PDB-6z8g: Crystal structure of VSG13 soaked in 0.5 M used to phase VSG13 to...

ID or keywords:

Entry

Database: PDB / ID: 6z8g

Title

Crystal structure of VSG13 soaked in 0.5 M used to phase VSG13 to solve the structure.

Components

Variant surface glycoprotein MITat 1.13

Keywords

MEMBRANE PROTEIN / Variant Surface Glycoprotein / Immune Recognition / Immune Evasion / Trypanosomiasis

Function / homology

Trypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / symbiont-mediated evasion of host immune response / side of membrane / plasma membrane / BROMIDE ION / Variant surface glycoprotein MITat 1.13

Function and homology information

Biological species

Trypanosoma brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.56 Å

Authors

Stebbins, C.E. / Hempelmann, A. / Van Straaten, M. / Zeelen, J.

Citation

Journal: Nat Microbiol / Year: 2021
Title: Structure of trypanosome coat protein VSGsur and function in suramin resistance.
Authors: Zeelen, J. / van Straaten, M. / Verdi, J. / Hempelmann, A. / Hashemi, H. / Perez, K. / Jeffrey, P.D. / Halg, S. / Wiedemar, N. / Maser, P. / Papavasiliou, F.N. / Stebbins, C.E.

History

Deposition	Jun 2, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_branch_descriptor / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6z8g.cif.gz	302.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6z8g_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6z8g_full_validation.pdf.gz	1.2 MB	Display
Data in XML	6z8g_validation.xml.gz	37 KB	Display
Data in CIF	6z8g_validation.cif.gz	51.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z8/6z8g ftp://data.pdbj.org/pub/pdb/validation_reports/z8/6z8g	HTTPS FTP

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Related structure data

Related structure data	6z79C 6z7bC 6z7cC 6z7dC 6z7eC 6z8hC C: citing same article (ref.)
Similar structure data	6z8h-d 4odx-d 3fz5-d 6v0y-d 1l9a-d 6a0z-d 7byd-2 6xqp-1 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	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Variant surface glycoprotein MITat 1.13

B: Variant surface glycoprotein MITat 1.13

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	74.148, 68.407, 157.759
Angle α, β, γ (deg.)	90.000, 92.170, 90.000
Int Tables number	5
Space group name H-M	C121
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein

Variant surface glycoprotein MITat 1.13

Mass: 53771.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural)

Trypanosoma brucei (eukaryote) / References: UniProt: Q58NS4

#2: Polysaccharide

alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...

Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}	LINUCS	PDB-CARE

#3: Chemical

...
ChemComp-BR / BROMIDE ION

Mass: 79.904 Da / Num. of mol.: 23
Source method: isolated from a genetically manipulated source
Formula: Br

#4: Chemical

ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO₄

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

Has protein modification

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal grow	Temperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Purified methylated VSG13 N-terminal domain was concentrated to 2.5 mg/ml in 10mM Tris.Cl pH 8.0. Crystals were grown at 23C by vapour diffusion using hanging drops formed from mixing a 1:1 ...Details: Purified methylated VSG13 N-terminal domain was concentrated to 2.5 mg/ml in 10mM Tris.Cl pH 8.0. Crystals were grown at 23C by vapour diffusion using hanging drops formed from mixing a 1:1 volume ratio of the protein with an equilibration buffer consisting of 1.8-2.0M (NH4)2SO4, 100mM Tris.Cl pH 8.5.

Crystal grow

Temperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Purified methylated VSG13 N-terminal domain was concentrated to 2.5 mg/ml in 10mM Tris.Cl pH 8.0. Crystals were grown at 23C by vapour diffusion using hanging drops formed from mixing a 1:1 ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9198 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 29, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9198 Å / Relative weight: 1
Reflection	Resolution: 1.56→52.55 Å / Num. obs: 109295 / % possible obs: 97.2 % / Redundancy: 4 % / B_iso Wilson estimate: 19.34 Å² / CC_1/2: 0.983 / Net I/σ(I): 18.77
Reflection shell	Resolution: 1.56→1.62 Å / Num. unique obs: 109295 / CC_1/2: 0.983

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
xia2		data reduction
SHELXDE		phasing
Aimless		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.56→52.55 Å / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.68
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2

	R_factor	Num. reflection	% reflection
R_free	0.233	3905	1.85 %
R_work	0.226	207180	-
obs	0.226	109077	95.7 %

