PDB-4yc1: Structure of the human TSG101-UEV domain in the P321 space group

ID or keywords:

Entry

Database: PDB / ID: 4yc1

Title

Structure of the human TSG101-UEV domain in the P321 space group

Components

Tumor susceptibility gene 101 protein

Keywords

CELL CYCLE / UEV domain Ubiquitin binding

Function / homology

Function and homology information

positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Model details

Crystals obtained at pH 4.5

Authors

Camara-Artigas, A.

Funding support

Spain, 1items

Citation

Journal: to be published
Title: Structure of the human TSG101-UEV Domain
Authors: Camara-Artigas, A.

History

Deposition	Feb 19, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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	4yc1.cif.gz	193.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4yc1.ent.gz	155.5 KB	Display	PDB format
PDBx/mmJSON format	4yc1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4yc1_validation.pdf.gz	451.3 KB	Display	wwPDB validaton report
Full document	4yc1_full_validation.pdf.gz	454 KB	Display
Data in XML	4yc1_validation.xml.gz	19.7 KB	Display
Data in CIF	4yc1_validation.cif.gz	27.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yc/4yc1 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/4yc1	HTTPS FTP

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Related structure data

Related structure data	2f0rS S: Starting model for refinement
Similar structure data	1m6z-3 4bjt-2 1yui-d 1udz-2 4bjt-3 7nlj-d 5sv2-d 5tfn-2 2mpo-d 1p2x-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2f0rS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (3) #234 - Jun 2019 MDM2 and Cancer similarity (3) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Tumor susceptibility gene 101 protein

B: Tumor susceptibility gene 101 protein

C: Tumor susceptibility gene 101 protein

hetero molecules

55.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tumor susceptibility gene 101 protein

hetero molecules

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

2

B: Tumor susceptibility gene 101 protein

hetero molecules

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

3

C: Tumor susceptibility gene 101 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	169.739, 169.739, 39.707
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

#1: Protein	Tumor susceptibility gene 101 protein / ESCRT-I complex subunit TSG101 / TSG101 Mass: 18241.164 Da / Num. of mol.: 3 / Fragment: UEV domain, residues 1-145 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: pRSETa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99816
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 224 / 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: 3.24 Å³/Da / Density % sol: 62.06 % / Description: hexagonal prism
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG4k, 0.2 Ammonium sulphate, 0.1 M Sodium Acetate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.97779 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2014

Radiation

Monochromator: Si(111) channel-cut crystal monochromator and a pair of KB mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97779 Å / Relative weight: 1

Reflection

Redundancy: 8.6 % / Number: 381505 / R_merge(I) obs: 0.059 / D res high: 2 Å / D res low: 19.67 Å / Num. obs: 44232 / % possible obs: 99.7 / Rejects: 110

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Redundancy
2	2.06	1	0.559	8.3
8.49	19.67	1	0.03	7.9

Reflection

Resolution: 2→19.67 Å / Num. obs: 44232 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / B_iso Wilson estimate: 31.85 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.059 / Net I/σ(I): 22.6 / Num. measured all: 381505 / Scaling rejects: 110

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	CC_1/2	% possible all
2-2.06	8.3	0.559	4.5	29916	3606	0.928	100
8.49-19.67	7.9	0.03	58.5	4499	571	0.999	91.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
Aimless	0.3.11	data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2F0R

2f0r

Resolution: 2→19.67 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1967	4133	4.83 %	Random selection
R_work	0.1639	81442	-	-
obs	0.1655	44065	99.06 %	-

Solvent computation

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

Displacement parameters

B_iso max: 160.51 Å² / B_iso mean: 48.8471 Å² / B_iso min: 17.56 Å²

Refinement step

Cycle: final / Resolution: 2→19.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3464	0	25	224	3713
B_iso mean	-	-	59.97	45.77	-
Num. residues	-	-	-	-	440

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	3581
X-RAY DIFFRACTION	f_angle_d	1.376	4901
X-RAY DIFFRACTION	f_chiral_restr	0.061	562
X-RAY DIFFRACTION	f_plane_restr	0.009	609
X-RAY DIFFRACTION	f_dihedral_angle_d	11.072	1314

