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

ID or keywords:

Entry

Database: PDB / ID: 4z1i

Title

Crystal structure of human Trap1 with AMPPNP

Components

Heat shock protein 75 kDa, mitochondrial

Keywords

CHAPERONE / Mitochondrial Hsp90 / AMPPNP

Function / homology

Function and homology information

translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.3 Å

Authors

Lee, C. / Park, H.K. / Ryu, J.H. / Kang, B.H.

Citation

Journal: 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

Deposition	Mar 27, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 29, 2015	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4z1i.cif.gz	723.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4z1i.ent.gz	619.8 KB	Display	PDB format
PDBx/mmJSON format	4z1i.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4z1i_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	4z1i_full_validation.pdf.gz	1.8 MB	Display
Data in XML	4z1i_validation.xml.gz	70.6 KB	Display
Data in CIF	4z1i_validation.cif.gz	93 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z1/4z1i ftp://data.pdbj.org/pub/pdb/validation_reports/z1/4z1i	HTTPS FTP

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Related structure data

Related structure data	4z1fC 4z1gC 4z1hC C: citing same article (ref.)
Similar structure data	4gnx-2 4gnx-1 4pca-d 5ki6-d 5tcy-d 4q5v-1 4gop-1 2y0e-2 5j6f-d 1xia-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#32 - Aug 2002
Chaperones
similarity (1)
#108 - Dec 2008
Hsp90
similarity (5)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

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

232 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Heat shock protein 75 kDa, mitochondrial

C: Heat shock protein 75 kDa, mitochondrial

hetero molecules

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

2

B: Heat shock protein 75 kDa, mitochondrial

D: Heat shock protein 75 kDa, mitochondrial

hetero molecules

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

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 number	170
Space group name H-M	P6₅

#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

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.6 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 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

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
HKL-2000		data processing
Coot		model building
PHENIX		phasing

Refinement

Resolution: 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

	R_factor	Num. reflection	% reflection
R_free	0.2847	1895	4.96 %
R_work	0.2199	-	-
obs	0.2231	38205	99.13 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.3→37.822 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14117	0	128	0	14245

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	14545
X-RAY DIFFRACTION	f_angle_d	1.679	19569
X-RAY DIFFRACTION	f_dihedral_angle_d	16.632	5451
X-RAY DIFFRACTION	f_chiral_restr	0.066	2184
X-RAY DIFFRACTION	f_plane_restr	0.008	2460

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 (%)
3.2963-3.3787	0.3705	132	0.2985	2536	X-RAY DIFFRACTION	98
3.3787-3.47	0.3674	132	0.2835	2525	X-RAY DIFFRACTION	97
3.47-3.572	0.3763	138	0.2716	2579	X-RAY DIFFRACTION	98
3.572-3.6872	0.3594	134	0.2587	2598	X-RAY DIFFRACTION	99
3.6872-3.8189	0.3039	137	0.2509	2603	X-RAY DIFFRACTION	100
3.8189-3.9717	0.3399	135	0.229	2615	X-RAY DIFFRACTION	100
3.9717-4.1522	0.2587	138	0.2163	2597	X-RAY DIFFRACTION	100
4.1522-4.3708	0.2515	140	0.1926	2599	X-RAY DIFFRACTION	100
4.3708-4.6442	0.2467	130	0.1843	2611	X-RAY DIFFRACTION	100
4.6442-5.002	0.2489	136	0.1931	2626	X-RAY DIFFRACTION	100
5.002-5.504	0.2635	135	0.2131	2617	X-RAY DIFFRACTION	100
5.504-6.2973	0.2574	133	0.2271	2604	X-RAY DIFFRACTION	100
6.2973-7.922	0.3232	137	0.221	2623	X-RAY DIFFRACTION	100
7.922-37.8241	0.2402	138	0.1895	2577	X-RAY DIFFRACTION	97

