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BMRB: 17536

2LAS

Molecular Determinants of Paralogue-Specific SUMO-SIM Recognition

Authors

Namanja, A., Li, Y., Su, Y., Wong, S., Lu, J., Colson, L., Wu, C., Li, S., Chen, Y.

Assembly

Complex of SUMO1 with RanBP2 M-IR2 SIM peptide

Entity

1. SUMO1 (polymer, Thiol state: all free), 97 monomers, 11132.40 Da Detail

MSDQEAKPST EDLGDKKEGE YIKLKVIGQD SSEIHFKVKM TTHLKKLKES YCQRQGVPMN SLRFLFEGQR IADNHTPKEL GMEEEDVIEV YQEQTGG

2. M-IR2 peptide (polymer, Thiol state: not present), 13 monomers, 1614.835 Da Detail

DNEIEVIIVW EKK

Total weight

12747.235 Da

Max. entity weight

11132.4 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 39.9 %, Completeness (bb): 63.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	39.9 % (529 of 1325)	28.2 % (198 of 701)	47.0 % (238 of 506)	78.8 % (93 of 118)
Backbone	63.8 % (417 of 654)	53.8 % (121 of 225)	63.0 % (203 of 322)	86.9 % (93 of 107)
Sidechain	26.8 % (207 of 773)	16.2 % (77 of 476)	45.5 % (130 of 286)	0.0 % (0 of 11)
Aromatic	14.1 % (11 of 78)	15.4 % (6 of 39)	13.2 % (5 of 38)	0.0 % (0 of 1)
Methyl	30.4 % (31 of 102)	27.5 % (14 of 51)	33.3 % (17 of 51)

1. SUMO1

MSDQEAKPST EDLGDKKEGE YIKLKVIGQD SSEIHFKVKM TTHLKKLKES YCQRQGVPMN SLRFLFEGQR IADNHTPKEL GMEEEDVIEV YQEQTGG

2. M-IR2 peptide

DNEIEVIIVW EKK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	SUMO1	[U-13C; U-15N; U-2H]		0.5 mM
2	M-IR2 peptide	natural abundance		1.0 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
5	SUMO1	[U-15N]; perdeuterated		0.5 mM
6	M-IR2 peptide	natural abundance		0.6 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	SUMO1	[U-15N; U-2H]		0.6 mM
10	M-IR2 peptide	natural abundance		0.4 mM
11	D2O	natural abundance		100 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2LAS, Strand ID: A, B Detail

Release date

2011-12-13

Citation

Insights into high affinity small ubiquitin-like modifier (SUMO) recognition by SUMO-interacting motifs (SIMs) revealed by a combination of NMR and peptide array analysis
Namanja, A.T., Li, Y., Su, Y., Wong, S., Lu, J., Colson, L.T., Wu, C., Li, S.S.C., Chen, Y.
J. Biol. Chem. (2012), 287, 3231-3240, PubMed 22147707 , DOI 10.1074/jbc.M111.293118 , Abstract

Related entities 1. SUMO1, : 3 : 51 entities Detail

Related entities 2. M-IR2 peptide, : 1 : 2 entities Detail

Interaction partners 2. M-IR2 peptide, : 67 interactors Detail

More details for 67 interactors identified by 31 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	SUMO1	[U-13C; U-15N; U-2H]		0.5 mM
2	M-IR2 peptide	natural abundance		1.0 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 3D HN(CO)CACB

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	SUMO1	[U-13C; U-15N; U-2H]		0.5 mM
2	M-IR2 peptide	natural abundance		1.0 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	SUMO1	[U-13C; U-15N; U-2H]		0.5 mM
2	M-IR2 peptide	natural abundance		1.0 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HNCA

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	SUMO1	[U-13C; U-15N; U-2H]		0.5 mM
2	M-IR2 peptide	natural abundance		1.0 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	SUMO1	[U-13C; U-15N; U-2H]		0.5 mM
2	M-IR2 peptide	natural abundance		1.0 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D 15N-edited NOESYHSQC

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
5	SUMO1	[U-15N]; perdeuterated		0.5 mM
6	M-IR2 peptide	natural abundance		0.6 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

7 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
5	SUMO1	[U-15N]; perdeuterated		0.5 mM
6	M-IR2 peptide	natural abundance		0.6 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

8 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
5	SUMO1	[U-15N]; perdeuterated		0.5 mM
6	M-IR2 peptide	natural abundance		0.6 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

9 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	SUMO1	[U-15N; U-2H]		0.6 mM
10	M-IR2 peptide	natural abundance		0.4 mM
11	D2O	natural abundance		100 %

10 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	SUMO1	[U-15N; U-2H]		0.6 mM
10	M-IR2 peptide	natural abundance		0.4 mM
11	D2O	natural abundance		100 %

11 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	SUMO1	[U-15N; U-2H]		0.6 mM
10	M-IR2 peptide	natural abundance		0.4 mM
11	D2O	natural abundance		100 %

12 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	SUMO1	[U-15N; U-2H]		0.6 mM
10	M-IR2 peptide	natural abundance		0.4 mM
11	D2O	natural abundance		100 %

13 2D 1H-13C HSQC-TOCSY

Instrument

Bruker Avance - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	SUMO1	[U-15N; U-2H]		0.6 mM
10	M-IR2 peptide	natural abundance		0.4 mM
11	D2O	natural abundance		100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17536_2las.nef
Input source #2: Coordindates	2las.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

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

-
V
|
V

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

--2710-------
DNEIEVIIVWEKK
|||||||||||||
DNEIEVIIVWEKK
--------10---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	101	0	0	100.0
B	B	13	0	0	100.0

Content subtype: combined_17536_2las.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	494		96.0 (chain: A, length: 101), 100.0 (chain: B, length: 13)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	148 (1)	noe	10.9 (chain: A, length: 101), 92.3 (chain: B, length: 13)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	64 (64)	.	30.7 (chain: A, length: 101), 100.0 (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: 101, Sequence coverage: 96.0%
  - Entity_assembly_ID: B, Chain length: 13, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 224
  - ¹H chemical shifts: 178
  - ¹⁵N chemical shifts: 92
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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: A
  - Chain_ID: B

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 10.9%
  - Entity_assembly_ID: B, Chain length: 13, Sequence coverage: 92.3%
- Total number of restraints: 143
- Weight of restraints: 1.0 (143)
- Potential type of restraints: square-well-parabolic (143)
- Range of distance target values: 2.15, 4.1 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 30.7%
  - Entity_assembly_ID: B, Chain length: 13, Sequence coverage: 100.0%
- Total number of restraints: 64
- Total number of restraints per polymer type: 64
- Weight of restraints: 1.0 (64)
- Potential type of restraints: square-well-parabolic (64)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: B

Keywords NMR, post-translational modification, protein-protein interaction, RanBP2, SIM, SUMO, SUMO binding motif, ubiquitin