442-5.0020.24891360.19312626X-RAY DIFFRACTION100
5.002-5.5040.26351350.21312617X-RAY DIFFRACTION100
5.504-6.29730.25741330.22712604X-RAY DIFFRACTION100
6.2973-7.9220.32321370.2212623X-RAY DIFFRACTION100
7.922-37.82410.24021380.18952577X-RAY DIFFRACTION97
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)
15.0609-2.8821-4.63448.03014.3989.32660.2252-0.8380.2647-0.06940.0632-0.5433-0.10421.5741-0.18850.5110.0476-0.09590.66710.16950.276121.7251114.501519.8719
22.95690.22170.27553.53331.41553.944-0.00120.3691-0.1234-0.15750.010.1553-0.32060.11620.00170.41120.11210.00010.3351-0.03960.354815.244388.6557-14.7817
37.1202-3.750.76322.31480.05161.56530.07420.21820.5405-0.3297-0.3050.7064-0.3344-0.62420.26520.78980.2544-0.14020.69480.00320.8411-10.1247103.745-16.0875
41.43920.62750.19073.1436-1.28951.48260.33690.3851-1.44750.8110.89070.24220.0198-0.8858-0.7340.57190.39150.06141.01430.08221.0705-27.7415107.0269-13.4114
53.53411.61325.20574.44160.42548.98670.5342-0.3927-0.2212-0.4223-0.0644-0.27861.0451-0.4208-0.55530.6008-0.01910.00490.5854-0.02340.356923.5904118.3089-41.3917
65.02580.0994-0.29723.00761.2633.283-0.0091-0.5815-0.237-0.0860.1368-0.1167-0.00330.1937-0.13680.2176-0.0716-0.09690.48330.03920.425138.385139.7883-6.2236
75.7788-2.9132-1.18961.90980.88923.0856-0.1301-0.7353-0.25390.24210.1449-0.1702-0.32360.1211-0.03530.3579-0.1021-0.06150.58460.0030.43529.6344144.7045-1.9192
88.1571-2.08010.75051.9895-0.42283.8147-0.1726-0.40450.01690.23470.06630.1335-0.2821-0.60220.01670.31620.00660.02830.4489-0.0450.3531-18.6821150.9226-8.1623
92.09011.66592.5535.61153.70637.81730.0958-0.0816-0.4025-0.00760.4703-0.81770.03990.5404-0.62380.48850.1183-0.06190.68440.00570.511924.718282.6245-14.2533
102.92170.2828-0.20431.99540.29722.8236-0.11850.01130.1786-0.2563-0.05450.1352-0.00680.0720.15050.6130.0508-0.09780.1885-0.03280.363612.3976108.272118.8461
115.43681.9228-0.30761.428-0.98481.6218-0.2076-0.0086-0.05510.01370.1260.15190.37-0.63790.04380.7872-0.0724-0.10980.5407-0.13350.5978-12.689893.186517.0733
123.91251.23561.66722.31870.42262.9681-0.17590.0101-0.2369-0.1986-0.06640.38270.538-1.11280.34011.0551-0.3531-0.10961.0882-0.21470.9049-36.436980.13355.0072
133.10730.25981.93971.18350.86893.35270.3289-0.1449-0.656-0.30390.4485-0.5286-0.54890.8731-0.55810.3681-0.10020.1170.9551-0.11050.607249.3827138.0472-7.3002
142.5618-0.39790.04393.45190.43583.86-0.11570.0751-0.1514-0.41280.14040.1123-0.0893-0.1585-0.03520.3759-0.1597-0.02710.2459-0.04050.374920.7046128.8718-39.3835
153.6029-4.6315-0.09346.1480.99522.23510.24160.34010.4801-0.6995-0.1859-0.4342-0.2435-0.2769-0.02060.6596-0.129-0.01760.4760.05420.478911.9282157.01-34.3593
161.79950.6131-0.81275.62022.42521.87790.1944-0.6381.01710.281-0.27190.0223-0.6368-0.23130.0510.8416-0.0539-0.08810.5973-0.13910.7995.363179.18-22.45
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 70 through 93)
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 297 )
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 434 )
4X-RAY DIFFRACTION4chain 'A' and (resid 435 through 454 )
5X-RAY DIFFRACTION5chain 'B' and (resid 70 through 93 )
6X-RAY DIFFRACTION6chain 'B' and (resid 94 through 297 )
7X-RAY DIFFRACTION7chain 'B' and (resid 298 through 434 )
8X-RAY DIFFRACTION8chain 'B' and (resid 435 through 553 )
9X-RAY DIFFRACTION9chain 'C' and (resid 70 through 93 )
10X-RAY DIFFRACTION10chain 'C' and (resid 94 through 297 )
11X-RAY DIFFRACTION11chain 'C' and (resid 298 through 434 )
12X-RAY DIFFRACTION12chain 'C' and (resid 435 through 553 )
13X-RAY DIFFRACTION13chain 'D' and (resid 70 through 93 )
14X-RAY DIFFRACTION14chain 'D' and (resid 94 through 297 )
15X-RAY DIFFRACTION15chain 'D' and (resid 298 through 434 )
16X-RAY DIFFRACTION16chain 'D' and (resid 435 through 550 )

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