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0001-2.0228	0.3496	136	0.2409	2704	2840	100
2.0228-2.0466	0.2866	172	0.2416	2702	2874	99
2.0466-2.0715	0.2948	134	0.2301	2765	2899	100
2.0715-2.0977	0.2696	134	0.2012	2733	2867	100
2.0977-2.1253	0.241	106	0.1949	2752	2858	100
2.1253-2.1543	0.2343	126	0.1955	2744	2870	100
2.1543-2.1851	0.2439	144	0.188	2745	2889	100
2.1851-2.2177	0.2098	143	0.1818	2742	2885	100
2.2177-2.2523	0.3887	100	0.3263	2462	2562	90
2.2523-2.2891	0.2691	144	0.2237	2505	2649	92
2.2891-2.3285	0.182	172	0.161	2756	2928	100
2.3285-2.3708	0.2541	140	0.1647	2708	2848	100
2.3708-2.4163	0.2136	134	0.159	2724	2858	100
2.4163-2.4656	0.2174	130	0.1647	2761	2891	99
2.4656-2.5191	0.2099	127	0.1636	2674	2801	98
2.5191-2.5775	0.2267	124	0.1592	2733	2857	100
2.5775-2.6419	0.1825	150	0.1659	2806	2956	100
2.6419-2.7131	0.2018	145	0.1688	2659	2804	100
2.7131-2.7927	0.2479	150	0.1673	2723	2873	100
2.7927-2.8826	0.2274	115	0.1723	2793	2908	100
2.8826-2.9853	0.1997	146	0.1762	2717	2863	100
2.9853-3.1044	0.2204	134	0.1751	2757	2891	100
3.1044-3.2451	0.1757	161	0.1733	2661	2822	99
3.2451-3.4153	0.1918	146	0.1738	2715	2861	100
3.4153-3.6281	0.1537	154	0.1566	2782	2936	100
3.6281-3.9062	0.2256	114	0.1439	2710	2824	99
3.9062-4.2956	0.1617	168	0.1276	2689	2857	100
4.2956-4.9087	0.1559	131	0.1208	2722	2853	99
4.9087-6.1529	0.1837	152	0.1507	2708	2860	100
6.1529-19.6758	0.1389	101	0.159	2790	2891	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	0.4663	0.37	-0.0183	0.2422	-0.0965	0.135	-0.3775	-0.6366	0.1697	0.1457	0.3463	0.1307	-0.2262	0.1872	-0.0818	0.2892	0.0964	-0.0051	0.5417	0.0024	0.2073	-45.1857	-53.0257	34.3426
2	0.0341	-0.043	-0.0363	0.0239	0.0239	0.0253	0.012	-0.0786	0.1093	0.0498	-0.0449	-0.1267	-0.2094	0.054	-0.0002	0.2427	0.0104	-0.0028	0.3816	-0.0302	0.2037	-45.0267	-50.4818	27.4086
3	0.4894	0.373	0.5887	1.4958	0.456	0.9491	-0.2189	-0.3107	-0.2485	-0.1793	0.0491	0.2124	0.4978	-0.4516	-0.6959	0.375	-0.0198	0.1792	0.2834	0.1071	0.3134	-52.1766	-63.1842	28.8171
4	0.1976	0.2648	-0.133	0.1855	-0.1983	0.1076	0.0089	-0.2201	-0.0197	-0.0416	-0.039	0.0504	0.2424	-0.1148	0	0.2525	0.0197	0.0303	0.3329	0.0047	0.3203	-59.4781	-57.6926	22.2441
5	0.5407	-0.396	0.1421	0.3962	-0.1036	0.6625	-0.0014	0.0521	-0.172	-0.0051	0.0044	0.0922	0.1235	0.07	-0	0.2263	0.0327	-0.0023	0.2738	-0.03	0.3151	-51.584	-62.6407	16.9612
6	0.1164	-0.231	-0.0947	0.2801	0.115	0.2907	-0.0033	0.07	0.0722	0.0153	0.1412	0.3149	0.0727	0.0142	-0.0002	0.195	-0.0112	-0.0295	0.2581	-0.001	0.2755	-61.3059	-56.7514	13.7385
7	0.0431	-0.0487	0.035	0.0034	-0.0006	-0.0127	0.1296	-0.3051	-0.0417	-0.4402	-0.0355	-0.0506	-0.2544	0.3911	-0.0005	0.397	0.0371	0.002	0.4843	-0.0356	0.3122	-56.3019	-41.968	-12.1732
8	0.2258	-0.1035	0.0283	0.0295	0.0182	0.0204	-0.1657	0.2911	-0.1509	-0.3235	0.3462	-0.2633	-0.5741	0.4702	0.0014	0.3434	-0.1315	0.0538	0.5225	-0.0044	0.2467	-42.9705	-34.9588	-0.5095
9	0.0662	0.0027	0.0536	0.0631	-0.0802	0.0562	0.2386	-0.1792	-0.309	-0.4207	-0.2551	-0.1981	0.2141	0.0949	-0.0003	0.2991	-0.0176	0.0448	0.4346	-0.0459	0.2596	-46.1574	-41.7207	4.5058
10	0.3392	-0.3449	0.1695	0.2978	-0.2551	0.4319	-0.0201	0.3296	0.1073	-0.1121	-0.0123	0.3504	-0.3112	-0.1581	-0.002	0.3551	-0.0173	-0.0155	0.3023	0.0303	0.2093	-56.2415	-32.5758	4.6871
11	0.2522	-0.4373	-0.0927	0.6135	-0.2104	0.6017	-0.0434	-0.0463	-0.0801	-0.1259	0.0327	0.0808	-0.226	0.0394	0.0002	0.3027	-0.0188	0.0055	0.3392	-0.0403	0.2956	-57.1172	-35.542	10.2822
12	0.0666	0.0361	-0.0948	0.0806	0.0643	0.1665	0.17	-0.0101	0.0399	-0.0238	0.0309	0.309	-0.3403	0.1009	-0.0002	0.3233	0.0222	-0.0257	0.3387	0.0222	0.4411	-64.7267	-28.5855	8.7532
13	0.1621	-0.0181	0.0474	-0.0156	-0.046	-0.0104	-0.0959	-0.1713	0.2048	0.0997	0.0416	0.2567	-0.2115	-0.0013	-0.0001	0.3176	0.0178	0.0211	0.3067	-0.0527	0.3545	-62.335	-30.2111	18.5131
