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BMRB: 17632

2LCT

Solution structure of the Vav1 SH2 domain complexed with a Syk-derived doubly phosphorylated peptide

Authors

Chen, C., Gorenstein, N., Post, C.

Assembly

Syk/Vav complex

Entity

1. Syk/Vav complex, entity 1 (polymer, Thiol state: all free), 107 monomers, 12316.99 Da Detail

GHMQDLSVHL WYAGPMERAG AESILANRSD GTFLVRQRVK DAAEFAISIK YNVEVKHIKI MTAEGLYRIT EKKAFRGLTE LVEFYQQNSL KDCFKSLDTT LQFPFKE

2. Syk/Vav complex, entity 2 (polymer, Thiol state: not present), 13 monomers, 1674.457 Da Detail

DTEVXESPXA DPE

Total weight

13991.447 Da

Max. entity weight

12316.99 Da

Source organism

Homo sapiens , Mus musculus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.3 %, Completeness: 79.2 %, Completeness (bb): 74.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.2 % (1109 of 1401)	88.2 % (643 of 729)	67.4 % (370 of 549)	78.0 % (96 of 123)
Backbone	74.3 % (520 of 700)	92.0 % (219 of 238)	58.9 % (205 of 348)	84.2 % (96 of 114)
Sidechain	83.9 % (682 of 813)	86.4 % (424 of 491)	82.4 % (258 of 313)	0.0 % (0 of 9)
Aromatic	81.0 % (102 of 126)	82.5 % (52 of 63)	80.6 % (50 of 62)	0.0 % (0 of 1)
Methyl	90.5 % (114 of 126)	92.1 % (58 of 63)	88.9 % (56 of 63)

1. entity 1

GHMQDLSVHL WYAGPMERAG AESILANRSD GTFLVRQRVK DAAEFAISIK YNVEVKHIKI MTAEGLYRIT EKKAFRGLTE LVEFYQQNSL KDCFKSLDTT LQFPFKE

2. entity 2

DTEVXESPXA DPE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

Protein Blocks Logo

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

Release date

2011-06-02

Citation

Two closely spaced tyrosines regulate NFAT signaling in B cells via Syk association with Vav
Chen, C., Martin, V.A., Gorenstein, N.M., Geahlen, R.L., Post, C.
Mol. Cell. Biol. (2011), 31, 2984-2996, PubMed 21606197 , DOI 10.1128/MCB.05043-11 , Abstract

Related entities 1. Syk/Vav complex, entity 1, : 3 : 181 entities Detail

Related entities 2. Syk/Vav complex, entity 2, : 1 : 15 entities Detail

Interaction partners 1. Syk/Vav complex, entity 1, : 24 interactors Detail

More details for 24 interactors identified by 20 citations

Experiments performed 14 experiments Detail

1 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

2 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

3 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

5 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

7 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

8 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

12 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

13 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

14 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1.1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 %
6	entity_2	natural abundance		1.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17632_2lct.nef
Input source #2: Coordindates	2lct.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:4:VAL:C	2:5:PTR:N	unknown	unknown	n/a
2:5:PTR:C	2:6:GLU:N	unknown	unknown	n/a
2:8:PRO:C	2:9:PTR:N	unknown	unknown	n/a
2:9:PTR:C	2:10:ALA:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	342	PTR	O-PHOSPHOTYROSINE	Assigned chemical shifts, Distance restraints, Coordinates
B	346	PTR	O-PHOSPHOTYROSINE	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760
GHMQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQRVKDAAEFAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQRVKDAAEFAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTT
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------
LQFPFKE
|||||||
LQFPFKE
-------

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

--340-----350
DTEVXESPXADPE
|||||||||||||
DTEVXESPXADPE
--------10---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	107	0	0	100.0
B	B	13	0	0	100.0

Content subtype: combined_17632_2lct.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1103		93.5 (chain: A, length: 107), 100.0 (chain: B, length: 13)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3849 (1)	noe	91.6 (chain: A, length: 107), 61.5 (chain: B, length: 13)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 93.5%
  - Entity_assembly_ID: B, Chain length: 13, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 653
  - ¹³C chemical shifts: 355
  - ¹⁵N chemical shifts: 95
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- 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
  - Chain_ID: B

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: 107, Sequence coverage: 91.6%
  - Entity_assembly_ID: B, Chain length: 13, Sequence coverage: 61.5%
- Total number of restraints: 3844
- Weight of restraints: 1.0 (3844)
- Potential type of restraints: square-well-parabolic (3844)
- Range of distance target values: 2.06, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords phosphopeptide, sh2 domain, vav1