BMRB Entry 5500

Name: Parkin binds the Rpn10 subunit of 26S proteasomes with the ubiquitin-like domain
Published: 2003-03-10

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PDB ID: 1iyf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR5500
MolProbity Validation Chart

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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:

Parkin binds the Rpn10 subunit of 26S proteasomes with the ubiquitin-like domain

Deposition date:

2002-08-13

Original release date:

2003-03-10

Authors:

Sakata, Eri; Yamaguchi, Yoshiki; Kurimoto, Eiji; Kikuchi, Jun; Yokoyama, Shigeyuki; Kawahara, Hiroyuki; Yokosawa, Hideyoshi; Hattori, Nobutaka; Mizuno, Yoshikuni; Tanaka, Keiji; Kato, Koichi

Citation:

Citation: Sakata, Eri; Yamaguchi, Yoshiki; Kurimoto, Eiji; Kikuchi, Jun; Yokoyama, Shigeyuki; Kawahara, Hiroyuki; Yokosawa, Hideyoshi; Hattori, Nobutaka; Mizuno, Yoshikuni; Tanaka, Keiji; Kato, Koichi. "Parkin binds the Rpn10 subunit of 26S proteasomes with the ubiquitin-like domain" EMBO Rep. 4, 301-306 (2003).

Assembly members:

Assembly members:
Parkin ubiquitin-like domain, polymer, 81 residues, 9235 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: GEX6P

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Parkin ubiquitin-like domain: GPLGSMIVFVRFNSSHGFPV EVDSDTSIFQLKEVVAKRQG VPADQLRVIFAGKELRNDWT VQNCDLDQQSIVHIVQRPWR K

Data sets:

assigned_chemical_shifts
- shift_set_1

Data type	Count
1H chemical shifts	148
13C chemical shifts	216
15N chemical shifts	72

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Ubl	1

Entities:

Entity 1, Ubl 81 residues - 9235 Da.

1

GLY

PRO

LEU

GLY

SER

MET

ILE

VAL

PHE

VAL

2

ARG

PHE

ASN

SER

HIS

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

ARG

ASN

ASP

TRP

THR

7

VAL

GLN

ASN

CYS

ASP

LEU

ASP

GLN

SER

8

ILE

VAL

HIS

ILE

VAL

GLN

ARG

PRO

TRP

ARG

9

LYS

Samples:

sample_1: Parkin ubiquitin-like domain, [U-98% 13C; U-98% 15N], 0.1 mM; potasium phosphate buffer 50 mM

Ex-cond_1: pH: 6.0; temperature: 303 K; ionic strength: 0.3 M

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	not available	not available	not available
2D 1H-13C HSQC	not available	not available	not available
3D CBCA(CO)NH	not available	not available	not available
3D CBCANH	not available	not available	not available
3D HCACO	not available	not available	not available
3D HNCA	not available	not available	not available
3D HN(CO)CA	not available	not available	not available
3D HNCO	not available	not available	not available
3D 15N-edited TOCSY	not available	not available	not available

Software:

XWINNMR v2.6 - raw spectral data processing, data analysis

CNS v1.1 - solution structure refinement

NMR spectrometers:

Bruker DRX 800 MHz

PDB	1IYF
DBJ	BAA25751 BAF43729 BAF85279 BAI46122
EMBL	CAH90914
GB	AAH22014 ABC74794 ABN46990 ACL68652 ACL98151
REF	NP_001125521 NP_001274591 NP_004553 NP_054642 NP_054643
SP	O60260
AlphaFold	O60260