14	0.057	0.1065	0.073	0.4184	0.056	-0.0681	0.0952	-0.0863	-0.414	0.094	-0.0534	0.023	-0.1518	0.0111	0.0002	0.2203	0.0038	0.0323	0.3003	-0.0363	0.2332	-54.7917	-41.0527	16.4764
15	0.0568	-0.0204	-0.0415	0.0303	-0.006	0.0249	0.1347	-0.23	-0.0537	-0.2331	0.1284	0.3312	0.0894	0.2017	-0.0001	0.2751	0.0751	-0.0621	0.3196	-0.0246	0.5863	-75.0214	-34.2012	14.9018
16	0.0002	0.0016	-0.0034	0.0067	0.0142	0.0168	-0.0214	0.0181	-0.0212	0.196	-0.1002	0.1376	-0.024	-0.2557	0.0002	0.89	-0.1762	0.0842	0.625	-0.0578	0.6786	-29.7112	-32.0373	34.7145
17	0.1064	0.089	0.0777	0.2731	-0.2412	0.5265	-0.3347	-0.3997	-0.2207	0.1018	-0.2651	0.1176	0.1307	-0.1032	-0.5311	0.739	-0.4383	0.2651	0.7473	-0.2312	0.5392	-39.3402	-33.1401	26.6108
18	0.0645	-0.1016	0.0453	0.1053	-0.0186	0.0466	-0.1531	-0.5338	-0.177	0.0139	-0.2436	-0.0908	0.2268	-0.4172	-0.0001	0.5749	-0.1584	0.0481	0.5409	-0.0148	0.5331	-26.7589	-32.5543	25.1949
19	0.0181	0.0719	-0.0335	0.3114	-0.0774	0.0557	0.3031	0.5218	-0.089	0.5184	-0.3399	-0.275	-0.0032	-0.2431	-0.0194	0.5438	-0.0738	0.0548	0.7071	-0.1077	0.5081	-33.5941	-20.2333	27.5262
20	0.1865	-0.3378	0.1968	0.3688	-0.2544	0.2653	0.1799	-0.0595	0.571	0.4444	-0.0651	-0.2494	-0.0514	-0.2502	0.0035	0.4255	-0.0861	0.0208	0.5147	-0.0233	0.7334	-24.2332	-16.0509	23.2794
21	0.0069	0.0068	-0.0618	0.2044	-0.2616	0.4516	-0.0387	-0.1093	0.441	-0.0027	-0.3088	0.1302	-0.1262	-0.3973	0	0.4388	-0.0691	-0.0405	0.4465	-0.0585	0.7029	-31.7839	-16.0588	19.2111
22	0.0347	0.0208	0.0521	0.0105	0.0114	0.0352	-0.2692	-0.3156	0.4887	-0.0978	0.1906	0.1535	0.0446	-0.2639	-0.0003	0.3693	-0.051	-0.0428	0.5018	0.0311	0.6071	-32.4551	-16.5332	12.8342
23	0.0922	-0.0681	0.0436	0.0494	0.0482	0.0182	0.1046	0.222	0.0746	0.2862	-0.0239	-0.3876	0.045	-0.0686	-0.0002	0.3844	-0.0834	0.0008	0.4235	0.0164	0.5285	-25.3877	-24.1067	13.3232
24	0.0124	0.0003	-0.0208	0.0246	-0.02	0.0226	0.4626	-0.029	-0.145	-0.2894	-0.1118	-0.3954	0.037	0.1063	-0.0002	0.6511	-0.0036	0.0193	0.4085	-0.0357	1.1925	-20.4603	-3.602	18.2315

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 17 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 31 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 32 through 48 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 49 through 75 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 76 through 123 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 124 through 145 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -3 through 4 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 17 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 18 through 29 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 30 through 63 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 64 through 85 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 86 through 94 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 95 through 115 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 116 through 137 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 138 through 145 )	B
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 3 through 11 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 12 through 17 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 18 through 31 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 32 through 48 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 49 through 75 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 76 through 104 )	C
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 105 through 115 )	C
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 116 through 137 )	C
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 138 through 145 )	C

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Open data

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi