[English] 日本語
Yorodumi
- PDB-6z7a: Variant Surface Glycoprotein VSGsur -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z7a
TitleVariant Surface Glycoprotein VSGsur
ComponentsVariant surface glycoprotein Sur
KeywordsMEMBRANE PROTEIN / Variant surface glycoprotein Suramin Trypanosomiasis Drug resistance Glycosylation
Function / homologyVariant surface glycoprotein C-terminal domain superfamily / plasma membrane / Variant surface glycoprotein Sur
Function and homology information
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsZeelen, J.P. / Straaten van, M. / Stebbins, C.E. / Hashemi, H.
CitationJournal: Nat Microbiol / Year: 2021
Title: A Parasite Coat Protein Binds Suramin to Confer Drug Resistance
Authors: Zeelen, J.P. / van Straaten, M. / Verdi, J. / Hempelmann, A. / Hashemi, H. / Perez, K. / Jeffrey, P.D. / Haelg, S. / Wiedemar, N. / Maeser, P. / Papavasiliou, F.N. / Stebbins, C.E.
History
DepositionMay 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Variant surface glycoprotein Sur
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5412
Polymers52,4681
Non-polymers1,0731
Water6,107339
1
A: Variant surface glycoprotein Sur
hetero molecules

A: Variant surface glycoprotein Sur
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0824
Polymers104,9362
Non-polymers2,1462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area10870 Å2
ΔGint8 kcal/mol
Surface area30380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.042, 71.062, 130.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein Variant surface glycoprotein Sur


Mass: 52468.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei rhodesiense (eukaryote)
Gene: VSGsur / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A291L8F4
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_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]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19-24 % PEG 400 100 mM TEA/HCl pH=7.5 10 % (v/v) Isopropanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.21→48.05 Å / Num. obs: 122573 / % possible obs: 91.43 % / Redundancy: 6.1 % / Biso Wilson estimate: 15.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09566 / Rpim(I) all: 0.04114 / Rrim(I) all: 0.1044 / Net I/σ(I): 8.57
Reflection shellResolution: 1.21→1.25 Å / Num. unique obs: 7073 / CC1/2: 0.174

-
Processing

Software
NameVersionClassification
AutoProcessdata collection
PHENIX1.17.1_3660refinement
Cootmodel building
pointlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z79

6z79


Resolution: 1.21→48.05 Å / SU ML: 0.1569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1866 6192 5.05 %
Rwork0.1659 116381 -
obs0.1669 122545 91.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.66 Å2
Refinement stepCycle: LAST / Resolution: 1.21→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 72 339 3046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01932864
X-RAY DIFFRACTIONf_angle_d1.54073927
X-RAY DIFFRACTIONf_chiral_restr0.2389479
X-RAY DIFFRACTIONf_plane_restr0.0116510
X-RAY DIFFRACTIONf_dihedral_angle_d15.08991072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.220.39771080.38911960X-RAY DIFFRACTION47.11
1.22-1.240.40431140.3742234X-RAY DIFFRACTION52.27
1.24-1.250.37321380.3752485X-RAY DIFFRACTION59.78
1.25-1.270.3591670.35952756X-RAY DIFFRACTION65.97
1.27-1.290.32841570.34793071X-RAY DIFFRACTION73.46
1.29-1.30.36631710.32853378X-RAY DIFFRACTION80.42
1.3-1.320.30021870.32863609X-RAY DIFFRACTION85.73
1.32-1.340.2972130.30513889X-RAY DIFFRACTION92.2
1.34-1.360.30842200.30434040X-RAY DIFFRACTION96.88
1.36-1.380.29592320.27474165X-RAY DIFFRACTION99.08
1.38-1.410.26212040.24244157X-RAY DIFFRACTION99.52
1.41-1.430.22642200.2284214X-RAY DIFFRACTION99.46
1.43-1.460.24962510.21384189X-RAY DIFFRACTION99.57
1.46-1.490.19962390.18674157X-RAY DIFFRACTION99.5
1.49-1.520.19062240.18054194X-RAY DIFFRACTION99.35
1.52-1.560.1942020.1684191X-RAY DIFFRACTION98.72
1.56-1.60.16592170.15354187X-RAY DIFFRACTION99.46
1.6-1.640.18082350.14754203X-RAY DIFFRACTION99.35
1.64-1.690.15862390.13214220X-RAY DIFFRACTION99.82
1.69-1.740.13762160.12254211X-RAY DIFFRACTION99.46
1.74-1.810.14552350.12034213X-RAY DIFFRACTION99.53
1.81-1.880.12322280.12094197X-RAY DIFFRACTION98.95
1.88-1.960.14892510.11764207X-RAY DIFFRACTION99.62
1.96-2.070.12372110.12164249X-RAY DIFFRACTION99.64
2.07-2.20.13662130.11864264X-RAY DIFFRACTION99.84
2.2-2.370.16552180.12354264X-RAY DIFFRACTION98.74
2.37-2.610.16712240.13314271X-RAY DIFFRACTION99.56
2.61-2.980.17612210.15044311X-RAY DIFFRACTION99.52
2.98-3.760.17682080.16724347X-RAY DIFFRACTION98.96
3.76-48.050.21242290.18774548X-RAY DIFFRACTION99.07

+
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