PDB-5o9m: Crystal structure of human Histamine-Releasing Factor (HRF/TCTP)c...

ID or keywords:

Entry

Database: PDB / ID: 5o9m

Title

Crystal structure of human Histamine-Releasing Factor (HRF/TCTP)containing a disulphide-linked dimer

Components

Translationally-controlled tumor protein

Keywords

IMMUNE SYSTEM / Immunoglobulin E / Allergy / Histamine Releasing Factor / TCTP / HRF / p23 / p21 / fortilin

Function / homology

Function and homology information

negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cytoplasmic microtubule / multivesicular body / response to virus / spindle pole / intracellular calcium ion homeostasis / calcium ion transport / regulation of apoptotic process / calcium ion binding / negative regulation of apoptotic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Dore, K.A. / Kashiwakura, J. / McDonnell, J.M. / Gould, H.J. / Kawakami, T. / Sutton, B.J. / Davies, A.M.

Funding support

United Kingdom, 1items

Citation

Journal: Mol. Immunol. / Year: 2017
Title: Crystal structures of murine and human Histamine-Releasing Factor (HRF/TCTP) and a model for HRF dimerisation in mast cell activation.
Authors: Dore, K.A. / Kashiwakura, J.I. / McDonnell, J.M. / Gould, H.J. / Kawakami, T. / Sutton, B.J. / Davies, A.M.

History

Deposition	Jun 19, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5o9m.cif.gz	149.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5o9m.ent.gz	117.8 KB	Display	PDB format
PDBx/mmJSON format	5o9m.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5o9m_validation.pdf.gz	444.1 KB	Display	wwPDB validaton report
Full document	5o9m_full_validation.pdf.gz	445.2 KB	Display
Data in XML	5o9m_validation.xml.gz	17 KB	Display
Data in CIF	5o9m_validation.cif.gz	25.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/5o9m ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o9m	HTTPS FTP

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Related structure data

Related structure data	5o9kC 5o9lC 1yz1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3cto-4 6lnp-2 5ejc-2 3hix-d 3p01-1 6hxt-d 6lnp-1 1r3f-d 3pnr-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

Deposited unit

A: Translationally-controlled tumor protein

B: Translationally-controlled tumor protein

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	47.527, 77.592, 99.325
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Translationally-controlled tumor protein / TCTP / Fortilin / Histamine-releasing factor / HRF / p23 Mass: 20690.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: protein contains a C-terminal His-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: TPT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13693
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.21 Å³/Da / Density % sol: 44.42 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES pH6.0 and 20% (w/v) PEG MME 2000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 23, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 1.4→19.86 Å / Num. obs: 72800 / % possible obs: 99.7 % / Redundancy: 7.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.066 / R_pim(I) all: 0.025 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.4→1.43 Å / Redundancy: 7.6 % / R_merge(I) obs: 1.112 / Num. unique obs: 3759 / CC_1/2: 0.703 / R_pim(I) all: 0.428 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YZ1

1yz1

Resolution: 1.4→19.855 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.85

	R_factor	Num. reflection	% reflection
R_free	0.1985	3666	5.04 %
R_work	0.1793	-	-
obs	0.1803	72706	99.58 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.4→19.855 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2509	0	5	301	2815

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	2656
X-RAY DIFFRACTION	f_angle_d	1.546	3600
X-RAY DIFFRACTION	f_dihedral_angle_d	13.9	994
X-RAY DIFFRACTION	f_chiral_restr	0.114	401
X-RAY DIFFRACTION	f_plane_restr	0.009	463

