BMRB Entry 16813

Name: Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain
Published: 2010-05-19

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PDB ID: 2knb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16813
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain

Deposition date:

2010-03-31

Original release date:

2010-05-19

Authors:

Trempe, Jean-Francois; Guennadi, Kozlov; Edna, Camacho; Kalle, Gehring

Citation:

Citation: Trempe, Jean-Francois; Chen, Carol X-Q; Grenier, Karl; Camacho, Edna Matta; Kozlov, Guennadi; McPherson, Peter; Gehring, Kalle; Fon, Edward. "SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination." Mol. Cell 36, 1034-1047 (2009).
PubMed: 20064468

Assembly members:

Assembly members:
Ubl, polymer, 81 residues, 8738.083 Da.
SH3, polymer, 71 residues, 7121.919 Da.

Natural source:

Natural source: Common Name: Norway rat Taxonomy ID: 10116 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Rattus norvegicus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-6p1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ubl: GPLGSMIVFVRFNSSYGFPV EVDSDTSIFQLKEVVAKRQG VPADQLRVIFAGKELQNHLT VQNCDLEQQSIVHIVQRPQR K
SH3: GSRRASVGSDQPCCRALYDF EPENEGELGFKEGDIITLTN QIDENWYEGMLHGQSGFFPI NYVEILVALPH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	406
15N chemical shifts	150
1H chemical shifts	833

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Ubl	1
2	SH3	2

Entities:

Entity 1, Ubl 81 residues - 8738.083 Da.

Residues 1-5 represent a non-native tag generated after 3C protease cleavage of N-terminal GST

1

GLY

PRO

LEU

GLY

SER

MET

ILE

VAL

PHE

VAL

2

ARG

PHE

ASN

SER

TYR

GLY

PHE

PRO

VAL

3

GLU

VAL

ASP

SER

ASP

THR

SER

ILE

PHE

GLN

4

LEU

LYS

GLU

VAL

ALA

LYS

ARG

GLN

GLY

5

VAL

PRO

ALA

ASP

GLN

LEU

ARG

VAL

ILE

PHE

6

ALA

GLY

LYS

GLU

LEU

GLN

ASN

HIS

LEU

THR

7

VAL

GLN

ASN

CYS

ASP

LEU

GLU

GLN

SER

8

ILE

VAL

HIS

ILE

VAL

GLN

ARG

PRO

GLN

ARG

9

LYS

Entity 2, SH3 71 residues - 7121.919 Da.

Residues 1-9 represent a non-native tag generated after thrombin protease cleavage of N-terminal GST

1

GLY

SER

ARG

ALA

SER

VAL

GLY

SER

ASP

2

GLN

PRO

CYS

ARG

ALA

LEU

TYR

ASP

PHE

3

GLU

PRO

GLU

ASN

GLU

GLY

GLU

LEU

GLY

PHE

4

LYS

GLU

GLY

ASP

ILE

THR

LEU

THR

ASN

5

GLN

ILE

ASP

GLU

ASN

TRP

TYR

GLU

GLY

MET

6

LEU

HIS

GLY

GLN

SER

GLY

PHE

PRO

ILE

7

ASN

TYR

VAL

GLU

ILE

LEU

VAL

ALA

LEU

PRO

8

HIS

Samples:

Ubl_SH3_D2O: Ubl, [U-99% 13C; U-99% 15N], 1.2 ± 0.1 mM; SH3 1.2 ± 0.1 mM; D2O 100%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

SH3_Ubl_D2O: SH3, [U-99% 13C; U-99% 15N], 1.2 mM; Ubl 1.2 mM; D2O 100%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

Ubl_SH3_H2O: Ubl, [U-99% 13C; U-99% 15N], 0.8 mM; SH3 1.6 mM; D2O 5%; H2O 95%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

SH3_Ubl_H2O: SH3, [U-99% 13C; U-99% 15N], 0.8 mM; Ubl 1.6 mM; D2O 5%; H2O 95%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

Ubl_SH3_H2OB: Ubl, [U-99% 15N], 0.8 mM; SH3 1.6 mM; D2O 5%; H2O 95%; polyacrylamide 4.5%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

SH3_Ubl_H2OB: SH3, [U-99% 15N], 0.8 mM; Ubl 1.6 mM; D2O 5%; H2O 95%; polyacrylamide 4.5%; HEPES 10 mM; NaCl 50 mM; DTT 1 mM; EDTA 0.1 mM

isotropic: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

polyacrylamide: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D CBCA(CO)NH	Ubl_SH3_H2O	isotropic	isotropic
3D HNCACB	Ubl_SH3_H2O	isotropic	isotropic
3D CBCA(CO)NH	SH3_Ubl_H2O	isotropic	isotropic
3D HNCACB	SH3_Ubl_H2O	isotropic	isotropic
2D 1H-15N HSQC	Ubl_SH3_H2O	isotropic	isotropic
2D 1H-15N HSQC	SH3_Ubl_H2O	isotropic	isotropic
3D HCCH-COSY	Ubl_SH3_D2O	isotropic	isotropic
3D HCCH-COSY	SH3_Ubl_D2O	isotropic	isotropic
3D 1H-13C NOESY	Ubl_SH3_D2O	isotropic	isotropic
3D 1H-13C NOESY	SH3_Ubl_D2O	isotropic	isotropic
2D 1H-13C HSQC	Ubl_SH3_D2O	isotropic	isotropic
2D 1H-13C HSQC	SH3_Ubl_D2O	isotropic	isotropic
2D 1H-15N IPAP-HSQC	Ubl_SH3_H2OB	anisotropic	polyacrylamide
2D 1H-15N IPAP-HSQC	SH3_Ubl_H2OB	anisotropic	polyacrylamide
2D 1H-15N IPAP-HSQC	Ubl_SH3_H2OB	isotropic	isotropic
2D 1H-15N IPAP-HSQC	SH3_Ubl_H2OB	isotropic	isotropic
3D 1H-13C NOESY coupled	Ubl_SH3_D2O	isotropic	isotropic
3D 1H-13C NOESY coupled	SH3_Ubl_D2O	isotropic	isotropic

Software:

NMRPipe v2.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.115, Goddard - chemical shift assignment, peak picking

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

NMR spectrometers:

Bruker Avance 600 MHz
Varian INOVA 800 MHz

PDB	2KNB 4K95 4ZYN 2KNB 3IQL
DBJ	BAA92431 BAC31888 BAE22364 BAE23963
GB	AAF34874 AAF68666 AAG37013 AAM21453 AAM21456 AAH18385 AAI23533 AAL37407 AAL37408 AIL95726
REF	NP_064478 NP_001070308 NP_062408 XP_001925192 XP_002920770 XP_003783082
SP	Q9JK66 Q62420
TPG	DAA26952
AlphaFold	Q9JK66 Q62420