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BMRB: 50107

1Z2W

1H, 13C and 15N chemical shift assignments for VPS29

Authors

Owen, D.J., Neuhaus, D., Yang, J., Crawley-Snowdon, H.

Assembly

VPS29

Entity

1. VPS29 (polymer, Thiol state: all free), 192 monomers, 21598.57 Da Detail

GSPEFGTRDR MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK TLAGDVHIVR GDFDENLNYP EQKVVTVGQF KIGLIHGHQV IPWGDMASLA LLQRQFDVDI LISGHTHKFE AFEHENKFYI NPGSATGAYN ALETNIIPSF VLMDIQASTV VTYVYQLIGD DVKVERIEYK KS

Formula weight

21598.57 Da

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 67.5 %, Completeness (bb): 79.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	67.5 % (1540 of 2281)	71.8 % (844 of 1175)	57.7 % (519 of 899)	85.5 % (177 of 207)
Backbone	79.5 % (903 of 1136)	94.6 % (370 of 391)	63.6 % (357 of 561)	95.7 % (176 of 184)
Sidechain	61.0 % (807 of 1322)	60.5 % (474 of 784)	64.5 % (332 of 515)	4.3 % (1 of 23)
Aromatic	33.2 % (67 of 202)	42.6 % (43 of 101)	23.0 % (23 of 100)	100.0 % (1 of 1)
Methyl	73.1 % (177 of 242)	75.2 % (91 of 121)	71.1 % (86 of 121)

1. entity 1

GSPEFGTRDR MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK TLAGDVHIVR GDFDENLNYP EQKVVTVGQF KIGLIHGHQV IPWGDMASLA LLQRQFDVDI LISGHTHKFE AFEHENKFYI NPGSATGAYN ALETNIIPSF VLMDIQASTV VTYVYQLIGD DVKVERIEYK KS

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details D2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
5	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
6	TRIS	[U-2H]		20 mM
7	sodium chloride	natural abundance		200 mM
8	DTT	[U-2H]		1 mM

Release date

2019-12-01

Citation

Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29
Crawley-Snowdon, H., Yang, J.C., Zaccai, N.R., Davis, L.J., Wartosch, L., Herman, E.K., Bright, N.A., Swarbrick, J.S., Collins, B.M., Jackson, L.P., Seaman, M., Luzio, J.P., Dacks, J.B., Neuhaus, D., Owen, D.J.
Nat. Commun. (2020), 11, 5031-5031, PubMed 33024112 , DOI 10.1038/s41467-020-18773-2 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 34461 released on 2020-01-06
    Title Solution structure and 1H, 13C and 15N chemical shift assignments for the complex of VPS29 with VARP 687-747
  BMRB: 50108 released on 2019-12-01
    Title 1H, 13C and 15N chemical shift assignments for VARP 687-747

Related entities 1. VPS29, : 1 : 4 : 27 : 38 entities Detail

Interaction partners 1. VPS29, : 15 interactors Detail

More details for 15 interactors identified by 4 citations

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

4 2D 1H-13C HSQC aliphatic constant time

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

5 2D 1H-13C HSQC aromatic constant time

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

6 3D CBCANH

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

7 3D CBCA(CO)NH

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

8 3D HNCA

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

9 3D HN(CO)CA

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

10 3D HBHANH

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

11 3D HBHA(CO)NH

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

12 3D [1H-13C-1H] HCCH-COSY

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

13 3D [1H-13C-1H] HCCH-TOCSY

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

14 3D [13C-13C-1H] HCCH-TOCSY

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

15 3D 15N NOESY-HSQC (150ms mixing time)

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

16 3D 13C NOESY aliphatic (150ms mixing time)

Instrument

Bruker Avance-1 - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details H2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
1	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
2	TRIS	[U-2H]		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	[U-2H]		1 mM

17 2D DQ-correlation

Instrument

Bruker Avance-III - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details D2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
5	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
6	TRIS	[U-2H]		20 mM
7	sodium chloride	natural abundance		200 mM
8	DTT	[U-2H]		1 mM

18 3D 13C NOESY-HSQC aromatic (150ms mixing time)

Instrument

Bruker Avance-III - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details D2O sample of 15N,13C-labelled VSP29

#	Name	Isotope labeling	Type	Concentration
5	VPS29	[U-98% 13C; U-98% 15N]		0.45 (±0.15) mM
6	TRIS	[U-2H]		20 mM
7	sodium chloride	natural abundance		200 mM
8	DTT	[U-2H]		1 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr50107_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr50107_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1722		97.9 (chain: 1, length: 192)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 192, Sequence coverage: 97.9%
- Total number of assignments
  - ¹H chemical shifts: 1026
  - ¹³C chemical shifts: 519
  - ¹⁵N chemical shifts: 177
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Keywords VARP, retromer, NMR complex structure, Zinc finger, endosome