BMRB Entry 16880

Name: Solution Structure of UBM2 of murine Polymerase iota in Complex with Ubiquitin
Published: 2010-10-14

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PDB ID: 2kwu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16880
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of UBM2 of murine Polymerase iota in Complex with Ubiquitin

Deposition date:

2010-04-19

Original release date:

2010-10-14

Authors:

Burschowsky, Daniel; Rudolf, Fabian; Rabut, Gwenael; Herrmann, Torsten; Peter, Matthias; Wider, Gerhard

Citation:

Citation: Burschowsky, Daniel; Rudolf, Fabian; Rabut, Gwenael; Herrmann, Torsten; Matthias, Peter; Wider, Gerhard. "Structural Analysis of the Conserved Ubiquitin-binding Motifs (UBMs) of the Translesion Polymerase iota in Complex with Ubiquitin." J. Biol. Chem. 286, 1364-1373 (2011).
PubMed: 20929865

Assembly members:

Assembly members:
DNA_polymerase_iota_UBM2, polymer, 50 residues, 4205.713 Da.
Ubiquitin, polymer, 76 residues, 8576.914 Da.

Natural source:

Natural source: Common Name: house mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-4T-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_polymerase_iota_UBM2: GSPEFDSAEEKLPFPPDIDP QVFYELPEEVQKELMAEWER AGAARPSAHR
Ubiquitin: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:

assigned_chemical_shifts
- UBM2_shift_list

Data type	Count
13C chemical shifts	432
15N chemical shifts	130
1H chemical shifts	907

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA polymerase iota UBM2	1
2	Ubiquitin	2

Entities:

Entity 1, DNA polymerase iota UBM2 50 residues - 4205.713 Da.

Residues 668-672 represent non-native cloning artifacts. Residues 673-674 and 711-717 represent flexible flanking regions that are not shown in the Structure.

1	GLY	SER	PRO	GLU	PHE	ASP	SER	ALA	GLU	GLU
2	LYS	LEU	PRO	PHE	PRO	PRO	ASP	ILE	ASP	PRO
3	GLN	VAL	PHE	TYR	GLU	LEU	PRO	GLU	GLU	VAL
4	GLN	LYS	GLU	LEU	MET	ALA	GLU	TRP	GLU	ARG
5	ALA	GLY	ALA	ALA	ARG	PRO	SER	ALA	HIS	ARG

Entity 2, Ubiquitin 76 residues - 8576.914 Da.

1

MET

GLN

ILE

PHE

VAL

LYS

THR

LEU

THR

GLY

2

LYS

THR

ILE

THR

LEU

GLU

VAL

GLU

PRO

SER

3

ASP

THR

ILE

GLU

ASN

VAL

LYS

ALA

LYS

ILE

4

GLN

ASP

LYS

GLU

GLY

ILE

PRO

ASP

GLN

5

GLN

ARG

LEU

ILE

PHE

ALA

GLY

LYS

GLN

LEU

6

GLU

ASP

GLY

ARG

THR

LEU

SER

ASP

TYR

ASN

7

ILE

GLN

LYS

GLU

SER

THR

LEU

HIS

LEU

VAL

8

LEU

ARG

LEU

ARG

GLY

Samples:

15NUBM2+ub: DNA polymerase iota UBM2, [U-99% 15N], 1 – 2 mM; Ubiquitin4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; D2O 5%

13C15NUBM2+ub: DNA polymerase iota UBM2, [U-95% 13C; U-99% 15N], 1 – 2 mM; Ubiquitin4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; D2O 5%

15NUbi+ubm2: DNA polymerase iota UBM24 – 8 mM; Ubiquitin, [U-99% 15N], 1 – 2 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; D2O 5%

13C15NUbi+ubm2: DNA polymerase iota UBM24 – 8 mM; Ubiquitin, [U-95% 13C; U-99% 15N], 1 – 2 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; D2O 5%

labUbi-overUBM2: DNA polymerase iota UBM21 – 2 mM; Ubiquitin, [U-95% 13C; U-99% 15N], 4 – 8 mM; sodium phosphate 25 mM; sodium chloride 25 mM; potassium chloride 100 mM; CHAPS 2 mM; PMSF 0.15 mM; sodium azide 0.2 % w/v; H2O 95%; D2O 5%

