BMRB Entry 17536

Name: Molecular Determinants of Paralogue-Specific SUMO-SIM Recognition
Published: 2011-12-14

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PDB ID: 2las
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17536
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Molecular Determinants of Paralogue-Specific SUMO-SIM Recognition

Deposition date:

2011-03-20

Original release date:

2011-12-14

Authors:

Namanja, Andrew; Li, Yi-Jia; Su, Yang; Wong, Steven; Lu, Jingjun; Colson, Loren; Wu, Chenggang; Li, Shawn; Chen, Yuan

Citation:

Citation: Namanja, Andrew; Li, Yi-Jia; Su, Yang; Wong, Steven; Lu, Jingjun; Colson, Loren; Wu, Chenggang; Li, Shawn; Chen, Yuan. "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." J. Biol. Chem. 287, 3231-3240 (2012).
PubMed: 22147707

Assembly members:

Assembly members:
SUMO1, polymer, 97 residues, 9099.442 Da.
M-IR2_peptide, polymer, 13 residues, 1616.870 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SUMO1: MSDQEAKPSTEDLGDKKEGE YIKLKVIGQDSSEIHFKVKM TTHLKKLKESYCQRQGVPMN SLRFLFEGQRIADNHTPKEL GMEEEDVIEVYQEQTGG
M-IR2_peptide: DNEIEVIIVWEKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	225
15N chemical shifts	92
1H chemical shifts	198

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SUMO1	1
2	M-IR2	2

Entities:

Entity 1, SUMO1 97 residues - 9099.442 Da.

1

MET

SER

ASP

GLN

GLU

ALA

LYS

PRO

SER

THR

2

GLU

ASP

LEU

GLY

ASP

LYS

GLU

GLY

GLU

3

TYR

ILE

LYS

LEU

LYS

VAL

ILE

GLY

GLN

ASP

4

SER

GLU

ILE

HIS

PHE

LYS

VAL

LYS

MET

5

THR

HIS

LEU

LYS

LEU

LYS

GLU

SER

6

TYR

CYS

GLN

ARG

GLN

GLY

VAL

PRO

MET

ASN

7

SER

LEU

ARG

PHE

LEU

PHE

GLU

GLY

GLN

ARG

8

ILE

ALA

ASP

ASN

HIS

THR

PRO

LYS

GLU

LEU

9

GLY

MET

GLU

ASP

VAL

ILE

GLU

VAL

10

TYR

GLN

GLU

GLN

THR

GLY

Entity 2, M-IR2 13 residues - 1616.870 Da.

1

ASP

ASN

GLU

ILE

GLU

VAL

ILE

VAL

TRP

2

GLU

LYS

Samples:

sample_1: SUMO1, [U-13C; U-15N; U-2H], 0.5 mM; M-IR2 peptide 1.0 mM; H2O 90%; D2O 10%

sample_2: SUMO1, [U-15N]; perdeuterated, 0.5 mM; M-IR2 peptide 0.6 mM; H2O 90%; D2O 10%

sample_3: SUMO1, [U-15N; U-2H], 0.6 mM; M-IR2 peptide 0.4 mM; D2O 100%

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D 15N-edited NOESYHSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC-TOCSY	sample_3	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker - collection, processing

SPARKY v3.113, Goddard - chemical shift assignment

HADDOCK v2.0, Bonvin - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - analysis, refinement

NMR spectrometers:

Bruker Avance 600 MHz

BMRB	16611 25299
PDB	1A5R 1TGZ 1WYW 1Y8R 1Z5S 2ASQ 2BF8 2G4D 2IO2 2IY0 2IY1 2KQS 2LAS 2MW5 2PE6 2UYZ 2VRR 3KYC 3KYD 3RZW 3UIP 4WJN 4WJO 4WJP 4WJQ
DBJ	BAB22172 BAB27379 BAB93477 BAC40739 BAE35024
EMBL	CAA67898 CAG31129 CAG46944 CAG46953 CAH92616
GB	AAB39999 AAB40388 AAB40390 AAC39959 AAC50733
REF	NP_001005781 NP_001005782 NP_001009672 NP_001030535 NP_001106146
SP	A7WLH8 P63165 P63166 Q2EF74 Q5E9D1
TPG	DAA32560
AlphaFold	A7WLH8 P63165 P63166 Q2EF74 Q5E9D1 Q59FH7