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 (%)
1.4-1.4184	0.3313	143	0.2937	2577	X-RAY DIFFRACTION	99
1.4184-1.4379	0.2875	144	0.2813	2637	X-RAY DIFFRACTION	99
1.4379-1.4584	0.3008	143	0.2679	2571	X-RAY DIFFRACTION	99
1.4584-1.4802	0.2742	141	0.2523	2630	X-RAY DIFFRACTION	99
1.4802-1.5033	0.2509	133	0.2518	2614	X-RAY DIFFRACTION	99
1.5033-1.5279	0.273	123	0.2428	2639	X-RAY DIFFRACTION	99
1.5279-1.5543	0.2816	138	0.2286	2597	X-RAY DIFFRACTION	99
1.5543-1.5825	0.2481	146	0.2183	2661	X-RAY DIFFRACTION	100
1.5825-1.6129	0.2426	139	0.1997	2623	X-RAY DIFFRACTION	100
1.6129-1.6458	0.2029	149	0.192	2631	X-RAY DIFFRACTION	100
1.6458-1.6816	0.1839	140	0.179	2630	X-RAY DIFFRACTION	100
1.6816-1.7207	0.1757	139	0.1776	2653	X-RAY DIFFRACTION	100
1.7207-1.7637	0.1992	133	0.1771	2658	X-RAY DIFFRACTION	100
1.7637-1.8114	0.1927	133	0.1743	2653	X-RAY DIFFRACTION	100
1.8114-1.8646	0.1951	130	0.174	2665	X-RAY DIFFRACTION	100
1.8646-1.9248	0.1833	145	0.1726	2616	X-RAY DIFFRACTION	100
1.9248-1.9935	0.2053	145	0.1727	2659	X-RAY DIFFRACTION	100
1.9935-2.0732	0.164	149	0.1664	2668	X-RAY DIFFRACTION	100
2.0732-2.1675	0.1792	136	0.1669	2638	X-RAY DIFFRACTION	98
2.1675-2.2816	0.1754	137	0.1647	2669	X-RAY DIFFRACTION	100
2.2816-2.4243	0.1932	138	0.1694	2675	X-RAY DIFFRACTION	100
2.4243-2.6111	0.2218	136	0.1829	2689	X-RAY DIFFRACTION	100
2.6111-2.8732	0.2272	137	0.1835	2708	X-RAY DIFFRACTION	100
2.8732-3.2873	0.1844	145	0.1779	2718	X-RAY DIFFRACTION	100
3.2873-4.1355	0.1698	160	0.1532	2706	X-RAY DIFFRACTION	99
4.1355-19.8571	0.1869	164	0.1689	2855	X-RAY DIFFRACTION	100

