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BMRB: 19266

2M8R

Pre-Fusion Solution NMR Structure of Neuronal SNARE Syntaxin 1A

Authors

Liang, B., Kiessling, V., Tamm, L.K.

Assembly

SNARE

Entity

1. SNARE (polymer, Thiol state: all free), 109 monomers, 12316.24 Da Detail

GSHMDSSISK QALSEIETRH SEIIKLENSI RELHDMFMDM AMLVESQGEM IDRIEYNVEH AVDYVERAVS DTKKAVKYQS KARRKKIMII ICCVILGIII ASTIGGIFG

Formula weight

12316.24 Da

Source organism

Rattus norvegicus

Exptl. method

Refine. method

distance geometry, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.9 %, Completeness (bb): 99.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.9 % (1232 of 1272)	97.7 % (646 of 661)	95.4 % (474 of 497)	98.2 % (112 of 114)
Backbone	99.5 % (651 of 654)	99.6 % (223 of 224)	100.0 % (321 of 321)	98.2 % (107 of 109)
Sidechain	94.9 % (684 of 721)	96.8 % (423 of 437)	91.8 % (256 of 279)	100.0 % (5 of 5)
Aromatic	70.0 % (42 of 60)	86.7 % (26 of 30)	53.3 % (16 of 30)
Methyl	97.8 % (133 of 136)	100.0 % (68 of 68)	95.6 % (65 of 68)

1. SNARE

GSHMDSSISK QALSEIETRH SEIIKLENSI RELHDMFMDM AMLVESQGEM IDRIEYNVEH AVDYVERAVS DTKKAVKYQS KARRKKIMII ICCVILGIII ASTIGGIFG

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	SNARE	[U-13C; U-15N; U-2H]		1 mM
2	DPC	natural abundance		100 mM
3	HEPES	natural abundance		10 mM
4	MES	natural abundance		10 mM
5	sodium acetate	natural abundance		10 mM
6	sodium chloride	natural abundance		150 mM
7	DTT	natural abundance		5 mM
8	EDTA	natural abundance		1 mM
9	H2O	natural abundance		95 %
10	D2O	natural abundance		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M8R, Strand ID: A Detail

Release date

2013-11-10

Citation

Prefusion structure of syntaxin-1A suggests pathway for folding into neuronal trans-SNARE complex fusion intermediate
Liang, B., Kiessling, V., Tamm, L.K.
Proc. Natl. Acad. Sci. U. S. A. (2013), 110, 19384-19389, PubMed 24218570 , DOI 10.1073/pnas.1314699110 , Abstract

Related entities 1. SNARE, : 4 : 76 entities Detail

Interaction partners 1. SNARE, : 24 interactors Detail

More details for 24 interactors identified by 13 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	SNARE	[U-13C; U-15N; U-2H]		1 mM
2	DPC	natural abundance		100 mM
3	HEPES	natural abundance		10 mM
4	MES	natural abundance		10 mM
5	sodium acetate	natural abundance		10 mM
6	sodium chloride	natural abundance		150 mM
7	DTT	natural abundance		5 mM
8	EDTA	natural abundance		1 mM
9	H2O	natural abundance		95 %
10	D2O	natural abundance		5 %

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	SNARE	[U-13C; U-15N; U-2H]		1 mM
2	DPC	natural abundance		100 mM
3	HEPES	natural abundance		10 mM
4	MES	natural abundance		10 mM
5	sodium acetate	natural abundance		10 mM
6	sodium chloride	natural abundance		150 mM
7	DTT	natural abundance		5 mM
8	EDTA	natural abundance		1 mM
9	H2O	natural abundance		95 %
10	D2O	natural abundance		5 %

