6Z7A

Variant Surface Glycoprotein VSGsur

PDB DOI: https://doi.org/10.2210/pdb6Z7A/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Trypanosoma brucei rhodesiense
Expression System: Trypanosoma brucei brucei
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2020-05-30 Released: 2021-05-26
Deposition Author(s): Zeelen, J.P., Straaten van, M., Stebbins, C.E., Hashemi, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free: 0.187
R-Value Work: 0.166
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A Parasite Coat Protein Binds Suramin to Confer Drug Resistance

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.

(2021) Nat Microbiol 6: 392-400

DOI: https://doi.org/10.1038/s41564-020-00844-1

Macromolecule Content

Total Structure Weight: 53.54 kDa
Atom Count: 3,142
Modelled Residue Count: 359
Deposited Residue Count: 491
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Variant surface glycoprotein Sur	A	491	Trypanosoma brucei rhodesiense	Mutation(s): 0 Gene Names: VSGsur Membrane Entity: Yes
UniProt
Find proteins for A0A291L8F4 (Trypanosoma brucei rhodesiense) Explore A0A291L8F4 Go to UniProtKB: A0A291L8F4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A291L8F4
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	B	6		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free: 0.187
R-Value Work: 0.166
R-Value Observed: 0.167
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.042	α = 90
b = 71.062	β = 90
c = 130.453	γ = 90

Software Package:

Software Name	Purpose
AutoProcess	data collection
PHENIX	refinement
Coot	model building
pointless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

Straaten van, M.

Revision History (Full details and data files)

Version 1.0: 2021-05-26
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.