BMRB Entry 30602

Name: NMR Structure of Branched K11/K48-Linked Tri-Ubiquitin
Published: 2019-10-15

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PDB ID: 6oq2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30602
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:

NMR Structure of Branched K11/K48-Linked Tri-Ubiquitin

Deposition date:

2019-04-25

Original release date:

2019-10-15

Authors:

Boughton, A.; Fushman, D.

Citation:

Citation: Boughton, A.; Krueger, S.; Fushman, D.. "Branching via K11 and K48 Bestows Ubiquitin Chains with a Unique Interdomain Interface and Enhanced Affinity for Proteasomal Subunit Rpn1" Structure 28, 29-43 (2020).
PubMed: 31677892

Assembly members:

Assembly members:
entity_1, polymer, 76 residues, 8660.873 Da.
entity_2, polymer, 76 residues, 8604.845 Da.
entity_3, polymer, 77 residues, 8691.918 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MQIFVKTLTGRTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGRQLEDGRTLSDYN IQRESTLHLVLRLRGG
entity_2: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGRQLEDGRTLSDYN IQKESTLHLVLRLRGG
entity_3: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGGD

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
15N chemical shifts	140
1H chemical shifts	140

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2
3	entity_3	3

Entities:

Entity 1, entity_1 76 residues - 8660.873 Da.

1

MET

GLN

ILE

PHE

VAL

LYS

THR

LEU

THR

GLY

2

ARG

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

ARG

GLU

SER

THR

LEU

HIS

LEU

VAL

8

LEU

ARG

LEU

ARG

GLY

Entity 2, entity_2 76 residues - 8604.845 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

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

Entity 3, entity_3 77 residues - 8691.918 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

ASP

Samples:

sample_1: entity_1, [U-15N-distal11], 120 uM; entity_2, [U-15N-distal11], 120 uM; entity_3, [U-15N-distal11], 120 uM

sample_2: entity_1, [U-15N-distal48], 100 uM; entity_2, [U-15N-distal48], 100 uM; entity_3, [U-15N-distal48], 100 uM

sample_3: entity_1, [U-15N-distal11], 60 uM; entity_2, [U-15N-distal11], 60 uM; entity_3, [U-15N-distal11], 60 uM

sample_4: entity_1, [U-15N-distal48], 110 uM; entity_2, [U-15N-distal48], 110 uM; entity_3, [U-15N-distal48], 110 uM

sample_conditions_1: ionic strength: 0 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - processing

Sparky, Goddard - peak picking

HADDOCK, Bonvin - refinement, structure calculation

NMR spectrometers:

Bruker AvanceIII 800 MHz
Bruker AvanceIII 600 MHz

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