4 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	SNARE	[U-13C; U-15N; U-2H]		1 mM
2	DPC	natural abundance		100 mM
3	HEPES	natural abundance		10 mM
4	MES	natural abundance		10 mM
5	sodium acetate	natural abundance		10 mM
6	sodium chloride	natural abundance		150 mM
7	DTT	natural abundance		5 mM
8	EDTA	natural abundance		1 mM
9	H2O	natural abundance		95 %
10	D2O	natural abundance		5 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	SNARE	[U-13C; U-15N; U-2H]		1 mM
2	DPC	natural abundance		100 mM
3	HEPES	natural abundance		10 mM
4	MES	natural abundance		10 mM
5	sodium acetate	natural abundance		10 mM
6	sodium chloride	natural abundance		150 mM
7	DTT	natural abundance		5 mM
8	EDTA	natural abundance		1 mM
9	H2O	natural abundance		95 %
10	D2O	natural abundance		5 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	SNARE	[U-13C; U-15N; U-2H]		1 mM
2	DPC	natural abundance		100 mM
3	HEPES	natural abundance		10 mM
4	MES	natural abundance		10 mM
5	sodium acetate	natural abundance		10 mM
6	sodium chloride	natural abundance		150 mM
7	DTT	natural abundance		5 mM
8	EDTA	natural abundance		1 mM
9	H2O	natural abundance		95 %
10	D2O	natural abundance		5 %

7 3D HNHA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

9 3D HCCH-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

10 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

11 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

12 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

13 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

14 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

15 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	SNARE	[U-100% 13C; U-100% 15N]		1 mM
12	DPC	[U-99% 2H]		100 mM
13	sodium chloride	natural abundance		150 mM
14	sodium azide	natural abundance		0.02 %
15	sodium phosphate	natural abundance		10 mM
16	H2O	natural abundance		95 %
17	D2O	natural abundance		5 %

16 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	SNARE	[U-13C; U-15N; U-2H]		1 mM
2	DPC	natural abundance		100 mM
3	HEPES	natural abundance		10 mM
4	MES	natural abundance		10 mM
5	sodium acetate	natural abundance		10 mM
6	sodium chloride	natural abundance		150 mM
7	DTT	natural abundance		5 mM
8	EDTA	natural abundance		1 mM
9	H2O	natural abundance		95 %
10	D2O	natural abundance		5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_19266_2m8r.nef
Input source #2: Coordindates	2m8r.cif
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

Sequence alignments

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

180-----190-------200-------210-------220-------230-------240-------250-------260-------270-------28
GSHMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVKYQSKARRKKIMIIICCVILGIII
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVKYQSKARRKKIMIIICCVILGIII
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0--------
ASTIGGIFG
|||||||||
ASTIGGIFG
---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	109	0	0	100.0

Content subtype: combined_19266_2m8r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1224		99.1 (chain: A, length: 109)
1	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	1853 (1)	noe	99.1 (chain: A, length: 109)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	182 (182)	.	88.1 (chain: A, length: 109)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	90 (90)	.	82.6 (chain: A, length: 109)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 642
  - ¹³C chemical shifts: 468
  - ¹⁵N chemical shifts: 114
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Tautomeric state of HIS
- 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: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_6
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 99.1%
- Total number of restraints: 1853
- Weight of restraints: 1.0 (1853)
- Potential type of restraints: square-well-parabolic (1853)
- Range of distance target values: 2.25, 4.15 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 88.1%
- Total number of restraints: 182
- Total number of restraints per polymer type: 182
- Weight of restraints: 1.0 (182)
- Potential type of restraints: square-well-parabolic (182)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 82.6%

180-----190-------200-------210-------220-------230-------240-------250-------260-------270-------28
GSHMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVKYQSKARRKKIMIIICCVILGIII
   ||||||||||||||||||||||||||||||||| |  |||| |||| ||||||||||||  || | || ||||| |  ||||||| ||| |||| ||
...MDSSISKQALSEIETRHSEIIKLENSIRELHDM.M..AMLV.SQGE.IDRIEYNVEHAV..VE.A.SD.KKAVK.Q..ARRKKIM.IIC.VILG.II

0--------
ASTIGGIFG
|||||||||
ASTIGGIFG

Total number of restraints: 90
Potential type of restraints: undefined (90)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords membrane protein, Prefusion, SNARE, Solution NMR, syntaxin