PDB-5o9l: Crystal structure of human Histamine-Releasing Factor (HRF/TCTP)

ID or keywords:

Entry

Database: PDB / ID: 5o9l

Title

Crystal structure of human Histamine-Releasing Factor (HRF/TCTP)

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 / intracellular calcium ion homeostasis / spindle pole / 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: 1.75 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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PDBx/mmCIF format	5o9l.cif.gz	144.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5o9l.ent.gz	114.5 KB	Display	PDB format
PDBx/mmJSON format	5o9l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/5o9l ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o9l	HTTPS FTP

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Related structure data

Related structure data	5o9kC 5o9mC 1yz1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6lan-d 2isb-d 6pbs-8 3juc-d 3ebm-1 3gs2-3 3q64-d 2acf-3 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

Deposited unit

A: Translationally-controlled tumor protein

B: Translationally-controlled tumor protein

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

1

A: Translationally-controlled tumor protein

defined by author
20.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Translationally-controlled tumor protein

defined by author
20.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.725, 58.952, 57.733
Angle α, β, γ (deg.)	90.00, 99.41, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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: human histamine-releasing factor with C-terminal His-tag Source: (gene. exp.) Homo sapiens (human) / Gene: TPT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13693
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H₂O

#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: human histamine-releasing factor with C-terminal His-tag
Source: (gene. exp.)

Homo sapiens (human) / Gene: TPT1 / Production host:

Escherichia coli (E. coli) / References: UniProt: P13693

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.02 Å³/Da / Density % sol: 39.03 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1M MMT pH4.0 and 25% w/v PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 1.75→24.53 Å / Num. obs: 33094 / % possible obs: 99.3 % / Redundancy: 4.5 % / CC_1/2: 0.988 / R_merge(I) obs: 0.124 / R_pim(I) all: 0.065 / Net I/σ(I): 11.7
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 3.4 % / R_merge(I) obs: 1.085 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1827 / CC_1/2: 0.342 / R_pim(I) all: 0.667 / % possible all: 97.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1yz1

1yz1

Resolution: 1.75→24.528 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 22.9

	R_factor	Num. reflection	% reflection
R_free	0.2209	1643	5 %
R_work	0.1884	-	-
obs	0.19	32846	98.61 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.75→24.528 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2526	0	0	215	2741

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2628
X-RAY DIFFRACTION	f_angle_d	0.632	3552
X-RAY DIFFRACTION	f_dihedral_angle_d	14.127	1590
X-RAY DIFFRACTION	f_chiral_restr	0.049	385
X-RAY DIFFRACTION	f_plane_restr	0.003	459

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 (%)
1.7501-1.8016	0.3211	133	0.2525	2528	X-RAY DIFFRACTION	97
1.8016-1.8597	0.2888	134	0.2421	2549	X-RAY DIFFRACTION	97
1.8597-1.9261	0.3403	134	0.3128	2523	X-RAY DIFFRACTION	96
1.9261-2.0032	0.2589	137	0.2309	2601	X-RAY DIFFRACTION	99
2.0032-2.0943	0.2605	138	0.1906	2612	X-RAY DIFFRACTION	100
2.0943-2.2047	0.2136	139	0.1821	2640	X-RAY DIFFRACTION	100
2.2047-2.3427	0.2915	131	0.2457	2508	X-RAY DIFFRACTION	95
2.3427-2.5234	0.2285	138	0.1867	2623	X-RAY DIFFRACTION	100
2.5234-2.7771	0.207	139	0.187	2641	X-RAY DIFFRACTION	100
2.7771-3.1782	0.2088	139	0.1802	2642	X-RAY DIFFRACTION	100
3.1782-4.0014	0.1956	139	0.1501	2637	X-RAY DIFFRACTION	100
4.0014-24.5308	0.1534	142	0.1521	2699	X-RAY DIFFRACTION	99