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	0.5133	-0.2404	0.2577	0.4614	-0.3219	0.2452	0.0389	-0.0261	-0.0057	0.0546	-0.0171	-0.0004	0.1334	0.066	0.0001	0.1097	0.0012	0.0014	0.1099	-0.0011	0.121	-8.9771	11.1196	-32.5703
2	0.2962	-0.3695	0.2026	0.5445	-0.5244	0.8217	0.1924	-0.4351	0.1108	0.4183	-0.0685	0.9858	-0.1063	-0.8061	0.285	-0.0124	0.0069	0.0103	0.3232	-0.0226	0.3277	-23.4266	16.4265	-32.28
3	0.2782	-0.4157	0.1987	1.043	0.2651	0.7689	-0.365	0.1652	0.5638	-0.1462	0.2489	0.0222	-0.2753	0.2386	-0.0026	0.1625	-0.0289	-0.0105	0.2052	-0.0203	0.186	-4.1014	26.9261	-29.2847
4	0.7693	-0.1534	-0.2024	0.3071	0.7505	1.3989	0.0297	0.1495	0.3374	-0.0187	-0.0054	-0.1564	-0.5402	0.2196	0.064	0.1205	-0.0282	-0.0079	0.1298	0.0343	0.1317	-3.679	24.2955	-36.5387
5	2.7808	-1.9948	-0.3169	2.5349	-0.135	3.3318	-0.2662	1.7279	-1.0716	-0.3005	0.2308	1.031	0.8715	-0.916	-0.7032	0.1443	-0.0422	-0.189	0.3432	0.0078	-0.1933	-17.8172	10.8274	-48.6616
6	0.9146	0.4893	0.4804	3.0296	0.1542	0.5268	0.0174	-0.345	-0.0414	0.7773	0.1859	0.2526	0.0702	-0.416	0.054	0.152	-0.0163	-0.049	0.2969	0.048	0.1839	-24.5831	16.5725	-44.8233
7	1.8983	0.871	0.596	1.2122	-0.6601	1.3393	-0.1144	-0.0171	0.2644	0.1924	0.0201	0.1257	-0.3148	0.0093	-0.0046	0.1383	0.0057	-0.009	0.1158	-0.0027	0.1181	-10.9658	22.7657	-39.6496
8	0.5285	0.2661	0.1664	0.1325	0.0776	0.3352	-0.0446	-0.0978	-0.1179	0.0292	0.0482	0.1608	0.14	-0.0966	0.001	0.1113	-0.0185	-0.0039	0.124	-0.0019	0.1593	-15.2007	13.9303	-34.796
9	0.1266	0.0638	-0.0072	0.0302	-0.0084	-0.0053	-0.3691	-0.4675	-0.4814	0.8343	0.3467	-0.3571	0.952	1.0268	0.0512	0.7191	0.2846	0.0427	0.3751	0.0846	0.3132	-3.5663	-2.4689	-17.6236
10	0.4956	-0.0662	0.2987	0.3786	0.2307	0.3668	0.0358	0.0096	-0.1831	0.0571	-0.0146	0.0797	0.3271	0.0139	-0.0001	0.1633	-0.0118	-0.0117	0.1044	0.0085	0.1276	0.0961	11.3902	-17.6391
11	1.1528	-0.5941	0.9072	0.8756	0.1191	1.3693	-0.077	0.1508	0.24	0.0522	-0.0375	-0.3633	-0.1163	0.6172	0.0256	0.1179	0.0198	-0.0097	0.1981	0.0271	0.1582	12.5051	17.1784	-17.2682
12	-0.3608	-0.1462	0.1705	0.3365	-0.1768	0.0059	0.0181	-0.0501	0.0233	0.0547	0.0271	0.3449	-0.0442	-0.1483	-0.0004	0.1996	0.0019	0.0191	0.1576	0.006	0.2367	-4.5669	43.4291	-19.7843
13	2.0618	0.7089	-0.8516	0.8378	0.5572	1.6732	0.0077	-0.5189	-0.1103	0.0998	-0.0047	-0.0459	0.2714	0.1306	0.0083	0.1666	0.0185	0.0069	0.1671	0.0027	0.0933	3.6886	15.545	-4.7073
14	0.9839	0.2922	-0.6576	1.337	-1.1669	1.4824	-0.4002	-0.057	-0.0597	-0.8597	0.2588	0.0882	0.4504	0.4403	-0.0725	0.2742	0.062	-0.113	0.2628	-0.0004	0.2306	15.618	16.4057	-4.9079
15	0.8549	-0.7223	0.3875	1.1114	0.0345	0.7344	-0.0216	-0.1243	-0.0137	0.0749	-0.0878	-0.0783	0.0144	0.003	0.0002	0.126	-0.0055	0.0011	0.1158	0.0036	0.0972	2.4143	22.5934	-10.1025
16	0.5656	-0.2106	0.12	0.1849	-0.2758	0.5294	0.0446	0.0209	-0.1728	-0.2043	-0.0347	-0.0324	0.3099	0.0914	-0.0153	0.1824	0.0332	-0.0218	0.1171	0.0192	0.1584	6.0631	13.1442	-14.8828
17	0.1177	-0.048	-0.0224	0.1905	-0.0784	0.0417	-0.0513	0.0852	0.0248	-0.4252	0.0977	0.2451	-0.1279	-0.1151	-0	0.2085	-0.0154	-0.0085	0.1212	-0.0073	0.172	-4.6937	1.2129	-31.7949

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 27 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 28 through 64 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 65 through 84 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 85 through 107 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 108 through 131 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 132 through 157 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 158 through 171 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 172 through 178 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 19 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 20 through 32 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 33 through 70 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 71 through 107 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 108 through 131 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 132 through 157 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 158 through 171 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 172 through 177 )

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