PDB-8q0p: Crystal Structure of an N-terminal Domain of Variant Surface Glyc...

ID or keywords:

Entry

Database: PDB / ID: 8q0p

Title

Crystal Structure of an N-terminal Domain of Variant Surface Glycoprotein 21 (VSG21) of Trypanosome brucei brucei Lister 427

Components

Variant surface glycoprotein MITat 1.21

Keywords

MEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Glycosylation MEMBRANE PROTEIN

Function / homology

Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / evasion of host immune response /

plasma membrane / Variant surface glycoprotein MITat 1.21

Function and homology information

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 Å

Authors

Zeelen, J.P. / Stebbins, C.E.

Funding support

Germany, 1items

Citation

Journal: Plos Negl Trop Dis / Year: 2023
Title: A structural classification of the variant surface glycoproteins of the African trypanosomey.
Authors: Dakovic, S. / Zeelen, J.P. / Gkeka, A. / Chandra, M. / van Straaten, M. / Foti, K. / Zhong, J. / Vlachou, E.P. / Aresta-Branco, F. / Verdi, J.P. / Papavasiliou, F.N. / Stebbins, C.E.

History

Deposition	Jul 28, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 13, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8q0p.cif.gz	549.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8q0p.ent.gz	445.1 KB	Display	PDB format
PDBx/mmJSON format	8q0p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q0/8q0p ftp://data.pdbj.org/pub/pdb/validation_reports/q0/8q0p	HTTPS FTP

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Related structure data

Related structure data	8ok4C 8ok5C 8ok6C 8ok7C 8ok8C 8onhC 8q0eC C: citing same article (ref.)
Similar structure data	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: Variant surface glycoprotein MITat 1.21

B: Variant surface glycoprotein MITat 1.21

C: Variant surface glycoprotein MITat 1.21

D: Variant surface glycoprotein MITat 1.21

E: Variant surface glycoprotein MITat 1.21

F: Variant surface glycoprotein MITat 1.21

298 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Variant surface glycoprotein MITat 1.21

B: Variant surface glycoprotein MITat 1.21

defined by author
Evidence: gel filtration
99.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Variant surface glycoprotein MITat 1.21

D: Variant surface glycoprotein MITat 1.21

defined by author
Evidence: gel filtration
99.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Variant surface glycoprotein MITat 1.21

F: Variant surface glycoprotein MITat 1.21

defined by author
Evidence: gel filtration
99.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	174.329, 84.422, 120.095
Angle α, β, γ (deg.)	90.00, 100.89, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Variant surface glycoprotein MITat 1.21 Mass: 49718.664 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: MITat 1.21 / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q58NS8
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 891 / 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 grow	Temperature: 295 K / Method: vapor diffusion / pH: 7 / Details: 100 mM Tris/HCl, 200 mM CaCL2, 20 % (W/V) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.01→48.53 Å / Num. obs: 111578 / % possible obs: 97.85 % / Redundancy: 7 % / CC_1/2: 0.996 / Net I/σ(I): 8.17
Reflection shell	Resolution: 2.01→2.082 Å / Num. unique obs: 10775 / CC_1/2: 0.53 / % possible all: 95.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
pointless		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.01→48.53 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2194	5579	5 %
R_work	0.1789	-	-
obs	0.1809	111578	97.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.01→48.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10006	0	0	891	10897

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	10215
X-RAY DIFFRACTION	f_angle_d	0.664	13936
X-RAY DIFFRACTION	f_dihedral_angle_d	5.438	1437
X-RAY DIFFRACTION	f_chiral_restr	0.044	1802
X-RAY DIFFRACTION	f_plane_restr	0.006	1784

