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- PDB-6z7c: Variant Surface Glycoprotein VSGsur mutant H122A -

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Basic information

Entry
Database: PDB / ID: 6z7c
TitleVariant Surface Glycoprotein VSGsur mutant H122A
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 / Variant surface glycoprotein Sur
Function and homology information
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsZeelen, J.P. / Straaten van, M. / Stebbins, C.E.
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 17, 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6362
Polymers52,4011
Non-polymers1,2351
Water5,927329
1
A: Variant surface glycoprotein Sur
hetero molecules

A: Variant surface glycoprotein Sur
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2724
Polymers104,8022
Non-polymers2,4702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area11430 Å2
ΔGint15 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.945, 70.919, 130.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-872-

HOH

21A-878-

HOH

31A-926-

HOH

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Components

#1: Protein Variant surface glycoprotein Sur


Mass: 52401.016 Da / Num. of mol.: 1 / Mutation: H122A
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-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
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: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.47→65.31 Å / Num. obs: 75184 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 17.97 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.112 / Net I/σ(I): 10.9 / Num. measured all: 990624
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
1.47-1.513.40.44883036520.8513.118
3.99-65.3812.762.35171640660.0120.041

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Coot0.9-per EL(ccpem)model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z79

6z79


Resolution: 1.64→65.25 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 2259 5.06 %
Rwork0.187 42348 -
obs0.1885 44607 81.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.85 Å2 / Biso mean: 37.7557 Å2 / Biso min: 14.14 Å2
Refinement stepCycle: final / Resolution: 1.64→65.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 83 329 3039
Biso mean--39.39 40.65 -
Num. residues----357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.670.4676120.32181831956
1.67-1.710.2644200.2638140112
1.71-1.760.2807610.2528983104431
1.76-1.80.2602950.26422214230968
1.8-1.860.26851750.23993079325497
1.86-1.920.24931650.22643135330098
1.92-1.980.26871670.20423163333099
1.98-2.060.20561710.17873192336399
2.06-2.160.21491750.16623147332298
2.16-2.270.17681620.16983188335099
2.27-2.410.2251750.17163186336199
2.41-2.60.22261750.18253223339899
2.6-2.860.23761650.19283237340299
2.86-3.280.2261680.197332633431100
3.28-4.130.19911690.170133123481100
4.13-65.250.2022040.188334623666100
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)
10.50090.34070.05321.1796-0.75653.21220.0752-0.24030.0280.3491-0.0991-0.0827-0.19930.2060.05740.1874-0.0041-0.02990.257-0.00810.18096.143344.540592.746
20.79350.30990.1411.1712-0.10393.34450.1097-0.28920.03240.4244-0.05370.0184-0.0505-0.2818-0.06860.1959-0.0171-0.00620.1790.00250.1483-0.568642.665593.9788
30.6647-0.07450.92251.67160.58273.01980.16270.1225-0.1049-0.4114-0.0203-0.02180.2628-0.0163-0.16840.31970.00870.00220.2031-0.00840.19373.307731.725444.277
46.7716-1.2324-2.04112.05660.12492.3030.0931-0.51850.55890.06770.0146-0.34-0.14010.2664-0.10570.2008-0.0436-0.04380.2442-0.03970.283711.100554.096678.8324
50.9458-0.4223-0.49431.84731.1073.55640.09250.2326-0.0105-0.5703-0.0212-0.18890.01550.123-0.07560.29070.02550.050.17310.00510.16093.531138.111942.9062
62.7851-0.54251.68910.7222-0.92791.5496-0.0694-0.36390.0880.11420.05930.1275-0.1765-0.35990.01870.16710.03530.020.2166-0.00390.237-10.220252.789576.8173
71.78720.20661.00931.4221-0.4411.90820.2049-0.09460.00930.2835-0.2090.1768-1.15540.41030.16050.5553-0.1343-0.03110.46020.06730.25895.28451.7084107.2579
82.04840.4584-0.33151.5023-0.34982.51520.5615-0.61980.30611.0985-0.6125-0.3585-0.55630.46220.15360.8005-0.2777-0.14220.53530.05560.31169.23147.0921119.9432
91.38462.2819-0.56143.9361-0.07094.34060.38-0.1502-0.69150.6992-0.47-1.04680.3186-0.08810.23090.5552-0.0645-0.16060.54180.15710.501111.094728.8431115.7657
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 138 )A86 - 138
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 181 )A139 - 181
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 197 )A182 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 269 )A198 - 269
6X-RAY DIFFRACTION6chain 'A' and (resid 270 through 302 )A270 - 302
7X-RAY DIFFRACTION7chain 'A' and (resid 303 through 322 )A303 - 322
8X-RAY DIFFRACTION8chain 'A' and (resid 323 through 383 )A323 - 383
9X-RAY DIFFRACTION9chain 'A' and (resid 388 through 409 )A388 - 409

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