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- PDB-5ly9: Structure of MITat 1.1 -

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Basic information

Entry
Database: PDB / ID: 5ly9
TitleStructure of MITat 1.1
ComponentsVariant surface glycoprotein MITAT 1.1
KeywordsIMMUNE SYSTEM / Trypanosoma / Mitat / VSG / immune response / Glycoprotein
Function / homologyVariant surface glycoprotein C-terminal domain superfamily / 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 1.1
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSchaefer, C. / Bartossek, T. / Jones, N. / Kuper, J. / Kisker, C. / Engstler, M.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationEN 305 Germany
German Research FoundationGRK 1114 Germany
German Research FoundationSFB630 Germany
CitationJournal: Nat Microbiol / Year: 2017
Title: Structural basis for the shielding function of the dynamic trypanosome variant surface glycoprotein coat.
Authors: Bartossek, T. / Jones, N.G. / Schafer, C. / Cvitkovic, M. / Glogger, M. / Mott, H.R. / Kuper, J. / Brennich, M. / Carrington, M. / Smith, A.S. / Fenz, S. / Kisker, C. / Engstler, M.
History
DepositionSep 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variant surface glycoprotein MITAT 1.1
B: Variant surface glycoprotein MITAT 1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,85511
Polymers79,2852
Non-polymers2,5699
Water16,466914
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13760 Å2
ΔGint-6 kcal/mol
Surface area27640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.507, 95.041, 103.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Variant surface glycoprotein MITAT 1.1 / VSG


Mass: 39642.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P26331

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 921 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 914 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 5.5-6.5 13-18% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.65→47.52 Å / Num. obs: 93995 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.126 / CC1/2: 0.675 / % possible all: 94.2

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→47.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.343 / SU ML: 0.103 / SU R Cruickshank DPI: 0.0905 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.094
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 4696 5 %RANDOM
Rwork0.1654 ---
obs0.1674 89212 99.61 %-
Displacement parametersBiso max: 103.94 Å2 / Biso mean: 28.862 Å2 / Biso min: 10.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--1.99 Å2-0 Å2
3----1.08 Å2
Refinement stepCycle: final / Resolution: 1.65→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 0 170 925 6601
Biso mean--38.64 42.16 -
Num. residues----732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025819
X-RAY DIFFRACTIONr_bond_other_d0.0020.025632
X-RAY DIFFRACTIONr_angle_refined_deg1.9292.0067907
X-RAY DIFFRACTIONr_angle_other_deg1.078313057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87725.799219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.225151019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9051522
X-RAY DIFFRACTIONr_chiral_restr0.1370.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026433
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021153
X-RAY DIFFRACTIONr_mcbond_it1.2571.9792945
X-RAY DIFFRACTIONr_mcbond_other1.2551.9782944
X-RAY DIFFRACTIONr_mcangle_it1.8692.9573681
LS refinement shellResolution: 1.648→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 331 -
Rwork0.28 6283 -
all-6614 -
obs--95.98 %
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)
10.05260.06340.24150.30020.61051.56790.0013-0.0137-0.02340.00150.00750.0440.0029-0.013-0.00880.05350.0064-0.00550.1069-0.01230.040849.963768.784117.3703
20.1241-0.04530.05810.09850.1680.50610.04940.016-0.0418-0.0046-0.00890.01690.02580.0202-0.04050.06880.0056-0.01960.0754-0.01860.044152.621958.1704-0.3334
30.1385-0.1128-0.58990.12910.40482.7036-0.01720.0176-0.01750.0083-0.00350.03790.077-0.02970.02070.0336-0.01950.00430.1233-0.00810.038250.504361.070134.37
41.8506-0.6293-0.21776.1208-4.4663.5155-0.10440.0026-0.15380.3909-0.0594-0.1293-0.25660.05260.16380.04970.02370.00210.05360.02480.03755.323456.610556.3396
50.62870.24-0.3240.0988-0.16680.56920.082-0.01520.10010.04260.01040.0503-0.107-0.0573-0.09240.04290.03210.03250.08010.00130.052450.878881.110546.8283
60.1181-0.01530.01210.10530.29480.87720.030.023-0.0130.00230.0225-0.015-0.01550.0811-0.05250.06030.00660.00250.0909-0.03020.035669.166968.070310.6169
70.3928-0.03230.13980.29470.21320.26870.00760.10380.0535-0.04650.0241-0.0406-0.07530.0966-0.03170.0552-0.01150.02610.131-0.00670.021268.1568.8737-12.6041
80.16980.28180.38090.63251.1922.95740.02920.06770.0652-0.07080.05230.0709-0.3619-0.0149-0.08150.12590.01720.06580.08470.00550.09269.560291.806330.459
90.70950.374-0.12940.6696-0.16450.60440.0864-0.1069-0.11540.0092-0.0594-0.0572-0.02880.099-0.0270.0329-0.0057-0.00930.0935-0.00870.030772.174276.481544.6539
103.52622.84241.52387.2279.237413.6549-0.1977-0.5072-0.0015-0.1355-0.12540.1951-0.04710.230.32310.08670.04220.00030.1942-0.03060.024857.695480.200563.1441
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 60
2X-RAY DIFFRACTION2A61 - 252
3X-RAY DIFFRACTION3A253 - 284
4X-RAY DIFFRACTION4A285 - 294
5X-RAY DIFFRACTION5A295 - 368
6X-RAY DIFFRACTION6B1 - 150
7X-RAY DIFFRACTION7B151 - 254
8X-RAY DIFFRACTION8B255 - 299
9X-RAY DIFFRACTION9B300 - 357
10X-RAY DIFFRACTION10B358 - 367

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