Solvent computation

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

Displacement parameters

B_iso max: 113.38 Å² / B_iso mean: 32.92 Å² / B_iso min: 15 Å²

Refinement step

Cycle: final / Resolution: 1.56→52.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5142	0	128	529	5799
B_iso mean	-	-	38.89	41.22	-
Num. residues	-	-	-	-	695

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.56-1.58	0.3981	87	0.3928	5067	5154	64
1.58-1.6	0.3437	106	0.3768	5136	5242	68
1.6-1.62	0.3613	128	0.3604	5998	6126	76
1.62-1.64	0.37	141	0.3427	6347	6488	84
1.64-1.67	0.332	124	0.336	7138	7262	92
1.67-1.69	0.3079	145	0.329	7645	7790	98
1.69-1.72	0.3399	129	0.3098	7687	7816	100
1.72-1.75	0.2822	140	0.3054	7761	7901	100
1.75-1.78	0.3024	164	0.3095	7590	7754	100
1.78-1.81	0.2521	131	0.2963	7867	7998	100
1.81-1.84	0.2575	142	0.288	7569	7711	100
1.84-1.88	0.2736	139	0.2781	7781	7920	100
1.88-1.92	0.2488	146	0.2725	7659	7805	100
1.92-1.97	0.2464	161	0.2585	7698	7859	100
1.97-2.01	0.2876	119	0.2548	7875	7994	100
2.01-2.07	0.3232	149	0.2557	7618	7767	100
2.07-2.13	0.243	145	0.2501	7734	7879	100
2.13-2.2	0.2666	137	0.2407	7830	7967	100
2.2-2.28	0.2988	130	0.2384	7715	7845	100
2.28-2.37	0.3006	143	0.2355	7676	7819	100
2.37-2.48	0.2414	167	0.2261	7678	7845	100
2.48-2.61	0.2479	144	0.2319	7759	7903	100
2.61-2.77	0.2303	130	0.2257	7763	7893	100
2.77-2.98	0.2392	153	0.2266	7771	7924	100
2.98-3.28	0.2119	144	0.2049	7648	7792	100
3.28-3.76	0.1701	159	0.1809	7727	7886	100
3.76-4.74	0.1605	166	0.159	7703	7869	100
4.74-52.55	0.1989	136	0.1937	7740	7876	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	0.0067	0.0108	0.0232	0.1019	0.156	0.2502	-0.1953	-0.0654	-0.2248	0.1152	-0.1103	0.2137	0.7037	-0.5246	0.125	0.5537	-0.2194	0.1315	0.3709	-0.0719	0.374	31.0539	46.7095	53.8033
2	2.0883	-0.008	-1.9166	0.3703	0.117	2.7603	-0.2063	-0.1416	-0.2158	0.1264	-0.0273	-0.0618	0.3327	0.0411	0.1485	0.3343	-0.0369	0.0061	0.1587	-0.0125	0.255	54.633	52.191	28.1601
3	1.7078	-0.4877	-1.6381	0.4768	0.5012	2.5195	0.0242	0.0968	-0.0482	-0.0248	-0.0931	-0.0177	0.1568	-0.2509	0.1286	0.2812	-0.0778	0.0063	0.1661	-0.0324	0.2264	48.0513	53.5506	23.6701
4	0.5649	-0.0629	-0.8731	0.6017	0.5769	2.7595	-0.2731	0.0188	-0.1639	0.1217	-0.0911	0.0308	0.6345	-0.4409	0.2033	0.2266	-0.098	-0.0077	0.4165	-0.0511	0.2338	23.6167	59.0101	73.9808
5	1.9772	-0.5033	-1.042	1.0363	0.4549	2.4589	-0.1665	-0.1687	-0.0873	0.1285	-0.0764	0.1089	0.5775	-0.2531	0.2244	0.3309	-0.0712	0.0491	0.356	-0.0243	0.2349	29.5126	55.8513	75.1999
6	0.0096	-0.0625	-0.1232	0.4096	0.8003	1.5958	-0.1326	-0.1785	-0.1335	0.2667	-0.0098	-0.0106	0.6915	-0.2511	0.1794	0.8106	-0.1001	0.1364	0.5189	0.0185	0.4267	35.6214	41.2564	54.2
7	1.4087	0.4498	-1.3119	1.7251	1.1086	3.9134	-0.1463	0.2835	-0.3539	-0.0756	-0.1252	0.1425	0.5355	-0.4551	0.2603	1.0049	-0.3403	0.1779	0.5718	-0.1167	0.4992	28.0243	42.2079	43.6644
8	0.2983	-0.206	-0.0655	0.5591	0.6125	0.8294	-0.0333	-0.1795	0.0009	0.2481	-0.1683	0.2224	0.2761	-0.4749	0.0983	0.4212	-0.3282	0.0764	0.6861	-0.1546	0.3013	15.3763	52.5908	70.6194
9	0.0157	0.1097	0.0621	0.7721	0.4391	0.2512	-0.0924	-0.0323	-0.1575	0.0849	-0.0563	0.2334	0.4101	-0.4811	0.0958	0.8209	-0.4097	0.312	0.9286	-0.1227	0.5166	5.4695	52.8621	91.5412
10	0.3402	0.1222	-0.2695	0.4482	-0.0498	0.5304	-0.134	0.0931	-0.1865	0.1265	-0.1667	0.1703	0.3989	-0.5752	0.1483	0.3409	-0.2658	0.0571	0.5773	-0.1142	0.3221	17.9042	52.3253	63.0978
