BMRB Entry 25979

Name: protein complex
Published: 2017-06-19

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PDB ID: 6co4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR25979
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: protein complex PubMed: 28598414

Deposition date: 2016-02-25 Original release date: 2017-06-19

Authors: Lu, Xiuxiu; Walters, Kylie

Citation: Lu, Xiuxiu; Nowicka, Urszula; Sridharan, Vinidhra; Liu, Fen; Randles, Leah; Hymel, David; Dyba, Marzena; Tarasov, Sergey; Tarasova, Nadya; Zhao, Xue Zhi; Hamazaki, Jun; Murata, Shigeo; Burke, Terrence; Walters, Kylie. "Structure of the Rpn13-Rpn2 complex provides insights for Rpn13 and Uch37 as anticancer targets." Nat. Commun. 8, 15540-15540 (2017).

Assembly members:
entity_1, polymer, 111 residues, 13104.049 Da.
entity_2, polymer, 14 residues, 1704.760 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: NKYLVEFRAGKMSLKGTTVT PDKRKGLVYIQQTDDSLIHF CWKDRTSGNVEDDLIIFPDD CEFKRVPQCPSGRVYVLKFK AGSKRLFFWMQEPKTDQDEE HCRKVNEYLNN
entity_2: QEPEPPEPFEYIDD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	545
15N chemical shifts	128
1H chemical shifts	836

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 111 residues - 13104.049 Da.

1

ASN

LYS

TYR

LEU

VAL

GLU

PHE

ARG

ALA

GLY

2

LYS

MET

SER

LEU

LYS

GLY

THR

VAL

THR

3

PRO

ASP

LYS

ARG

LYS

GLY

LEU

VAL

TYR

ILE

4

GLN

THR

ASP

SER

LEU

ILE

HIS

PHE

5

CYS

TRP

LYS

ASP

ARG

THR

SER

GLY

ASN

VAL

6

GLU

ASP

LEU

ILE

PHE

PRO

ASP

7

CYS

GLU

PHE

LYS

ARG

VAL

PRO

GLN

CYS

PRO

8

SER

GLY

ARG

VAL

TYR

VAL

LEU

LYS

PHE

LYS

9

ALA

GLY

SER

LYS

ARG

LEU

PHE

TRP

MET

10

GLN

GLU

PRO

LYS

THR

ASP

GLN

ASP

GLU

11

HIS

CYS

ARG

LYS

VAL

ASN

GLU

TYR

LEU

ASN

12

ASN

PRO

Entity 2, entity_2 14 residues - 1704.760 Da.

1

GLN

GLU

PRO

GLU

PRO

GLU

PRO

PHE

GLU

2

TYR

ILE

ASP

Samples:

sample_1: entity_1, [U-13C; U-15N], 0.7 mM; entity_2, [U-13C; U-15N], 0.7 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 2 mM; sodium azide 0.1%; H2O 90%; D2O, [U-2H], 10%

sample_2: entity_1, [U-13C; U-15N], 0.7 mM; entity_2, [U-13C; U-15N], 0.7 mM; potassium phosphate 20 mM; sodium chloride 50 mM; DTT 2 mM; sodium azide 0.1%; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 0.05 M; pH: 6.5; pressure: 1 atm; temperature: 298.2 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D half-filtered NOESY	sample_2	isotropic	sample_conditions_1

Software:

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

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

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

TOPSPIN, Bruker Biospin - collection

TALOS, Cornilescu, Delaglio and Bax - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 850 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts