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- PDB-6z7b: Variant Surface Glycoprotein VSGsur bound to suramin -

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Basic information

Entry
Database: PDB / ID: 6z7b
TitleVariant Surface Glycoprotein VSGsur bound to suramin
ComponentsVariant surface glycoprotein Sur
KeywordsMEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Drug resistance Glycosylation VSG
Function / homologyVariant surface glycoprotein C-terminal domain superfamily / side of membrane / plasma membrane / Chem-SVR / Variant surface glycoprotein Sur
Function and homology information
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsZeelen, J.P. / Straaten van, M. / Stebbins, C.E. / Jeffrey, P.
CitationJournal: 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
DepositionMay 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variant surface glycoprotein Sur
B: Variant surface glycoprotein Sur
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3525
Polymers104,9362
Non-polymers4,4163
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14260 Å2
ΔGint2 kcal/mol
Surface area32810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.688, 79.219, 118.029
Angle α, β, γ (deg.)90.000, 90.780, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Variant surface glycoprotein Sur


Mass: 52468.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei rhodesiense (eukaryote)
Gene: VSGsur / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A291L8F4
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN


Mass: 1297.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C51H40N6O23S6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19-24 % PEG 400 100 mM TEA/HCl pH=7.5 10 % (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→48.35 Å / Num. obs: 81517 / % possible obs: 99.91 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 12.25
Reflection shellResolution: 1.86→1.926 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.32 / Num. unique obs: 8077 / CC1/2: 0.725 / % possible all: 99.77

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
SCALAdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z79

6z79


Resolution: 1.86→48.35 Å / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 25.05 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.222 3941 4.83 %
Rwork0.1899 77607 -
obs0.1961 81517 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.85 Å2 / Biso mean: 21.5358 Å2 / Biso min: 2.32 Å2
Refinement stepCycle: final / Resolution: 1.86→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5626 0 296 648 6570
Biso mean--32.26 24.78 -
Num. residues----758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.890.36041890.31983886407595
1.89-1.930.31811830.27753819400295
1.93-1.960.3182120.26873861407394
1.96-20.25482100.23873807401794
2-2.050.22882150.21753852406795
2.05-2.090.23521820.2153908409096
2.09-2.150.23571960.20213858405495
2.15-2.210.21661670.19933908407596
2.21-2.270.23271970.20363854405195
2.27-2.340.22181820.20833870405296
2.34-2.430.21951850.20223877406295
2.43-2.520.23471970.20673901409895
2.52-2.640.21621700.20593922409296
2.64-2.780.22261930.20013836402995
2.78-2.950.24471830.19783905408896
2.95-3.180.22182210.18623848406995
3.18-3.50.25011770.16853927410496
3.5-4.010.20672120.16243890410295
4.01-5.050.17242020.14963910411295
5.05-48.350.21442370.18293968420594
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.3686-0.0656-0.17280.5273-0.27230.2747-0.0578-0.17390.0710.15130.0389-0.0233-0.10720.10940.06390.049-0.0243-0.00690.07-0.01760.109713.462734.727724.7574
20.4492-0.13350.06410.6137-0.17511.607-0.0138-0.05690.0193-0.0126-0.00940.00040.10810.03420.01680.001-0.0001-0.00780.0169-0.0030.073310.414227.70499.5624
30.5722-0.16450.01050.6175-0.330.31590.11020.13530.1352-0.2313-0.1028-0.07280.02070.0590.0320.080.0030.02890.05740.01210.093713.735634.3171-11.6008
40.85870.2099-0.7120.2510.3682.3239-0.04180.25930.0025-0.367-0.1205-0.2360.15440.40310.00260.44210.15640.14260.35390.12050.164921.208828.6337-38.1151
50.0782-0.03810.37711.4280.1882.06430.0309-0.04210.0769-0.0024-0.06180.31440.0664-0.3757-0.00440.0621-0.0011-0.00880.0747-0.00890.1829-3.924637.10333.9861
60.8015-0.11311.03450.5899-0.49941.572-0.0896-0.28150.03660.2203-0.0490.0234-0.2805-0.35490.16220.09970.00730.00210.1374-0.0020.13794.52136.686226.1194
76.1748-0.8642-1.42292.83650.71483.71-0.2831-0.2294-0.49920.6734-0.0130.7656-0.0768-0.8740.14670.37750.07090.10920.3449-0.03420.3107-2.360534.367955.1926
83.6095-0.42320.3191.3893-0.7922.3605-0.1351-0.33660.27790.39060.0409-0.2082-0.38040.29010.08390.366-0.0287-0.070.3264-0.02860.1515.669336.843653.3497
92.0762-1.25932.78945.7732-1.34393.7840.1818-0.18170.0150.0354-0.126-0.56020.21710.5633-0.06320.16510.0241-0.03240.2940.00390.168325.823821.149548.2246
100.3306-0.0765-0.00630.40220.35522.342-0.014-0.1267-0.0420.08220.01560.01480.0655-0.08270.04170.058-0.0074-0.0070.07180.01250.097812.474912.693923.1588
110.3364-0.0154-0.01170.4413-0.11761.76370.0166-0.03250.02-0.0162-0.0277-0.03130.06950.11080.02930.01210.00780.00890.0262-0.00140.102815.141721.73039.5021
120.5291-0.2120.07030.1980.21770.45230.06810.0373-0.0723-0.0976-0.00360.02030.05670.028-0.02060.0539-0.0084-0.00910.03490.00210.109112.985414.5514-4.6363
130.4499-0.28790.31490.5966-0.17971.44770.05430.1053-0.0112-0.2434-0.0567-0.0766-0.0010.0460.07480.14190.01240.01710.0679-0.00340.092417.130121.5387-15.8151
141.03550.627-0.41461.8771-0.68820.2902-0.0709-0.1857-0.04660.2141-0.0833-0.15920.38450.14530.07790.23550.0752-0.01030.2557-0.00790.119620.55776.967744.065
152.20050.4672-0.05782.2195-0.08242.28810.0136-0.2035-0.09730.24480.04460.1180.3046-0.0928-0.04970.2626-0.03560.00160.238-0.01280.07499.11686.157950.4873
164.80860.6764-2.73695.28950.74674.19270.0353-0.14970.09010.3255-0.08650.6281-0.3113-0.6481-0.0180.2070.04910.01140.2579-0.0010.1938-0.327622.538348.5768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 85 )A30 - 85
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 162 )A86 - 162
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 231 )A163 - 231
4X-RAY DIFFRACTION4chain 'A' and (resid 232 through 259 )A232 - 259
5X-RAY DIFFRACTION5chain 'A' and (resid 260 through 288 )A260 - 288
6X-RAY DIFFRACTION6chain 'A' and (resid 289 through 322 )A289 - 322
7X-RAY DIFFRACTION7chain 'A' and (resid 323 through 344 )A323 - 344
8X-RAY DIFFRACTION8chain 'A' and (resid 345 through 386 )A345 - 386
9X-RAY DIFFRACTION9chain 'A' and (resid 387 through 411 )A387 - 411
10X-RAY DIFFRACTION10chain 'B' and (resid 30 through 85 )B30 - 85
11X-RAY DIFFRACTION11chain 'B' and (resid 86 through 162 )B86 - 162
12X-RAY DIFFRACTION12chain 'B' and (resid 163 through 213 )B163 - 213
13X-RAY DIFFRACTION13chain 'B' and (resid 214 through 302 )B214 - 302
14X-RAY DIFFRACTION14chain 'B' and (resid 303 through 344 )B303 - 344
15X-RAY DIFFRACTION15chain 'B' and (resid 345 through 386 )B345 - 386
16X-RAY DIFFRACTION16chain 'B' and (resid 387 through 412 )B387 - 412

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