11	0.0151	-0.0688	-0.1134	0.33	0.6308	1.2472	-0.0496	-0.0383	-0.1092	-0.0798	-0.1568	0.1068	0.5135	-0.2347	0.1524	0.4521	-0.0864	0.023	0.2097	-0.0202	0.2738	51.2161	43.3118	18.717
12	1.2076	-0.3272	-0.7389	1.4289	0.4282	0.7159	-0.0127	0.3225	-0.2617	-0.1316	-0.0573	-0.0847	0.505	-0.2574	-0.0049	0.6022	-0.0664	0.0561	0.1024	-0.0556	0.307	56.5732	39.3583	7.3976
13	0.7447	0.2175	-0.3935	1.1058	0.0907	1.5332	-0.0026	-0.1948	-0.1298	0.0854	-0.0169	-0.3534	0.3397	0.2258	0.0329	0.213	0.0127	-0.0309	0.1571	-0.0093	0.2906	69.7191	55.9162	23.6112
14	2.4877	-1.3563	-2.534	4.2011	0.9214	6.0068	0.0232	0.1185	-0.2188	-0.3002	0.0289	-0.0641	0.2042	0.183	-0.062	0.3861	-0.0498	0.1151	0.4125	-0.112	0.4554	71.8477	66.4364	9.9487
15	0.9561	-0.2898	-1.0623	0.3809	0.3639	2.0629	0.1218	0.0757	0.1027	-0.0035	-0.0126	0.051	-0.2436	-0.393	0.0379	0.1842	-0.027	-0.0346	0.2474	-0.0126	0.2434	39.8044	72.1493	43.191
16	1.3573	-0.1416	-0.5325	1.774	-0.2337	4.191	0.0666	0.116	-0.0508	-0.2795	0.0867	-0.1866	-0.1353	0.191	0.031	0.2417	-0.0571	-0.0339	0.1431	-0.0065	0.22	58.3869	66.9143	12.4592
17	0.9673	0.1803	-1.0437	0.6972	-0.3453	3.2622	-0.0187	-0.0621	0.0018	-0.172	0.032	-0.0705	-0.0167	0.0623	0.0227	0.1912	-0.0422	-0.0263	0.147	-0.0237	0.2264	59.5599	69.1979	24.2586
18	1.6724	0.0192	-0.9607	0.409	-0.0931	1.3393	-0.1342	-0.0047	-0.1029	-0.0819	-0.0148	0.0457	0.1709	-0.2446	0.0815	0.1445	-0.059	-0.0319	0.2673	-0.0252	0.1956	36.4192	64.2948	52.7666
19	3.7513	0.5364	-0.7714	1.3888	-0.5544	2.7579	0.0963	-0.0468	0.1787	0.1198	0.0237	0.152	-0.044	-0.4948	-0.0038	0.128	0.018	-0.0201	0.635	-0.0201	0.2723	16.6477	67.1508	69.8643
20	0.9636	0.4103	-0.4316	0.4227	-0.4116	1.2669	-0.0573	-0.0123	-0.0152	0.1312	-0.1788	0.22	0.1598	-0.5165	-0.0657	0.1091	-0.4225	0.1056	1.2027	-0.2895	0.444	2.5755	61.0165	83.6307
21	1.2641	0.3662	0.4567	0.8168	0.0579	0.7475	0.0253	-0.1285	0.1496	0.0004	-0.1832	0.218	0.0324	-0.4192	-0.1328	0.108	-0.0522	-0.0485	0.7442	-0.0933	0.2925	13.8639	67.0165	64.52
22	0.8635	0.6599	-1.6247	0.7988	-0.8138	3.7019	0.0491	-0.1127	0.0466	-0.0599	0.0393	-0.1392	-0.336	-0.0257	0.0012	0.3136	-0.0324	0.0075	0.3031	-0.0484	0.3205	41.1587	78.4676	55.1837
23	1.5067	-0.0789	-0.6711	0.3259	0.1548	1.4494	-0.018	-0.2711	0.1138	0.2987	-0.0328	0.2468	-0.134	-0.7001	0.0082	0.056	0.0244	-0.0285	0.7792	-0.095	0.2744	13.9877	70.7535	84.915
24	-0.088	-0.1007	-0.0983	0.2369	0.0984	0.995	-0.017	0.0181	0.0094	0.0075	0.0149	0.0257	-0.1275	-0.2977	0.0103	0.1155	-0.0077	-0.0547	0.2877	-0.0265	0.192	35.6849	71.5202	61.3193
25	0.9668	-0.3637	-0.4189	1.4505	0.0517	1.2725	0.0801	-0.0204	0.0203	-0.4518	-0.137	-0.2226	-0.1481	0.3296	-0.0914	0.2446	-0.0574	0.0126	0.2125	-0.041	0.3597	74.3588	77.0197	18.9116
26	2.6007	0.2529	-0.6137	0.7832	-0.215	1.1095	0.0658	-0.0117	0.5309	-0.1108	0.045	0.0516	-0.4765	0.1659	-0.0627	0.3671	-0.0515	-0.0224	0.1139	-0.01	0.2977	60.9495	84.8055	16.3934
27	0.7884	-0.1826	-0.3846	1.2964	0.3348	1.8269	-0.0784	0.1872	-0.0461	-0.2478	-0.0911	0.2228	0.1613	-0.3316	0.0824	0.2567	-0.0617	-0.0394	0.1997	-0.021	0.2417	50.137	62.7454	8.1125
28	1.1711	0.5679	-0.3527	1.6243	0.282	2.4433	-0.0821	0.1581	-0.101	-0.2705	-0.0247	-0.2561	0.2952	0.2109	0.0542	0.3955	-0.0276	0.0865	0.1934	0.0278	0.3448	63.3143	53.5508	4.3126