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 (%)
2.01-2.03	0.3685	164	0.3219	3100	X-RAY DIFFRACTION	87
2.03-2.05	0.3366	184	0.3098	3501	X-RAY DIFFRACTION	97
2.05-2.08	0.343	183	0.3139	3465	X-RAY DIFFRACTION	97
2.08-2.11	0.336	186	0.3099	3566	X-RAY DIFFRACTION	97
2.11-2.13	0.3479	183	0.2898	3468	X-RAY DIFFRACTION	97
2.13-2.16	0.3076	184	0.2583	3503	X-RAY DIFFRACTION	97
2.16-2.19	0.2818	182	0.2533	3478	X-RAY DIFFRACTION	97
2.19-2.23	0.2755	187	0.2348	3540	X-RAY DIFFRACTION	97
2.23-2.26	0.3091	183	0.2346	3477	X-RAY DIFFRACTION	97
2.26-2.3	0.274	185	0.2199	3509	X-RAY DIFFRACTION	97
2.3-2.34	0.2633	185	0.2094	3508	X-RAY DIFFRACTION	98
2.34-2.38	0.2608	185	0.2056	3522	X-RAY DIFFRACTION	98
2.38-2.43	0.2946	188	0.2071	3558	X-RAY DIFFRACTION	98
2.43-2.48	0.2605	184	0.2096	3526	X-RAY DIFFRACTION	98
2.48-2.53	0.2471	185	0.2011	3519	X-RAY DIFFRACTION	98
2.53-2.59	0.2786	186	0.2102	3520	X-RAY DIFFRACTION	98
2.59-2.65	0.2461	187	0.2073	3549	X-RAY DIFFRACTION	98
2.65-2.72	0.2636	187	0.1991	3559	X-RAY DIFFRACTION	98
2.72-2.81	0.2211	186	0.1955	3540	X-RAY DIFFRACTION	98
2.81-2.9	0.2401	187	0.1863	3545	X-RAY DIFFRACTION	98
2.9-3	0.2658	189	0.1949	3589	X-RAY DIFFRACTION	98
3-3.12	0.2419	187	0.1854	3561	X-RAY DIFFRACTION	98
3.12-3.26	0.2288	188	0.1923	3568	X-RAY DIFFRACTION	99
3.26-3.43	0.232	188	0.1827	3576	X-RAY DIFFRACTION	99
3.43-3.65	0.1737	189	0.1537	3581	X-RAY DIFFRACTION	99
3.65-3.93	0.2006	189	0.1577	3590	X-RAY DIFFRACTION	99
3.93-4.32	0.1959	189	0.1392	3604	X-RAY DIFFRACTION	99
4.32-4.95	0.1625	191	0.128	3625	X-RAY DIFFRACTION	99
4.95-6.23	0.1793	192	0.1561	3638	X-RAY DIFFRACTION	99
6.23-48.53	0.1596	196	0.1453	3714	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	3.2646	-1.9001	-1.5178	5.094	2.4507	4.833	0.0781	0.7376	-0.1828	-0.4579	-0.1371	-0.3177	0.1547	0.0235	0.0242	0.319	0.0019	0.1436	0.3916	-0.0531	0.4432	-6.0418	-35.7844	-69.1426
2	2.0795	-0.723	-0.9817	1.2282	0.5953	1.4855	0.0258	-0.0544	0.3325	0.0287	0.0582	-0.1288	-0.1257	0.0074	-0.1009	0.2773	0.0089	0.0594	0.2039	0.0317	0.3722	-22.0981	-13.4216	-46.7133
3	6.0745	-1.7013	-2.8276	3.0263	0.8249	2.1041	-0.0733	0.131	-0.1223	-0.235	-0.0193	-0.0744	-0.0181	0.2084	0.1247	0.3016	-0.0053	0.1089	0.3392	0.0053	0.4476	2.0366	-32.3155	-60.8557
4	2.0566	-1.8435	-1.8197	4.0388	3.1962	4.855	-0.5487	0.058	-0.9433	0.2035	0.1251	-0.1177	0.9257	0.3507	0.1968	0.5157	0.0325	0.1434	0.3778	-0.095	0.5983	-11.9029	-49.7343	-57.5115
5	2.6178	-1.9284	-2.3501	3.675	3.0091	6.061	-0.0949	0.5451	-0.5277	-0.3579	0.0495	-0.2312	0.3366	0.0809	-0.0465	0.406	-0.0552	0.2016	0.4106	-0.1599	0.5214	-11.9527	-44.759	-66.3381
6	1.0201	-0.3722	-0.0882	2.1898	0.9129	1.0759	-0.1393	-0.2334	0.0198	0.3953	0.1199	-0.1935	0.2225	0.1101	-0.0118	0.3661	0.0403	0.0462	0.2946	-0.0047	0.3739	-21.9785	-22.098	-34.5637
7	1.1896	0.7201	0.5225	2.2085	0.6851	1.5955	-0.0672	0.2795	-0.1205	-0.0956	0.1093	-0.0076	0.1335	-0.056	0.0183	0.3453	-0.0522	0.0937	0.3436	-0.0256	0.3792	-25.4479	-42.8449	-60.8711
