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- PDB-8b3w: Structure of metacyclic VSG (mVSG) 1954 from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 8b3w
TitleStructure of metacyclic VSG (mVSG) 1954 from Trypanosoma brucei
ComponentsVariant surface glycoprotein 1954
KeywordsMEMBRANE PROTEIN / VSG / trypanosome / trypanosoma / metacyclic
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 / plasma membrane / BROMIDE ION / Variant surface glycoprotein 1954
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.681 Å
AuthorsChandra, M. / Stebbins, C.E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: Plos Negl Trop Dis / Year: 2023
Title: Structural similarities between the metacyclic and bloodstream form variant surface glycoproteins of the African trypanosome.
Authors: Chandra, M. / Dakovic, S. / Foti, K. / Zeelen, J.P. / van Straaten, M. / Aresta-Branco, F. / Tihon, E. / Lubbehusen, N. / Ruppert, T. / Glover, L. / Papavasiliou, F.N. / Stebbins, C.E.
History
DepositionSep 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Variant surface glycoprotein 1954
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2728
Polymers37,3681
Non-polymers9047
Water4,504250
1
A: Variant surface glycoprotein 1954
hetero molecules

A: Variant surface glycoprotein 1954
hetero molecules

A: Variant surface glycoprotein 1954
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,81524
Polymers112,1043
Non-polymers2,71121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area13370 Å2
ΔGint-42 kcal/mol
Surface area38930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.614, 69.614, 115.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

21A-670-

HOH

31A-695-

HOH

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Components

#1: Protein Variant surface glycoprotein 1954


Mass: 37367.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: M4T0T6
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 1500, 0.4M Sodium Bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9198 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.681→60.29 Å / Num. obs: 70911 / % possible obs: 99.79 % / Redundancy: 19.3 % / CC1/2: 0.999 / Net I/σ(I): 7.45
Reflection shellResolution: 1.681→1.741 Å / Num. unique obs: 3705 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
PHENIX1.19-4092-000refinement
PHENIX1.19-4092-000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.681→60.288 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 3536 4.99 %
Rwork0.1718 --
obs0.1736 70911 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.681→60.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 34 250 2793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012640
X-RAY DIFFRACTIONf_angle_d1.0223577
X-RAY DIFFRACTIONf_dihedral_angle_d13.3691602
X-RAY DIFFRACTIONf_chiral_restr0.058411
X-RAY DIFFRACTIONf_plane_restr0.006462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.681-1.70370.36891750.36042408X-RAY DIFFRACTION88
1.7037-1.72810.36811520.34452642X-RAY DIFFRACTION99
1.7281-1.75390.338940.3272723X-RAY DIFFRACTION100
1.7539-1.78130.35841500.32672717X-RAY DIFFRACTION100
1.7813-1.81050.32731240.30392701X-RAY DIFFRACTION100
1.8105-1.84170.36511800.29912702X-RAY DIFFRACTION100
1.8417-1.87520.31551660.28472701X-RAY DIFFRACTION100
1.8752-1.91130.27751520.25352626X-RAY DIFFRACTION100
1.9113-1.95030.29011440.23692722X-RAY DIFFRACTION100
1.9503-1.99270.21291140.20782768X-RAY DIFFRACTION100
1.9927-2.0390.26211340.1942712X-RAY DIFFRACTION100
2.039-2.090.21521840.17392652X-RAY DIFFRACTION100
2.09-2.14650.18391640.1652640X-RAY DIFFRACTION100
2.1465-2.20970.21081200.16012772X-RAY DIFFRACTION100
2.2097-2.2810.18421300.16442695X-RAY DIFFRACTION100
2.281-2.36260.20351460.14652749X-RAY DIFFRACTION100
2.3626-2.45720.20651320.13642699X-RAY DIFFRACTION100
2.4572-2.5690.18341220.13882721X-RAY DIFFRACTION100
2.569-2.70440.19471420.14052713X-RAY DIFFRACTION100
2.7044-2.87390.17411520.13622724X-RAY DIFFRACTION100
2.8739-3.09580.18111280.13662684X-RAY DIFFRACTION100
3.0958-3.40730.14951360.12732734X-RAY DIFFRACTION100
3.4073-3.90020.16841360.12362702X-RAY DIFFRACTION100
3.9002-4.91360.16511260.13172733X-RAY DIFFRACTION100
4.9136-60.2880.18571330.19072735X-RAY DIFFRACTION100
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)
10.3116-0.06080.17610.26550.00484.54850.0428-0.0522-0.03740.08250.0769-0.04810.29010.1963-0.08710.18370.0269-0.01960.1474-0.00180.1856.448626.854310.1813
21.86440.12550.76211.59490.82263.1333-0.0387-0.4061-0.3170.271-0.0337-0.21670.4480.1503-0.01510.58290.1065-0.10280.45590.10410.40818.999318.12645.8361
31.3545-0.0793-0.51431.16910.65711.9585-0.1054-0.1223-0.05830.30350.01840.0850.1722-0.2540.03690.336-0.0016-0.02330.3210.03910.201-0.344827.72839.5976
40.55620.0186-0.08410.67420.06850.6471-0.01280.0652-0.103-0.04980.01960.03660.0282-0.0105-0.00070.1371-0.0035-0.00240.1322-0.00810.1702-2.984821.7699-13.6065
50.77430.44081.58520.63681.54216.1736-0.0054-0.0970.00260.111-0.0008-0.0548-0.0040.02030.07010.22010.0117-0.01420.20580.00140.19851.161632.794622.6925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 135 )
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 160 )
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 340 )
5X-RAY DIFFRACTION5chain 'A' and (resid 341 through 383 )

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