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- PDB-2vsg: A Structural Motif in the Variant Surface Glycoproteins of Trypan... -

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Basic information

Entry
Database: PDB / ID: 2vsg
TitleA Structural Motif in the Variant Surface Glycoproteins of Trypanosoma Brucei
ComponentsVARIANT SURFACE GLYCOPROTEIN ILTAT 1.24
KeywordsMEMBRANE PROTEIN / VSG / TRYPANOSOME / ANTIGENIC VARIATION
Function / homology
Function and homology information


evasion of host immune response / side of membrane / plasma membrane
Similarity search - Function
Variant Surface Glycoprotein, subunit A; domain 2 / Variant Surface Glycoprotein, subunit A, domain 2 / Variant Surface Glycoprotein; Chain A domain 1 / Variant Surface Glycoprotein, subunit A domain 1 / Trypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / Alpha-Beta Complex / Orthogonal Bundle ...Variant Surface Glycoprotein, subunit A; domain 2 / Variant Surface Glycoprotein, subunit A, domain 2 / Variant Surface Glycoprotein; Chain A domain 1 / Variant Surface Glycoprotein, subunit A domain 1 / Trypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Variant surface glycoprotein ILTAT 1.24
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.7 Å
AuthorsBlum, M.L. / Down, J.A. / Metcalf, P. / Freymann, D.M. / Wiley, D.C.
Citation
Journal: Nature / Year: 1993
Title: A structural motif in the variant surface glycoproteins of Trypanosoma brucei.
Authors: Blum, M.L. / Down, J.A. / Gurnett, A.M. / Carrington, M. / Turner, M.J. / Wiley, D.C.
#1: Journal: Thesis / Year: 1990
Title: The Structure of a Vsg Variable Domain from Trypanosoma Brucei at 2.7 A Resolution
Authors: Blum, M.L.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Crystallization of Amino-Terminal Domains and Domain Fragments of Variant Surface Glycoproteins from Trypanosoma Brucei Brucei
Authors: Metcalf, P. / Down, J.A. / Turner, M. / Wiley, D.C.
#3: Journal: Nature / Year: 1987
Title: Two Variant Surface Glycoproteins of Trypanosoma Brucei of Diffrent Sequence Classes Have Similar 6 Angstrom Resolution X-Ray Structures
Authors: Metcalf, P. / Blum, M. / Freymann, D. / Turner, M. / Wiley, D.C.
History
DepositionNov 19, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VARIANT SURFACE GLYCOPROTEIN ILTAT 1.24
B: VARIANT SURFACE GLYCOPROTEIN ILTAT 1.24


Theoretical massNumber of molelcules
Total (without water)76,5732
Polymers76,5732
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-34 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.100, 98.800, 172.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.991703, 0.074356, 0.104862), (0.067064, -0.396666, 0.91551), (0.109669, 0.914946, 0.388388)
Vector: 8.485, 11.029, -7.882)

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Components

#1: Protein VARIANT SURFACE GLYCOPROTEIN ILTAT 1.24 / VSG


Mass: 38286.742 Da / Num. of mol.: 2 / Fragment: N-TERMINAL VARIABLE DOMAIN / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Variant: ILTAT 1.24 / References: UniProt: P26329
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 7

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.96 %
Description: PHASES TO 4.2 A WERE OBTAINED BY SIRAS, IMPROVED BY NCS AVERAGING, AND EXTENDED TO 3.8 A. A PARTIAL MODEL WAS BUILT, AND RESOLUTION EXTENDED TO 2.7 A BY NCS AVERAGING AND PHASE COMBINATION.
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Aug 5, 1986 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→10 Å / Num. all: 24682 / Num. obs: 24682 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.102
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 3.64 % / Rsym value: 0.39
Reflection
*PLUS
Num. measured all: 107903 / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
BUDDHAdata collection
ROTAVATAdata reduction
Agrovatadata reduction
BRICOGNEmodel building
X-PLORrefinement
BUDDHAdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.7→6 Å / Isotropic thermal model: RESTRAINED / σ(F): 2
Details: SEE REMARK 6 THIS STRUCTURE WAS REFINED BEFORE THE USE OF THE FREE R WAS INTRODUCED. IT IS MISSING SOME OF THE QUALITY INDICATORS NOW WIDELY USED. RELATIVELY LARGE DEVIATIONS FROM STANDARD ...Details: SEE REMARK 6 THIS STRUCTURE WAS REFINED BEFORE THE USE OF THE FREE R WAS INTRODUCED. IT IS MISSING SOME OF THE QUALITY INDICATORS NOW WIDELY USED. RELATIVELY LARGE DEVIATIONS FROM STANDARD GEOMETRY CAN BE ASCRIBED TO BOTH THE LIMITED RESOLUTION OF THE DATA AND THE STATE OF THE ART WHEN THE STRUCTURE WAS REFINED, AND MAY BE INDICATIVE OF SOME OVERFITTING. NEVERTHELESS THE ELECTRON DENSITY MAP WAS WELL DEFINED AND ALLOWED, FOR EXAMPLE, IDENTIFICATION OF THREE SEQUENCING ERRORS WHICH WERE SUBSEQUENTLY VERIFIED.
RfactorNum. reflection% reflection
Rwork0.203 --
obs-21676 81 %
Displacement parametersBiso mean: 34.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5372 0 0 83 5455
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS

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