BMRB Entry 28042

Name: ubiquitin receptor protein complex
Published: 2020-03-03

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PDB ID: 6uyi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR28042
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:

ubiquitin receptor protein complex

Deposition date:

2019-11-13

Original release date:

2020-03-03

Authors:

Lu, Xiuxiu; Walters, Kylie

Citation:

Citation: Lu, Xiuxiu; Ebelle, Danielle; Matsuo, Hiroshi; Walters, Kylie. "An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure" Structure 28, 495-506.e3 (2020).
PubMed: 32160516

Assembly members:

Assembly members:
ubiquitin_receptor_A, polymer, 136 residues, Formula weight is not available
ubiquitin_receptor_B, polymer, 36 residues, Formula weight is not available
ubiquitin_receptor_C, polymer, 77 residues, Formula weight is not available
ubiquitin_receptor_D, polymer, 76 residues, Formula weight is not available

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: pRSET

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ubiquitin_receptor_A: GPGSMTTSGALFPSLVPGSR GASNKYLVEFRAGKMSLKGT TVTPDKRKGLVYIQQTDDSL IHFCWKDRTSGNVEDDLIIF PDDCEFKRVPQCPSGRVYVL KFKAGSKRLFFWMQEPKTDQ DEEHCRKVNEYLNNPP
ubiquitin_receptor_B: MPGALGASGSSGHELSALGP GSQEPEPPEPFEYIDD
ubiquitin_receptor_C: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGGD
ubiquitin_receptor_D: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGRQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	1165
15N chemical shifts	207
1H chemical shifts	1930

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ubiquitin receptor, chain A	1
2	ubiquitin receptor, chain B	2
3	ubiquitin receptor, chain C	3
4	ubiquitin receptor, chain D	4

Entities:

Entity 1, ubiquitin receptor, chain A 136 residues - Formula weight is not available

1

GLY

PRO

GLY

SER

MET

THR

SER

GLY

ALA

2

LEU

PHE

PRO

SER

LEU

VAL

PRO

GLY

SER

ARG

3

GLY

ALA

SER

ASN

LYS

TYR

LEU

VAL

GLU

PHE

4

ARG

ALA

GLY

LYS

MET

SER

LEU

LYS

GLY

THR

5

THR

VAL

THR

PRO

ASP

LYS

ARG

LYS

GLY

LEU

6

VAL

TYR

ILE

GLN

THR

ASP

SER

LEU

7

ILE

HIS

PHE

CYS

TRP

LYS

ASP

ARG

THR

SER

8

GLY

ASN

VAL

GLU

ASP

LEU

ILE

PHE

9

PRO

ASP

CYS

GLU

PHE

LYS

ARG

VAL

PRO

10

GLN

CYS

PRO

SER

GLY

ARG

VAL

TYR

VAL

LEU

11

LYS

PHE

LYS

ALA

GLY

SER

LYS

ARG

LEU

PHE

12

PHE

TRP

MET

GLN

GLU

PRO

LYS

THR

ASP

GLN

13

ASP

GLU

HIS

CYS

ARG

LYS

VAL

ASN

GLU

14

TYR

LEU

ASN

PRO

Entity 2, ubiquitin receptor, chain B 36 residues - Formula weight is not available

1

MET

PRO

GLY

ALA

LEU

GLY

ALA

SER

GLY

SER

2

SER

GLY

HIS

GLU

LEU

SER

ALA

LEU

GLY

PRO

3

GLY

SER

GLN

GLU

PRO

GLU

PRO

GLU

PRO

4

PHE

GLU

TYR

ILE

ASP

Entity 3, ubiquitin receptor, chain C 77 residues - Formula weight is not available

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

ASP

Entity 4, ubiquitin receptor, chain D 76 residues - Formula weight is not available

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

ARG

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:

sample_1: Rpn13, [U-13C], 0.6 mM; Rpn2 0.6 mM; proximal ubiquitin of Diubiquitin, [U-13C], 0.72 mM; proximal ubiquitin of Diubiquitin, [U-13C], 0.72 mM

sample_2: Rpn13, [U-13C], 0.6 mM; Rpn2 0.6 mM; distal ubiquitin of Diubiquitin, [U-13C], 0.72 mM; distal ubiquitin of Diubiquitin, [U-13C], 0.72 mM

sample_conditions_1: ionic strength: 0.11 M; pH: 6.5; pressure: 1 atm; temperature: 298.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D half-filtered 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D half-filtered 1H-13C NOESY	sample_2	isotropic	sample_conditions_1

Software:

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

XEASY, Bartels et al. - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

Bruker Avance 850 MHz
Bruker Avance 900 MHz

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