8	5.8584	-4.9121	-0.4432	4.1581	0.324	0.3565	-0.0196	-0.0003	-1.4156	0.0199	-0.3453	2.2812	0.0911	-0.5034	0.2357	0.7056	-0.0596	0.1965	0.6855	-0.1657	1.0385	-3.968	-15.2344	-20.3607
9	5.6327	-2.1599	0.6642	4.8427	-0.9801	1.8797	-0.0172	-0.1182	0.1994	-0.1466	-0.0126	0.6765	-0.3787	-0.3998	0.0719	0.3332	0.0351	0.0718	0.4225	-0.064	0.4661	-7.2024	1.6163	-20.1731
10	2.7761	-1.1536	-0.8257	0.925	0.6779	0.8549	-0.0811	0.0688	-0.2917	0.0414	-0.024	0.0069	0.1482	-0.0586	0.0869	0.3545	-0.0144	0.1118	0.2921	-0.0055	0.4058	22.4414	-22.2017	-23.9339
11	3.5488	-0.8188	-1.5618	2.7258	0.4565	1.1925	0.0052	-0.1194	-0.1587	0.0408	-0.1361	0.2053	0.0733	-0.202	0.1346	0.3361	0.0113	0.1173	0.3783	-0.04	0.3629	2.2073	-7.4981	-9.044
12	6.0531	-6.8138	6.2079	9.0988	-5.806	8.125	-1.076	-1.4984	2.7148	0.0846	0.8192	-0.9142	-1.2991	-1.3967	0.2576	0.6044	0.0958	0.0044	0.8308	-0.0872	0.9654	19.8192	11.0974	-21.846
13	9.4732	-6.3732	0.737	5.8458	-1.0506	1.3183	-0.1425	-0.682	0.6059	0.1174	0.1784	0.1474	-0.1838	-0.1929	-0.0637	0.3483	0.0307	0.0219	0.3363	-0.0879	0.5903	5.7637	11.1609	-18.3594
14	3.3988	-4.2003	1.9738	5.4902	-1.6354	2.7263	0.1673	0.1151	0.1527	-0.2606	-0.161	0.2649	-0.0539	-0.3109	0.0252	0.3382	0.0348	0.0927	0.3977	0.0137	0.4981	5.8563	3.3565	-24.1095
15	2.6252	-1.8494	0.0412	2.9838	0.165	0.4557	-0.1102	-0.1385	0.1161	0.2176	0.0665	-0.2514	0.0394	0.0892	0.0506	0.3422	0.0039	0.0894	0.2844	0.0057	0.3766	35.2027	-15.7378	-20.3577
16	4.8852	-1.7107	-0.6177	4.907	0.1579	2.4377	-0.0943	0.5822	0.5584	-0.0781	0.0103	-0.035	-0.2573	-0.2065	0.0753	0.2875	-0.0389	0.0057	0.3758	0.0915	0.3171	12.0009	4.8603	-33.2321
17	3.9206	2.7294	-0.188	5.6602	2.6086	4.0266	-0.236	-0.5659	0.4561	0.7049	0.3661	-1.1432	-0.5486	2.7101	-0.1957	0.5892	0.0249	-0.112	1.059	-0.118	0.9175	-11.3539	-32.7753	-15.1453
18	5.9627	0.0417	4.6803	2.2472	-0.5164	7.5299	0.2659	-0.6119	-0.0847	0.6397	-0.1275	-0.4702	0.5225	0.5464	-0.1936	0.5438	-0.0066	-0.1291	0.6162	-0.0345	0.5954	-11.8261	-40.3927	-2.4259
19	5.2565	-0.3414	3.8279	2.3942	-0.1349	6.6492	0.0747	-0.7713	-0.039	0.6249	0.1659	-0.324	-0.0917	-0.2316	-0.0564	0.5292	-0.0041	-0.0573	0.4549	-0.0309	0.5016	-21.7472	-37.5744	-3.7763
20	2.1992	0.7884	1.3962	0.9857	0.419	2.4323	-0.0245	0.1319	-0.1268	-0.0659	0.1403	-0.2056	0.0579	0.0349	-0.1292	0.3179	-0.0127	0.0812	0.2701	-0.014	0.3766	-35.5706	-41.2968	-39.1586
21	5.0355	2.355	2.5308	2.5834	1.4135	4.2375	0.1891	-0.1302	0.2916	0.1235	-0.0429	0.1235	-0.4477	0.3311	0.1278	0.4397	-0.0883	0.0486	0.4491	-0.0328	0.4691	-23.8514	-26.1387	-19.4298
22	7.9439	0.6048	4.4262	3.8634	0.683	7.7226	-0.1056	-0.6595	0.5389	0.5689	0.0133	-0.2717	-0.6754	0.3731	0.0962	0.5232	-0.032	0.0341	0.4778	-0.0736	0.4007	-23.4512	-27.3908	-7.5073
23	5.7287	-0.0623	1.9858	2.0367	1.5331	3.7563	0.1574	-2.8272	-1.0376	0.5541	0.4231	-0.0566	0.6502	-1.6802	-0.6811	0.7787	-0.0444	0.0101	0.9401	0.1774	0.6641	-39.1162	-50.5179	-0.4318
24	4.9652	0.575	4.9231	2.2369	0.1336	9.2465	0.1443	-0.7505	-0.2721	0.8008	0.06	-0.4647	0.162	-0.1343	-0.239	0.8015	0.0199	-0.1298	0.5547	0.0183	0.4851	-23.4983	-45.5703	6.9994