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	4.1476	-0.8196	1.6192	2.1389	-0.1958	3.0511	0.04	0.1403	-0.2943	-0.1577	-0.0007	-0.092	0.3171	0.1703	-0.0439	0.1159	0.0184	-0.0105	0.0807	0.0109	0.1365	9.8876	4.2872	58.0592
2	3.0662	-0.5858	-0.2583	2.2822	1.0696	2.0765	-0.1323	-0.4846	-0.1846	0.2793	-0.0141	0.1252	-0.0365	0.0583	0.0932	0.1563	-0.0012	-0.015	0.1791	0.012	0.1671	10.8889	10.6715	67.5132
3	3.4936	2.4009	-2.5276	3.6131	-2.3218	2.0008	0.0315	0.0172	-0.2826	0.0029	-0.2199	-0.4873	0.0262	0.0471	0.2176	0.191	0.0043	-0.0255	0.2063	0.01	0.1951	18.9763	20.4288	58.7447
4	1.0522	0.3767	-0.6161	1.0802	-0.2674	0.3057	0.1206	0.0581	0.0525	-0.0225	-0.1124	-0.1245	-0.0295	0.0055	-0.0243	0.1057	0.0062	-0.0104	0.1425	0.0166	0.1449	13.9852	19.8983	53.9151
5	0.9747	0.09	0.1029	3.9331	-1.238	1.2815	-0.0139	0.2608	-0.273	0.0358	0.123	0.543	0.0083	-0.2928	-0.0625	0.0841	-0.0063	-0.0104	0.1909	0.0078	0.1928	-5.6723	9.8024	58.7206
6	1.1823	-0.065	-0.4029	2.7931	-0.2583	1.246	0.1067	-0.301	-0.1412	0.2347	-0.2764	0.1467	0.0114	-0.2476	0.0163	0.2024	-0.0086	0.0183	0.2613	0.0077	0.1749	-5.9044	10.1491	68.1797
7	1.7405	-0.1696	-0.0824	1.8349	-0.7185	2.5234	0.1238	-0.0826	0.1642	0.2319	-0.1422	-0.0601	-0.1754	-0.0694	-0.0132	0.1266	-0.0136	-0.0181	0.0964	-0.0059	0.1063	6.8743	20.2949	59.2455
8	1.5871	0.3923	0.0289	1.8354	-0.2316	1.2233	0.0158	-0.1097	-0.1252	0.3406	-0.0087	0.0366	0.0791	0.0021	-0.0025	0.1399	-0.0076	-0.0033	0.1546	0.0117	0.0986	8.3084	8.7717	63.7044
9	3.2512	-0.4219	0.9575	1.98	-0.3355	2.3402	0.0182	0.6458	0.7279	-0.425	-0.1898	0.4923	0.0579	-0.123	0.1164	0.2668	0.0533	-0.0721	0.2343	0.0281	0.3153	20.2521	0.9543	55.2508
10	3.3144	1.7557	-0.5003	1.7884	-0.4455	2.0593	-0.1712	0.4488	0.2225	-0.2119	0.2471	0.1889	0.004	-0.3789	0.0176	0.1026	0.0308	-0.0069	0.0811	0.0114	0.1322	-1.6744	25.8678	31.1613
11	4.776	0.6115	1.0996	1.9723	-0.0969	2.2239	0.2272	-0.4919	-0.6765	0.3855	-0.1795	-0.4843	0.0342	-0.0692	0.0573	0.127	-0.0175	-0.0267	0.179	0.0022	0.1496	2.6105	19.6473	43.1847
12	1.7686	1.5867	3.4978	2.0557	2.9152	7.5486	-0.0738	0.2646	0.32	-0.3093	-0.2901	0.3579	-0.3064	-0.1453	0.3131	0.2436	-0.004	-0.0352	0.2483	-0.0639	0.2529	-12.7742	9.1351	26.6058
13	1.2699	1.049	0.5892	1.3837	-0.0186	0.4847	-0.0568	0.1529	-0.0079	-0.0139	-0.0316	0.1933	0.0087	-0.0892	0.0852	0.1085	-0.0043	-0.0045	0.1399	-0.0141	0.1082	-2.5551	12.6048	26.5689
14	0.7567	0.0271	-0.0334	5.4131	0.9755	1.5241	-0.0307	0.0999	0.1405	0.2324	0.1411	-0.6534	-0.033	0.3102	-0.0614	0.1104	-0.0067	0.0212	0.1554	-0.0197	0.1794	16.5514	22.4217	30.3497
15	0.9375	0.0636	0.4883	1.3619	-0.0331	1.6393	-0.0396	-0.0046	-0.0134	0.323	0.0224	-0.2601	-0.0915	0.2455	0.063	0.1381	0.0009	0.0055	0.1496	0.0378	0.1346	13.0795	17.7546	37.5092
16	0.8949	-0.4968	0.1653	2.4218	0.6016	1.5728	0.0141	0.0296	0.0516	-0.1244	-0.0086	0.087	0.1365	-0.029	0.0003	0.0888	0.0055	0.0006	0.0895	0.0023	0.0739	2.4023	17.7226	33.3045
17	1.8977	0.248	0.1342	1.573	-0.0155	0.7773	-0.0504	0.2972	-0.6924	-0.2106	-0.0661	-0.1202	0.6229	0.5493	0.0572	0.2073	0.0826	0.0203	0.3417	-0.0031	0.3621	-10.3046	31.2306	25.7627

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 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 106 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 107 through 127 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 128 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 180 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 18 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 19 through 32 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 33 through 65 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 66 through 84 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 85 through 106 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 107 through 136 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 137 through 171 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 172 through 180 )

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