[English] 日本語
Yorodumi
- PDB-8ok8: Variant Surface Glycoprotein VSG615 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ok8
TitleVariant Surface Glycoprotein VSG615
ComponentsVariant surface glycoprotein 615
KeywordsMEMBRANE PROTEIN / Variant surface glycoprotein / Trypanosomiasis / Glycosylation
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 / Variant surface glycoprotein C-terminal domain superfamily / plasma membrane / alpha-D-glucopyranose / Variant surface glycoprotein 615
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsZeelen, J.P. / Stebbins, C.E. / Chandra, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos Negl Trop Dis / Year: 2023
Title: A structural classification of the variant surface glycoproteins of the African trypanosomey.
Authors: Dakovic, S. / Zeelen, J.P. / Gkeka, A. / Chandra, M. / van Straaten, M. / Foti, K. / Zhong, J. / Vlachou, E.P. / Aresta-Branco, F. / Verdi, J.P. / Papavasiliou, F.N. / Stebbins, C.E.
History
DepositionMar 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Variant surface glycoprotein 615
C: Variant surface glycoprotein 615
E: Variant surface glycoprotein 615
G: Variant surface glycoprotein 615
I: Variant surface glycoprotein 615
K: Variant surface glycoprotein 615
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,18522
Polymers239,6496
Non-polymers3,53516
Water21612
1
A: Variant surface glycoprotein 615
C: Variant surface glycoprotein 615
E: Variant surface glycoprotein 615
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,41210
Polymers119,8253
Non-polymers1,5877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Variant surface glycoprotein 615
I: Variant surface glycoprotein 615
K: Variant surface glycoprotein 615
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,77212
Polymers119,8253
Non-polymers1,9489
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.280, 111.230, 108.590
Angle α, β, γ (deg.)90.00, 91.65, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Variant surface glycoprotein 615


Mass: 39941.555 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: M4SXH7
#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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 23 % PEG 4000, 100 mM NaCacodylate, 10 mM ZnCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.22→77.68 Å / Num. obs: 30929 / % possible obs: 92.38 % / Redundancy: 6 % / Biso Wilson estimate: 85.19 Å2 / CC1/2: 0.978 / Net I/σ(I): 3.71
Reflection shellResolution: 3.22→3.335 Å / Num. unique obs: 3271 / CC1/2: 0.127

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.22→77.68 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3247 1524 4.94 %
Rwork0.3072 --
obs0.308 30848 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.22→77.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13875 0 222 12 14109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01314272
X-RAY DIFFRACTIONf_angle_d0.93519284
X-RAY DIFFRACTIONf_dihedral_angle_d18.4635154
X-RAY DIFFRACTIONf_chiral_restr0.0762233
X-RAY DIFFRACTIONf_plane_restr0.0132518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.320.40451580.38322810X-RAY DIFFRACTION98
3.32-3.440.36751070.38242693X-RAY DIFFRACTION97
3.47-3.580.41451090.38922215X-RAY DIFFRACTION98
3.58-3.740.3281170.36382179X-RAY DIFFRACTION76
3.74-3.940.3311190.33362317X-RAY DIFFRACTION80
3.94-4.190.35391270.32512854X-RAY DIFFRACTION99
4.19-4.510.31031580.29442817X-RAY DIFFRACTION99
4.51-4.960.31251400.29792836X-RAY DIFFRACTION99
4.97-5.680.30081760.30862852X-RAY DIFFRACTION99
5.68-7.160.36711680.30512842X-RAY DIFFRACTION99
7.16-77.680.27321450.24212909X-RAY DIFFRACTION98

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more