BMRBj - BMREntryMaster

Found 1 Document (0.595 seconds)

BMRB: 25767

NMR structure of the Vta1NTD-Did2(176-204) complex

Authors

Shen, J., Yang, Z., Wang, J., Vild, C.

Assembly

Vta1NTD-Did2(176-204) complex

Entity

1. Vta1NTD-Did2(176-204) complex, entity 1 (polymer), 167 monomers, 19037.83 Da Detail

MASNAARVVA TAKDFDKVGL GIIGYYLQLY AVELILSEED RSQEMTALAT ELLDTIEAFK KEIGGESEAE DSDKSLHVMN TLIHDQEKAK IYMLNFTMSL YNEKLKQLKD GPWDVMLKRS LWCCIDLFSC ILHLWKENIS ETSTNSLQKR IKYCKIYLSK LAKGEIG

2. Vta1NTD-Did2(176-204) complex, entity 2 (polymer, Thiol state: not present), 29 monomers, 3334.735 Da Detail

NVPEIKAKEV NVDDEKEDKL AQRLRALRG

Total weight

22372.564 Da

Max. entity weight

19037.83 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 83.2 %, Completeness (bb): 92.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.2 % (1948 of 2341)	86.2 % (1052 of 1221)	78.1 % (710 of 909)	88.2 % (186 of 211)
Backbone	92.7 % (1086 of 1172)	92.7 % (370 of 399)	92.7 % (537 of 579)	92.3 % (179 of 194)
Sidechain	76.6 % (1039 of 1356)	83.0 % (682 of 822)	67.7 % (350 of 517)	41.2 % (7 of 17)
Aromatic	38.2 % (55 of 144)	72.2 % (52 of 72)	0.0 % (0 of 69)	100.0 % (3 of 3)
Methyl	92.4 % (220 of 238)	97.5 % (116 of 119)	87.4 % (104 of 119)

1. entity 1

MASNAARVVA TAKDFDKVGL GIIGYYLQLY AVELILSEED RSQEMTALAT ELLDTIEAFK KEIGGESEAE DSDKSLHVMN TLIHDQEKAK IYMLNFTMSL YNEKLKQLKD GPWDVMLKRS LWCCIDLFSC ILHLWKENIS ETSTNSLQKR IKYCKIYLSK LAKGEIG

2. entity 2

NVPEIKAKEV NVDDEKEDKL AQRLRALRG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0, Details 1.5mM uniformly 15N-/13C double labeled or 15N-/13C-/70% 2H triple labeled Vta1NTD plus 1.8 mM unlabeled Did2176-204

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0, Details 1.5 mM uniformly labeled 15N-/13C-labeled Did2176-204 in complex with 1.8 mM unlabeled Vta1NTD

#	Name	Isotope labeling	Concentration
9	entity_1	natural abundance	1.8 mM
10	entity_2	[U-13C; U-15N]	1.5 mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	100 mM
13	DTT	[U-100% 2H]	5 mM
14	D2O	[U-100% 2H]	10 %
15	sodium azide	natural abundance	0.02 %

Release date

2016-09-28

Citation

NMR studies on the interactions between yeast Vta1 and Did2 during the multivesicular bodies sorting pathway
Shen, J., Yang, Z., Wang, J., Zhao, B., Lan, W., Wang, C., Zhang, X., Wild, C.J., Liu, M., Xu, Z., Cao, C.
Sci. Rep. (2016), 6, 38710-38710, PubMed 27924850 , DOI 10.1038/srep38710 , Abstract

Related entities 1. Vta1NTD-Did2(176-204) complex, entity 1, : 1 : 1 entities Detail

Related entities 2. Vta1NTD-Did2(176-204) complex, entity 2, : 1 : 1 entities Detail

Experiments performed 17 experiments Detail

1 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0, Details 1.5mM uniformly 15N-/13C double labeled or 15N-/13C-/70% 2H triple labeled Vta1NTD plus 1.8 mM unlabeled Did2176-204

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

2 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

5 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

6 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

7 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

8 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

12 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0, Details 1.5 mM uniformly labeled 15N-/13C-labeled Did2176-204 in complex with 1.8 mM unlabeled Vta1NTD

#	Name	Isotope labeling	Concentration
9	entity_1	natural abundance	1.8 mM
10	entity_2	[U-13C; U-15N]	1.5 mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	100 mM
13	DTT	[U-100% 2H]	5 mM
14	D2O	[U-100% 2H]	10 %
15	sodium azide	natural abundance	0.02 %

13 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	entity_1	natural abundance	1.8 mM
10	entity_2	[U-13C; U-15N]	1.5 mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	100 mM
13	DTT	[U-100% 2H]	5 mM
14	D2O	[U-100% 2H]	10 %
15	sodium azide	natural abundance	0.02 %