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 28:45)	A	28 - 45
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 46:80)	A	46 - 80
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 81:111)	A	81 - 111
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 112:152)	A	112 - 152
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 153:166)	A	153 - 166
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 167:179)	A	167 - 179
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 180:187)	A	180 - 187
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 188:205)	A	188 - 205
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 206:217)	A	206 - 217
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 218:280)	A	218 - 280
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 281:298)	A	281 - 298
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 299:334)	A	299 - 334
13	X-RAY DIFFRACTION	13	(CHAIN A AND RESID 335:379)	A	335 - 379
14	X-RAY DIFFRACTION	14	(CHAIN A AND RESID 380:384)	A	380 - 384
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 28:65)	B	28 - 65
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 66:79)	B	66 - 79
17	X-RAY DIFFRACTION	17	(CHAIN B AND RESID 80:103)	B	80 - 103
18	X-RAY DIFFRACTION	18	(CHAIN B AND RESID 104:129)	B	104 - 129
19	X-RAY DIFFRACTION	19	(CHAIN B AND RESID 130:135)	B	130 - 135
20	X-RAY DIFFRACTION	20	(CHAIN B AND RESID 136:149)	B	136 - 149
21	X-RAY DIFFRACTION	21	(CHAIN B AND RESID 150:172)	B	150 - 172
22	X-RAY DIFFRACTION	22	(CHAIN B AND RESID 175:190)	B	175 - 190
23	X-RAY DIFFRACTION	23	(CHAIN B AND RESID 191:217)	B	191 - 217
24	X-RAY DIFFRACTION	24	(CHAIN B AND RESID 218:296)	B	218 - 296
25	X-RAY DIFFRACTION	25	(CHAIN B AND RESID 297:318)	B	297 - 318
26	X-RAY DIFFRACTION	26	(CHAIN B AND RESID 319:338)	B	319 - 338
27	X-RAY DIFFRACTION	27	(CHAIN B AND RESID 339:378)	B	339 - 378
28	X-RAY DIFFRACTION	28	(CHAIN B AND RESID 379:384)	B	379 - 384

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