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	5.0609	-2.8821	-4.6344	8.0301	4.398	9.3266	0.2252	-0.838	0.2647	-0.0694	0.0632	-0.5433	-0.1042	1.5741	-0.1885	0.511	0.0476	-0.0959	0.6671	0.1695	0.2761	21.7251	114.5015	19.8719
2	2.9569	0.2217	0.2755	3.5333	1.4155	3.944	-0.0012	0.3691	-0.1234	-0.1575	0.01	0.1553	-0.3206	0.1162	0.0017	0.4112	0.1121	0.0001	0.3351	-0.0396	0.3548	15.2443	88.6557	-14.7817
3	7.1202	-3.75	0.7632	2.3148	0.0516	1.5653	0.0742	0.2182	0.5405	-0.3297	-0.305	0.7064	-0.3344	-0.6242	0.2652	0.7898	0.2544	-0.1402	0.6948	0.0032	0.8411	-10.1247	103.745	-16.0875
4	1.4392	0.6275	0.1907	3.1436	-1.2895	1.4826	0.3369	0.3851	-1.4475	0.811	0.8907	0.2422	0.0198	-0.8858	-0.734	0.5719	0.3915	0.0614	1.0143	0.0822	1.0705	-27.7415	107.0269	-13.4114
5	3.5341	1.6132	5.2057	4.4416	0.4254	8.9867	0.5342	-0.3927	-0.2212	-0.4223	-0.0644	-0.2786	1.0451	-0.4208	-0.5553	0.6008	-0.0191	0.0049	0.5854	-0.0234	0.3569	23.5904	118.3089	-41.3917
6	5.0258	0.0994	-0.2972	3.0076	1.263	3.283	-0.0091	-0.5815	-0.237	-0.086	0.1368	-0.1167	-0.0033	0.1937	-0.1368	0.2176	-0.0716	-0.0969	0.4833	0.0392	0.4251	38.385	139.7883	-6.2236
7	5.7788	-2.9132	-1.1896	1.9098	0.8892	3.0856	-0.1301	-0.7353	-0.2539	0.2421	0.1449	-0.1702	-0.3236	0.1211	-0.0353	0.3579	-0.1021	-0.0615	0.5846	0.003	0.4352	9.6344	144.7045	-1.9192
8	8.1571	-2.0801	0.7505	1.9895	-0.4228	3.8147	-0.1726	-0.4045	0.0169	0.2347	0.0663	0.1335	-0.2821	-0.6022	0.0167	0.3162	0.0066	0.0283	0.4489	-0.045	0.3531	-18.6821	150.9226	-8.1623
9	2.0901	1.6659	2.553	5.6115	3.7063	7.8173	0.0958	-0.0816	-0.4025	-0.0076	0.4703	-0.8177	0.0399	0.5404	-0.6238	0.4885	0.1183	-0.0619	0.6844	0.0057	0.5119	24.7182	82.6245	-14.2533
10	2.9217	0.2828	-0.2043	1.9954	0.2972	2.8236	-0.1185	0.0113	0.1786	-0.2563	-0.0545	0.1352	-0.0068	0.072	0.1505	0.613	0.0508	-0.0978	0.1885	-0.0328	0.3636	12.3976	108.2721	18.8461
11	5.4368	1.9228	-0.3076	1.428	-0.9848	1.6218	-0.2076	-0.0086	-0.0551	0.0137	0.126	0.1519	0.37	-0.6379	0.0438	0.7872	-0.0724	-0.1098	0.5407	-0.1335	0.5978	-12.6898	93.1865	17.0733
12	3.9125	1.2356	1.6672	2.3187	0.4226	2.9681	-0.1759	0.0101	-0.2369	-0.1986	-0.0664	0.3827	0.538	-1.1128	0.3401	1.0551	-0.3531	-0.1096	1.0882	-0.2147	0.9049	-36.4369	80.1335	5.0072
13	3.1073	0.2598	1.9397	1.1835	0.8689	3.3527	0.3289	-0.1449	-0.656	-0.3039	0.4485	-0.5286	-0.5489	0.8731	-0.5581	0.3681	-0.1002	0.117	0.9551	-0.1105	0.6072	49.3827	138.0472	-7.3002
14	2.5618	-0.3979	0.0439	3.4519	0.4358	3.86	-0.1157	0.0751	-0.1514	-0.4128	0.1404	0.1123	-0.0893	-0.1585	-0.0352	0.3759	-0.1597	-0.0271	0.2459	-0.0405	0.3749	20.7046	128.8718	-39.3835
15	3.6029	-4.6315	-0.0934	6.148	0.9952	2.2351	0.2416	0.3401	0.4801	-0.6995	-0.1859	-0.4342	-0.2435	-0.2769	-0.0206	0.6596	-0.129	-0.0176	0.476	0.0542	0.4789	11.9282	157.01	-34.3593
16	1.7995	0.6131	-0.8127	5.6202	2.4252	1.8779	0.1944	-0.638	1.0171	0.281	-0.2719	0.0223	-0.6368	-0.2313	0.051	0.8416	-0.0539	-0.0881	0.5973	-0.1391	0.799	5.363	179.18	-22.45

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 70 through 93)
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 94 through 297 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 298 through 434 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 435 through 454 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 70 through 93 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 94 through 297 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 298 through 434 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 435 through 553 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 70 through 93 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 94 through 297 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 298 through 434 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 435 through 553 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 70 through 93 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 94 through 297 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 298 through 434 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 435 through 550 )

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