14 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	entity_1	natural abundance	1.8 mM
10	entity_2	[U-13C; U-15N]	1.5 mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	100 mM
13	DTT	[U-100% 2H]	5 mM
14	D2O	[U-100% 2H]	10 %
15	sodium azide	natural abundance	0.02 %

15 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	entity_1	natural abundance	1.8 mM
10	entity_2	[U-13C; U-15N]	1.5 mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	100 mM
13	DTT	[U-100% 2H]	5 mM
14	D2O	[U-100% 2H]	10 %
15	sodium azide	natural abundance	0.02 %

16 3D 13C-F1 edited NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	1.5 mM
2	entity_1	[U-13C; U-15N; U-70% 2H]	1.5 mM
3	entity_2	natural abundance	1.8 mM
4	sodium phosphate	natural abundance	25 mM
5	sodium chloride	natural abundance	100 mM
6	DTT	[U-100% 2H]	5 mM
7	D2O	[U-100% 2H]	10 %
8	sodium azide	natural abundance	0.02 %

17 3D 13C-F1 edited NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	entity_1	natural abundance	1.8 mM
10	entity_2	[U-13C; U-15N]	1.5 mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	100 mM
13	DTT	[U-100% 2H]	5 mM
14	D2O	[U-100% 2H]	10 %
15	sodium azide	natural abundance	0.02 %

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr25767_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: bmr25767_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2177		100.0 (chain: 1, length: 167), 100.0 (chain: 2, length: 29)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 167, Sequence coverage: 100.0%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MASNAARVVATAKDFDKVGLGIIGYYLQLYAVELILSEEDRSQEMTALATELLDTIEAFKKEIGGESEAEDSDKSLHVMNTLIHDQEKAKIYMLNFTMSL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MASNAARVVATAKDFDKVGLGIIGYYLQLYAVELILSEEDRSQEMTALATELLDTIEAFKKEIGGESEAEDSDKSLHVMNTLIHDQEKAKIYMLNFTMSL

-------110-------120-------130-------140-------150-------160-------
YNEKLKQLKDGPWDVMLKRSLWCCIDLFSCILHLWKENISETSTNSLQKRIKYCKIYLSKLAKGEIG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
YNEKLKQLKDGPWDVMLKRSLWCCIDLFSCILHLWKENISETSTNSLQKRIKYCKIYLSKLAKGEIG

Entity_assembly_ID: 2, Chain length: 29, Sequence coverage: 100.0%

--------10--------20---------
NVPEIKAKEVNVDDEKEDKLAQRLRALRG
|||||||||||||||||||||||||||||
NVPEIKAKEVNVDDEKEDKLAQRLRALRG

Total number of assignments
- ¹H chemical shifts: 1304
- ¹³C chemical shifts: 688
- ¹⁵N chemical shifts: 185

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
7	ARG	HH11	7.121
7	ARG	HH12	7.121
17	LYS	HZ1	7.116
17	LYS	HZ2	7.116
17	LYS	HZ3	7.116
41	ARG	HH11	7.154
41	ARG	HH12	7.154
50	THR	HG1	5.441
77	HIS	HD1	7.059
123	CYS	HG	2.03
155	LYS	HZ1	7.532
155	LYS	HZ2	7.532
155	LYS	HZ3	7.532

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1036	918	88.6
¹³C chemical shifts	780	595	76.3
¹⁵N chemical shifts	184	164	89.1

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	341	328	96.2
¹³C chemical shifts	334	310	92.8
¹⁵N chemical shifts	166	157	94.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	695	590	84.9
¹³C chemical shifts	446	285	63.9
¹⁵N chemical shifts	18	7	38.9

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	108	103	95.4
¹³C chemical shifts	108	83	76.9

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	52	72.2
¹³C chemical shifts	69	0	0.0
¹⁵N chemical shifts	3	3	100.0

Entity_assemble_ID: 2

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
- Chain_ID: 2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	185	133	71.9
¹³C chemical shifts	129	93	72.1
¹⁵N chemical shifts	34	21	61.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	45	77.6
¹³C chemical shifts	58	46	79.3
¹⁵N chemical shifts	28	21	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	127	88	69.3
¹³C chemical shifts	71	47	66.2
¹⁵N chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0
¹³C chemical shifts	17	13	76.5

Keywords Endosomal Sorting Complexes Required for Transport, MIT-interacting motif 1 (MIM1), Multivesicular Bodies, Protein Structure, Saccharomyces cerevisiae Proteins, microtubule-interacting and transport (MIT) domain

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Found 1 Document (0.595 seconds)

BMRB: 25767

Sample #1

Sample #2

Related entities 1. Vta1NTD-Did2(176-204) complex, entity 1, : 1 : 1 entities Detail

Related entities 2. Vta1NTD-Did2(176-204) complex, entity 2, : 1 : 1 entities Detail

Experiments performed 17 experiments Detail

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Chemical shift validation 4 contents Detail