PDB-5tvx: Crystal structure of mitochondrial Hsp90 (TRAP1) with ATP in abse...

ID or keywords:

Entry

Database: PDB / ID: 5tvx

Title

Crystal structure of mitochondrial Hsp90 (TRAP1) with ATP in absence of Mg, fully hydrolyzed

Components

TNF receptor-associated protein 1

Keywords

CHAPERONE / Hsp90 / ATP / TRAP1

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

Biological species

Danio rerio (zebrafish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Elnatan, D. / Betegon, M. / Agard, D.A.

Funding support

United States, 1items

Citation

Journal: Elife / Year: 2017
Title: Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1.
Authors: Elnatan, D. / Betegon, M. / Liu, Y. / Ramelot, T. / Kennedy, M.A. / Agard, D.A.

History

Deposition	Nov 10, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Nov 20, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5tvx.cif.gz	481.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5tvx.ent.gz	396.1 KB	Display	PDB format
PDBx/mmJSON format	5tvx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tv/5tvx ftp://data.pdbj.org/pub/pdb/validation_reports/tv/5tvx	HTTPS FTP

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Related structure data

Related structure data	5tthC 5tvuC 5tvwC 4ipeS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6xg6-d 6d14-d 4ipe-d 5tvw-d 4iyn-d 5tvu-d 5fn3-d 6ppp-d 3kl3-d 5nbd-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #108 - Dec 2008 Hsp90 similarity (5)

Deposited unit

B: TNF receptor-associated protein 1

A: TNF receptor-associated protein 1

hetero molecules

150 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	178.491, 96.820, 125.780
Angle α, β, γ (deg.)	90.00, 134.18, 90.00
Int Tables number	5
Space group name H-M	C121
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	TNF receptor-associated protein 1 / Trap1 protein Mass: 74635.625 Da / Num. of mol.: 2 / Fragment: UNP residues 73-719 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trap1 / Variant: delta1-72 / Plasmid: pET151DTOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A8WFV1
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.09 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M NaK Tartrate, 20% (v/v) PEG3350, 36 mM hexamine cobalt, 5 mM ATP, 5 mM EDTA

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Data collection

Diffraction	Mean temperature: 91.4 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1159 Å / Relative weight: 1
Reflection	Resolution: 1.99→40.54 Å / Num. obs: 77629 / % possible obs: 99.6 % / Redundancy: 1.9 % / Net I/σ(I): 7.8

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Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
iMOSFLM	7.2.1	data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IPE

4ipe

Resolution: 2.2→39.97 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.47

	R_factor	Num. reflection	% reflection
R_free	0.2365	3992	5.15 %
R_work	0.1885	-	-
obs	0.1909	77583	99.54 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.2→39.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9570	0	54	374	9998

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9800
X-RAY DIFFRACTION	f_angle_d	0.965	13214
X-RAY DIFFRACTION	f_dihedral_angle_d	17.375	5989
X-RAY DIFFRACTION	f_chiral_restr	0.052	1472
X-RAY DIFFRACTION	f_plane_restr	0.006	1689

