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- PDB-6elc: Crystal Structure of O-linked Glycosylated VSG3 -

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Basic information

Entry
Database: PDB / ID: 6elc
TitleCrystal Structure of O-linked Glycosylated VSG3
ComponentsVariant surface glycoprotein
KeywordsIMMUNE SYSTEM / trypanosome / VSG / sleeping sickness / antigen
Function / homologyTrypanosome variant surface glycoprotein, B-type, N-terminal domain / Trypanosomal VSG domain / Trypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / side of membrane / plasma membrane / alpha-D-glucopyranose / Variant surface glycoprotein
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsStebbins, C.E.
Funding support United States, United Kingdom, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI085973 United States
Wellcome Trust101842 United Kingdom
Wellcome Trust097045 United Kingdom
National Institutes of Health United States
CitationJournal: Nat Microbiol / Year: 2018
Title: African trypanosomes evade immune clearance by O-glycosylation of the VSG surface coat.
Authors: Pinger, J. / Nesic, D. / Ali, L. / Aresta-Branco, F. / Lilic, M. / Chowdhury, S. / Kim, H.S. / Verdi, J. / Raper, J. / Ferguson, M.A.J. / Papavasiliou, F.N. / Stebbins, C.E.
History
DepositionSep 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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
Revision 2.1Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_audit_support / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Variant surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8633
Polymers53,9341
Non-polymers9292
Water8,557475
1
A: Variant surface glycoprotein
hetero molecules

A: Variant surface glycoprotein
hetero molecules

A: Variant surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,5909
Polymers161,8033
Non-polymers2,7876
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area14420 Å2
ΔGint12 kcal/mol
Surface area41540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.854, 129.854, 129.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-1053-

HOH

21A-1116-

HOH

31A-1137-

HOH

41A-1145-

HOH

51A-1162-

HOH

61A-1170-

HOH

71A-1171-

HOH

81A-1175-

HOH

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Components

#1: Protein Variant surface glycoprotein / VSG3 MITat1.3 VSG224


Mass: 53934.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: B3GVK1
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 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-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hanging drops formed from mixing a 1:1 volume ratio of the protein with an equilibration buffer consisting of 16-22% polyethylene glycol (PEG) molecular weight 3350 Da, 200-325mM NaCl, and ...Details: Hanging drops formed from mixing a 1:1 volume ratio of the protein with an equilibration buffer consisting of 16-22% polyethylene glycol (PEG) molecular weight 3350 Da, 200-325mM NaCl, and 100mM Tris pH 8.2 (tris(hydroxymethyl)aminomethane)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9194 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 1.41→91.82 Å / Num. obs: 68683 / % possible obs: 97.9 % / Observed criterion σ(I): 19.1 / Redundancy: 4.1 % / CC1/2: 0.999 / Rpim(I) all: 0.022 / Net I/σ(I): 19.1
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2732 / CC1/2: 0.407 / Rpim(I) all: 0.725 / % possible all: 73.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSJune 17, 2015data reduction
XDSJune 17, 2015data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→91.82 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.036 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16921 3462 5.1 %RANDOM
Rwork0.13003 ---
obs0.13193 64954 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.203 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.41→91.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 61 475 3188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022762
X-RAY DIFFRACTIONr_bond_other_d0.0020.022613
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.9773761
X-RAY DIFFRACTIONr_angle_other_deg1.05136026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2475354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75325.877114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62715445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2681512
X-RAY DIFFRACTIONr_chiral_restr0.1210.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023148
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02586
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5531.9311422
X-RAY DIFFRACTIONr_mcbond_other2.5531.9291421
X-RAY DIFFRACTIONr_mcangle_it3.1572.9051774
X-RAY DIFFRACTIONr_mcangle_other3.1562.9061775
X-RAY DIFFRACTIONr_scbond_it3.7172.4071340
X-RAY DIFFRACTIONr_scbond_other3.7172.4071340
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3323.4571988
X-RAY DIFFRACTIONr_long_range_B_refined4.60418.6963706
X-RAY DIFFRACTIONr_long_range_B_other4.2817.6893454
X-RAY DIFFRACTIONr_rigid_bond_restr2.91735373
X-RAY DIFFRACTIONr_sphericity_free30.2475117
X-RAY DIFFRACTIONr_sphericity_bonded11.40255684
LS refinement shellResolution: 1.41→1.446 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 215 -
Rwork0.24 3859 -
obs--79.38 %

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