Sample_conditions: ionic strength: 0.189 M; pH: 6.0; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	13C15NUBM2+ub	isotropic	Sample_conditions
3D 1H-15N NOESY	15NUBM2+ub	isotropic	Sample_conditions
3D 1H-15N TOCSY	15NUBM2+ub	isotropic	Sample_conditions
3D 1H-13C NOESY	13C15NUBM2+ub	isotropic	Sample_conditions
3D HCCH-COSY	13C15NUBM2+ub	isotropic	Sample_conditions
2D 1H-15N HSQC	15NUBM2+ub	isotropic	Sample_conditions
2D 1H-13C HSQC	13C15NUBM2+ub	isotropic	Sample_conditions
3D HNCACB	13C15NUbi+ubm2	isotropic	Sample_conditions
3D 1H-15N NOESY	15NUbi+ubm2	isotropic	Sample_conditions
3D 1H-15N TOCSY	15NUbi+ubm2	isotropic	Sample_conditions
3D 1H-13C NOESY	13C15NUbi+ubm2	isotropic	Sample_conditions
3D HCCH-COSY	13C15NUbi+ubm2	isotropic	Sample_conditions
2D 1H-15N HSQC	15NUbi+ubm2	isotropic	Sample_conditions
2D 1H-13C HSQC	13C15NUbi+ubm2	isotropic	Sample_conditions
3D 1H-13C-filtered-13C-edited NOESY	13C15NUBM2+ub	isotropic	Sample_conditions
3D 1H-13C-filtered-13C-edited NOESY	13C15NUbi+ubm2	isotropic	Sample_conditions
3D 1H-13C-filtered-13C-edited NOESY	labUbi-overUBM2	isotropic	Sample_conditions

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

TOPSPIN v2.1, Bruker Biospin - collection, processing

Molmol v2k.2, Koradi, Billeter and Wuthrich - geometry optimization

UNIO v1.0.4, T. Herrmann - chemical shift assignment, peak picking, structure solution

DYANA, Guntert, Braun and Wuthrich - structure solution

CARA v1.8.4, R. Keller - chemical shift assignment, data analysis

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 750 MHz
Bruker Avance 900 MHz

Related Database Links:

PDB	2KWU 1AAR 1CMX 1D3Z 1F9J 1FXT 1G6J 1GJZ 1NBF 1OGW 1P3Q 1Q5W 1S1Q 1TBE 1UBI 1UBQ 1UZX 1V80 1V81 1VX7 1WR6 1WRD 1XD3 1XQQ 1YD8 1YIW 1YJ1 1YX5 1YX6 1ZGU 2AYO 2BGF 2C7M 2C7N 2D3G 2DEN 2DX5 2FCM 2FCN 2FCQ 2FCS 2FID 2FIF 2FUH 2G45 2GMI 2HD5 2HTH 2IBI 2J7Q 2JF5 2JRI 2JY6 2JZZ 2K25 2K39 2K6D 2K8B 2K8C 2KDE 2KDF 2KHW 2KJH 2KLG 2KN5 2KOX 2KTF 2KWU 2KWV 2KX0 2L0F 2L0T 2L3Z 2LD9 2LJ5 2LVO 2LVP 2LVQ 2LZ6 2MBB 2MBH 2MBO 2MBQ 2MCN 2MJ5 2MJB 2MOR 2MRE 2MUR 2NR2 2O6V 2OJR 2OOB 2PE9 2PEA 2QHO 2RR9 2RSU 2RU6 2W9N 2WDT 2WWZ 2WX0 2WX1 2XBB 2XEW 2XK5 2Y5B 2Z59 2ZCB 2ZCC 2ZNV 2ZVN 2ZVO 3A1Q 3A33 3A9J 3A9K 3AI5 3ALB 3AUL 3AXC 3B08 3B0A 3BY4 3C0R 3DVG 3DVN 3EEC 3EFU 3EHV 3H1U 3H7P 3H7S 3HM3 3I3T 3IFW 3IHP 3JSV 3JVZ 3JW0 3K9O 3K9P 3KVF 3KW5 3LDZ 3M3J 3MHS 3MTN 3N30 3N32 3NHE 3NOB 3NS8 3O65 3OFI 3OJ3 3OJ4 3ONS 3PHD 3PHW 3PRM 3PRP 3PT2 3PTF 3Q3F 3RUL 3TBL 3TMP 3U30 3UGB 3VDZ 3VFK 3VHT 3VUW 3VUX 3VUY 3ZLZ 3ZNH 3ZNI 3ZNZ 4A18 4A19 4A1B 4A1D 4ADX 4AP4 4AUQ 4BBN 4BOS 4BOZ 4BVU 4CXC 4CXD 4DDG 4DDI 4DHJ 4DHZ 4FJV 4HXD 4I6N 4IG7 4IUM 4JIO 4JQW 4K1R 4K7S 4K7U 4K7W 4KSK 4KSL 4KZX 4KZY 4KZZ 4LCD 4LDT 4LJO 4LJP 4M0W 4MDK 4MM3 4MSM 4MSQ 4NQK 4NQL 4P4H 4PIG 4PIH 4PIJ 4PQT 4RF0 4RF1 4UN2 4UPX 4UQ1 4UQ4 4UQ5 4W20 4W22 4W23 4W25 4W27 4W28 4WUR 4WZP
BMRB	11505 11547 15047 15410 15689 15866 15907 16228 16582 16626 16763 16885 16895 17059 17181 17239 17333 17439 17769 17919 18582 18583 18584 18610 18611 18737 19394 19399 19406 19412 19447 25070 25230 4245 4375 4983 5101 5387 6457 6466 6470 6488 68 7111
DBJ	BAA03983 BAA09860 BAA11842 BAA11843 BAA23486
EMBL	CAA25706 CAA26488 CAA28495 CAA30183 CAA30815
GB	AAA02769 AAA28154 AAA28997 AAA28998 AAA28999
PIR	I50437 I51568 I65237 JN0790 S13928
PRF	0412265A 1101405A 1212243A 1212243B 1212243C
REF	NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286
SP	P0C273 P0C275 P0C276 P0CG47 P0CG48
TPD	FAA00319
TPG	DAA18802 DAA20663 DAA20672 DAA24675 DAA28295
AlphaFold	P0C273 P0C275 P0C276 P0CG47 P0CG48

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1	GLY	SER	PRO	GLU	PHE	ASP	SER	ALA	GLU	GLU
2	LYS	LEU	PRO	PHE	PRO	PRO	ASP	ILE	ASP	PRO
3	GLN	VAL	PHE	TYR	GLU	LEU	PRO	GLU	GLU	VAL
4	GLN	LYS	GLU	LEU	MET	ALA	GLU	TRP	GLU	ARG
5	ALA	GLY	ALA	ALA	ARG	PRO	SER	ALA	HIS	ARG

1	GLY	SER	PRO	GLU	PHE	ASP	SER	ALA	GLU	GLU
2	LYS	LEU	PRO	PHE	PRO	PRO	ASP	ILE	ASP	PRO
3	GLN	VAL	PHE	TYR	GLU	LEU	PRO	GLU	GLU	VAL
4	GLN	LYS	GLU	LEU	MET	ALA	GLU	TRP	GLU	ARG
5	ALA	GLY	ALA	ALA	ARG	PRO	SER	ALA	HIS	ARG

1	GLY	SER	PRO	GLU	PHE	ASP	SER	ALA	GLU	GLU
2	LYS	LEU	PRO	PHE	PRO	PRO	ASP	ILE	ASP	PRO
3	GLN	VAL	PHE	TYR	GLU	LEU	PRO	GLU	GLU	VAL
4	GLN	LYS	GLU	LEU	MET	ALA	GLU	TRP	GLU	ARG
5	ALA	GLY	ALA	ALA	ARG	PRO	SER	ALA	HIS	ARG