BMRBj - BMREntryMaster

	Total	¹H	¹⁵N
All	97.0 % (523 of 539)	96.9 % (442 of 456)	97.6 % (81 of 83)
Backbone	96.0 % (214 of 223)	95.3 % (143 of 150)	97.3 % (71 of 73)
Sidechain	97.8 % (309 of 316)	97.7 % (299 of 306)	100.0 % (10 of 10)
Aromatic	100.0 % (5 of 5)	100.0 % (5 of 5)
Methyl	100.0 % (22 of 22)	100.0 % (22 of 22)

1. Variant surface glycoprotein MITAT 1.1

GSKKQQTESA ENKEKICNAA KDNQKACENL KEKGCVFNTE SNKCELKKDV KEKLEKESKE TEGKDEKANT TGS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.5 mM [U-15N] Variant surface glycoprotein MITat1.1, 50 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Variant surface glycoprotein MITat1.1	[U-15N]	0.5 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.5 mM Variant surface glycoprotein MITat1.1, 50 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	Variant surface glycoprotein MITat1.1	natural abundance	0.5 mM
7	sodium chloride	natural abundance	150 mM
8	sodium phosphate	natural abundance	50 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

Protein Blocks Logo

Calculated from 35 models in PDB: 5M4T, Strand ID: A Detail

Release date

2016-11-10

Citation

Structural basis for the shielding function of the dynamic trypanosome variant surface glycoprotein coat
Bartossek, T., Jones, N.G., Schafer, C., Cvitkovic, M., Glogger, M., Mott, H.R., Kuper, J., Brennich, M., Carrington, M., Smith, A.S., Fenz, S., Kisker, C., Engstler, M.
Nat. Microbiol. (2017), 2, 1523-1532, PubMed 28894098 , DOI 10.1038/s41564-017-0013-6 , Abstract

Related entities 1. Variant surface glycoprotein MITAT 1.1, : 1 entities Detail

Experiments performed 7 experiments Detail

1 3D HNHA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.5 mM [U-15N] Variant surface glycoprotein MITat1.1, 50 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Variant surface glycoprotein MITat1.1	[U-15N]	0.5 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 2D 1H-15N HSQC

Instrument

Bruker DRX - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Variant surface glycoprotein MITat1.1	[U-15N]	0.5 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 3D 1H-15N TOCSY

Instrument

Bruker DRX - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Variant surface glycoprotein MITat1.1	[U-15N]	0.5 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

4 3D 1H-15N NOESY

Instrument

Bruker DRX - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Variant surface glycoprotein MITat1.1	[U-15N]	0.5 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

5 2D DQF-COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.5 mM Variant surface glycoprotein MITat1.1, 50 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	Variant surface glycoprotein MITat1.1	natural abundance	0.5 mM
7	sodium chloride	natural abundance	150 mM
8	sodium phosphate	natural abundance	50 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

6 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Variant surface glycoprotein MITat1.1	natural abundance	0.5 mM
7	sodium chloride	natural abundance	150 mM
8	sodium phosphate	natural abundance	50 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

7 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Variant surface glycoprotein MITat1.1	natural abundance	0.5 mM
7	sodium chloride	natural abundance	150 mM
8	sodium phosphate	natural abundance	50 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34055_5m4t.nef
Input source #2: Coordindates	5m4t.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:387:CYS:SG	A:405:CYS:SG	unknown	unknown	2.028
A:397:CYS:SG	A:414:CYS:SG	unknown	unknown	2.029

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-------380-------390-------400-------410-------420-------430-------440---
GSKKQQTESAENKEKICNAAKDNQKACENLKEKGCVFNTESNKCELKKDVKEKLEKESKETEGKDEKANTTGS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSKKQQTESAENKEKICNAAKDNQKACENLKEKGCVFNTESNKCELKKDVKEKLEKESKETEGKDEKANTTGS
--------10--------20--------30--------40--------50--------60--------70---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	73	0	0	100.0

Content subtype: combined_34055_5m4t.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	528		97.3 (chain: A, length: 73)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2181 (1)	noe	95.9 (chain: A, length: 73)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 97.3%
- Total number of assignments
  - ¹H chemical shifts: 447
  - ¹⁵N chemical shifts: 81
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	456	447	98.0
¹⁵N chemical shifts	83	81	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	150	145	96.7
¹⁵N chemical shifts	73	71	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	306	302	98.7
¹⁵N chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	22	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 95.9%
- Total number of restraints: 2109
- Weight of restraints: 1.0 (2109)
- Potential type of restraints: square-well-parabolic (2109)
- Range of distance target values: 1.7, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Membrane protein, variant surface glycoprotein immune evasion Trypanosoma brucei GPI-anchored protein

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Found 1 Document (0.633 seconds)

BMRB: 34055

Sample #1

Sample #2

Related entities 1. Variant surface glycoprotein MITAT 1.1, : 1 entities Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 3 contents Detail