25	1.6444	-0.5671	2.5713	0.8642	-1.6167	6.2336	-0.0497	-0.2507	0.1709	0.1954	0.1001	-0.1024	-0.1333	-0.3043	-0.0701	0.3712	0.0196	0.028	0.2896	-0.0097	0.348	-38.8882	-38.8136	-25.6624
26	3.4971	-0.2259	1.9645	3.2012	-5.1113	8.9249	-0.286	-0.4472	0.1581	0.6167	0.2569	0.1739	-0.6579	-0.618	0.0547	0.7511	0.0833	0.1241	0.4495	-0.0765	0.5041	-40.4266	-31.8376	-10.8594
27	1.5498	0.0074	0.8482	0.8371	-0.7957	4.0309	0.0362	-0.0395	-0.1355	0.0254	0.1789	0.1682	0.1016	-0.4414	-0.2216	0.3179	-0.0298	0.0596	0.3204	0.0003	0.3433	-49.3725	-44.7655	-30.9478
28	2.8945	0.6527	0.9378	4.7082	-3.2995	9.0685	0.2731	-0.5897	-0.8762	-0.0149	0.4023	0.2947	0.8838	-0.329	-0.5514	0.4904	0.0329	0.0036	0.3455	0.0875	0.4857	-36.1744	-57.3749	-12.1271
29	2.7677	0.3052	1.0835	2.9284	-1.3384	5.5316	0.1892	-0.3534	-0.5206	0.5172	-0.0609	-0.4807	0.4834	0.4112	-0.1606	0.4527	0.0305	-0.099	0.3741	0.0314	0.5183	-26.3701	-55.8263	-6.984

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 22 through 132 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 133 through 250 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 251 through 294 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 23 through 61 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 62 through 132 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 133 through 238 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 239 through 292 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 22 through 34 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 35 through 106 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 107 through 250 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 251 through 294 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 23 through 34 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 35 through 94 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 95 through 132 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 133 through 250 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 251 through 293 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 22 through 34 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 35 through 94 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 95 through 132 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 133 through 238 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 239 through 250 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 251 through 293 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 23 through 34 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 35 through 106 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 107 through 160 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 161 through 170 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 171 through 238 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 239 through 251 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 252 through 293 )

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About Yorodumi

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Yorodumi