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2-2.2259	0.3848	135	0.3523	2487	X-RAY DIFFRACTION	99
2.2259-2.253	0.404	159	0.3676	2521	X-RAY DIFFRACTION	99
2.253-2.2816	0.3793	166	0.3432	2457	X-RAY DIFFRACTION	99
2.2816-2.3116	0.3753	171	0.3176	2501	X-RAY DIFFRACTION	100
2.3116-2.3432	0.3575	159	0.2913	2495	X-RAY DIFFRACTION	100
2.3432-2.3767	0.3159	133	0.2816	2558	X-RAY DIFFRACTION	100
2.3767-2.4122	0.2717	132	0.2654	2524	X-RAY DIFFRACTION	100
2.4122-2.4499	0.2981	110	0.262	2525	X-RAY DIFFRACTION	100
2.4499-2.49	0.3266	155	0.2676	2518	X-RAY DIFFRACTION	100
2.49-2.533	0.3049	169	0.2472	2507	X-RAY DIFFRACTION	100
2.533-2.579	0.3405	163	0.2425	2514	X-RAY DIFFRACTION	100
2.579-2.6286	0.3317	107	0.2392	2581	X-RAY DIFFRACTION	100
2.6286-2.6822	0.3068	154	0.2239	2510	X-RAY DIFFRACTION	100
2.6822-2.7406	0.2824	106	0.2233	2566	X-RAY DIFFRACTION	100
2.7406-2.8043	0.3253	124	0.2177	2538	X-RAY DIFFRACTION	100
2.8043-2.8744	0.2956	119	0.2184	2526	X-RAY DIFFRACTION	100
2.8744-2.9521	0.2981	102	0.2182	2569	X-RAY DIFFRACTION	100
2.9521-3.0389	0.2627	160	0.2173	2531	X-RAY DIFFRACTION	100
3.0389-3.137	0.2171	124	0.2069	2557	X-RAY DIFFRACTION	100
3.137-3.249	0.3047	126	0.204	2557	X-RAY DIFFRACTION	100
3.249-3.3791	0.2623	145	0.1897	2546	X-RAY DIFFRACTION	100
3.3791-3.5328	0.2286	122	0.1793	2569	X-RAY DIFFRACTION	100
3.5328-3.7189	0.2162	116	0.1694	2563	X-RAY DIFFRACTION	100
3.7189-3.9517	0.1934	114	0.1598	2570	X-RAY DIFFRACTION	100
3.9517-4.2565	0.1623	126	0.1432	2580	X-RAY DIFFRACTION	100
4.2565-4.6843	0.1712	179	0.131	2497	X-RAY DIFFRACTION	99
4.6843-5.3607	0.2166	120	0.1464	2583	X-RAY DIFFRACTION	99
5.3607-6.7486	0.2082	139	0.1833	2571	X-RAY DIFFRACTION	100
6.7486-39.9766	0.1877	157	0.1587	2570	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.6779	-0.6868	0.6267	2.9205	0.3088	2.6852	0.024	-0.3966	0.0382	0.0756	0.0215	-0.2575	0.0385	0.0286	-0.0406	0.2768	-0.0419	-0.021	0.3267	-0.0164	0.3355	99.8171	19.1243	148.1051
2	2.5795	-0.7332	1.7914	2.0033	-0.6941	4.8772	-0.0024	0.307	-0.0999	-0.3677	-0.133	0.3667	0.1113	-0.1557	0.1556	0.4494	0.0052	-0.0383	0.3045	-0.0814	0.4206	83.854	32.9008	121.9046
3	0.8924	-0.4851	-0.9227	1.6646	-0.6174	1.8713	-0.2532	-0.04	1.1251	-0.9481	-0.2452	1.0228	-0.866	-1.3487	0.513	1.1504	0.3282	-0.5458	1.0391	-0.1926	1.298	62.9939	42.3761	101.8733
4	2.7796	-1.6167	-0.4647	3.4665	0.2967	2.4505	-0.1279	0.4356	0.3365	-0.2619	-0.3546	0.869	-0.485	-0.8495	0.4328	0.7502	0.0207	-0.311	0.9181	0.0543	0.8072	58.0489	21.7264	79.0881
5	4.2485	0.2876	0.9819	1.9404	0.1013	2.6341	0.107	-0.6693	0.1812	0.3975	-0.2628	0.3732	0.0409	-0.1309	0.1282	0.3855	-0.1099	0.1827	0.5274	-0.1458	0.6153	63.5977	22.0446	156.2874
6	1.3302	-0.5622	-1.024	2.6103	0.5727	3.4847	0.1879	0.1079	0.3164	-0.0546	-0.0352	-0.0456	-0.1033	0.0861	-0.1145	0.2635	0.0208	0.0385	0.3183	0.0427	0.4003	66.377	6.5943	124.6148
7	3.4911	0.2381	-1.0053	2.4352	-0.0556	3.6266	-0.4785	0.0197	-0.3243	-0.1851	0.3128	0.234	0.5784	0.1573	0.1723	0.5418	-0.0385	0.0177	0.3947	0.0543	0.2844	75.5813	-3.2486	96.0738
8	3.0349	-0.4865	-0.326	1.7999	-0.8314	3.3763	-0.1974	0.6338	0.291	-0.4857	0.0752	0.1503	-0.0511	0.0243	0.1386	0.7062	-0.1605	-0.1126	0.5929	0.1316	0.3079	79.3637	10.4895	75.689

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 109 through 302 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 323 through 482 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 497 through 564 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 593 through 717 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 109 through 301 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 318 through 482 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 498 through 573 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 585 through 717 )

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