BMRB Entry 25576

Name: Solution structure of human SUMO1
Published: 2016-04-18

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PDB ID: 2n1v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25576
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of human SUMO1

Deposition date:

2015-04-24

Original release date:

2016-04-18

Authors:

Naik, Mandar; Naik, Nandita; Shih, Hsiu-Ming; Huang, Tai-huang

Citation:

Citation: Naik, Mandar; Naik, Nandita; Shih, Hsiu-Ming; Huang, Tai-huang. "Structures of human SUMO" .

Assembly members:

Assembly members:
SUMO1, polymer, 111 residues, 11149.640 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: pCDFDuet-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SUMO1: MGSSHHHHHHSQDPMSDQEA KPSTEDLGDKKEGEYIKLKV IGQDSSEIHFKVKMTTHLKK LKESYCQRQGVPMNSLRFLF EGQRIADNHTPKELGMEEED VIEVYQEQTGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts

Data type	Count
13C chemical shifts	433
15N chemical shifts	104
1H chemical shifts	697

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	human SUMO1	1

Entities:

Entity 1, human SUMO1 111 residues - 11149.640 Da.

Residues 1-14 (MGSSHHHHHHSQDP) represent a non-native purification tag. These residues were neither assigned nor included in structure calculation.

1

MET

GLY

SER

HIS

2

SER

GLN

ASP

PRO

MET

SER

ASP

GLN

GLU

ALA

3

LYS

PRO

SER

THR

GLU

ASP

LEU

GLY

ASP

LYS

4

LYS

GLU

GLY

GLU

TYR

ILE

LYS

LEU

LYS

VAL

5

ILE

GLY

GLN

ASP

SER

GLU

ILE

HIS

PHE

6

LYS

VAL

LYS

MET

THR

HIS

LEU

LYS

7

LEU

LYS

GLU

SER

TYR

CYS

GLN

ARG

GLN

GLY

8

VAL

PRO

MET

ASN

SER

LEU

ARG

PHE

LEU

PHE

9

GLU

GLY

GLN

ARG

ILE

ALA

ASP

ASN

HIS

THR

10

PRO

LYS

GLU

LEU

GLY

MET

GLU

ASP

11

VAL

ILE

GLU

VAL

TYR

GLN

GLU

GLN

THR

GLY

12

GLY

Samples:

CN: SUMO1, [U-100% 13C; U-100% 15N], 0.5 – 1 mM; potassium phosphate 10 ± 1 mM; potassium chloride 100 ± 1 mM; DTT 2 ± 0.05 mM; EDTA 0.1 ± 0.005 mM; sodium azide 0.001 ± 0.001 %; H2O 90%; D2O 10%

N: SUMO1, [U-100% 15N], 0.5 – 1 mM; potassium phosphate 10 ± 1 mM; potassium chloride 100 ± 1 mM; DTT 2 ± 0.05 mM; EDTA 0.1 ± 0.005 mM; sodium azide 0.001 ± 0.001 %; H2O 90%; D2O 10%

Phage: SUMO1, [U-100% 15N], 0.5 – 1 mM; potassium phosphate 10 ± 1 mM; potassium chloride 100 ± 1 mM; DTT 2 ± 0.05 mM; EDTA 0.1 ± 0.005 mM; sodium azide 0.001 ± 0.001 %; Pf1 phage 10 ± 0.1 w/v; H2O 90%; D2O 10%

Unlabeled: SUMO10.5 – 1 mM; potassium phosphate 10 ± 1 mM; potassium chloride 100 ± 1 mM; DTT 2 ± 0.05 mM; EDTA 0.1 ± 0.005 mM; sodium azide 0.001 ± 0.001 %; H2O 90%; D2O 10%

Default: pH: 6.5; pressure: 1 atm; temperature: 290 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	N	isotropic	Default
2D 1H-13C HSQC	CN	isotropic	Default
3D HNCO	CN	isotropic	Default
3D HNCA	CN	isotropic	Default
3D HN(CO)CA	CN	isotropic	Default
3D HNCACB	CN	isotropic	Default
3D CBCA(CO)NH	CN	isotropic	Default
3D HCCH-TOCSY	CN	isotropic	Default
3D HCCH-COSY	CN	isotropic	Default
3D HBHAcoNH	CN	isotropic	Default
2D-hbCBcgcdHD	CN	isotropic	Default
2D-hbCBcgcdceHE	CN	isotropic	Default
3D 1H-15N TOCSY	CN	isotropic	Default
2D 1H-1H NOESY	Unlabeled	isotropic	Default
3D 1H-15N NOESY	CN	isotropic	Default
3D 1H-13C NOESY	CN	isotropic	Default
2D 1H-15N HSQC IPAP	Phage	anisotropic	Default

Software:

TOPSPIN v3.2, Bruker Biospin - collection, processing

SPARKY v3.113, Goddard - chemical shift assignment, data analysis, peak picking

CYANA v3.9, Guntert, Mumenthaler and Wuthrich - geometry optimization, structure solution

X-PLOR_NIH v2.34, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz
Bruker Avance 800 MHz
Bruker Avance 850 MHz

UNP	P63165
PDB	1A5R
AlphaFold	Q93068