BMRB Entry 18688

Name: Backbone amide chemical shifts of gp78 RING bound to Ube2g2:G2BR
Published: 2013-08-26

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PDB ID: 2lxp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18688
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Backbone amide chemical shifts of gp78 RING bound to Ube2g2:G2BR

Deposition date:

2012-08-30

Original release date:

2013-08-26

Authors:

Das, Ranabir; Linag, Yuhe; Mariano, Jennifer; Li, Jess; Huang, Tao; King, Aaren; Weissman, Allan; Ji, Xinhua; Byrd, R. Andrew

Citation:

Citation: Das, Ranabir; Liang, Yu-He; Mariano, Jennifer; Li, Jess; Huang, Tao; King, Aaren; Tarasov, Sergey; Weissman, Allan; Ji, Xinhua; Byrd, R. Andrew. "Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine." EMBO J. 32, 2504-2516 (2013).
PubMed: 23942235

Assembly members:

Assembly members:
entity_1, polymer, 156 residues, 17556.293 Da.
entity_2, polymer, 27 residues, 3365.939 Da.
entity_3, polymer, 58 residues, 6473.385 Da.
entity_ZN, non-polymer, 65.409 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: pET3a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AGTALKRLMAEYKQLTLNPP EGIVAGPMNEENFFEWEALI MGPEDTCFEFGVFPAILSFP LDYPLSPPKMRFTCEMFHPN IYPDGRVCISILHAPGSAER WSPVQSVEKILLSVVSMLAE PNDESGANVDASKMWRDDRE QFYKIAKQIVQKSLGL
entity_2: SADERQRMLVQRKDELLQQA RKRFLNK
entity_3: AVATPEELAVNNDDCAICWD SMQAARKLPCGHLFHNSCLR SWLEQDTSCPTCRMSLNI

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
15N chemical shifts	55
1H chemical shifts	55

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
3	entity_3	3
4	ZINC ION_1	4
5	ZINC ION_2	4

Entities:

Entity 1, entity_1 156 residues - 17556.293 Da.

1

ALA

GLY

THR

ALA

LEU

LYS

ARG

LEU

MET

ALA

2

GLU

TYR

LYS

GLN

LEU

THR

LEU

ASN

PRO

3

GLU

GLY

ILE

VAL

ALA

GLY

PRO

MET

ASN

GLU

4

GLU

ASN

PHE

GLU

TRP

GLU

ALA

LEU

ILE

5

MET

GLY

PRO

GLU

ASP

THR

CYS

PHE

GLU

PHE

6

GLY

VAL

PHE

PRO

ALA

ILE

LEU

SER

PHE

PRO

7

LEU

ASP

TYR

PRO

LEU

SER

PRO

LYS

MET

8

ARG

PHE

THR

CYS

GLU

MET

PHE

HIS

PRO

ASN

9

ILE

TYR

PRO

ASP

GLY

ARG

VAL

CYS

ILE

SER

10

ILE

LEU

HIS

ALA

PRO

GLY

SER

ALA

GLU

ARG

11

TRP

SER

PRO

VAL

GLN

SER

VAL

GLU

LYS

ILE

12

LEU

SER

VAL

SER

MET

LEU

ALA

GLU

13

PRO

ASN

ASP

GLU

SER

GLY

ALA

ASN

VAL

ASP

14

ALA

SER

LYS

MET

TRP

ARG

ASP

ARG

GLU

15

GLN

PHE

TYR

LYS

ILE

ALA

LYS

GLN

ILE

VAL

16

GLN

LYS

SER

LEU

GLY

LEU

Entity 2, entity_2 27 residues - 3365.939 Da.

1

SER

ALA

ASP

GLU

ARG

GLN

ARG

MET

LEU

VAL

2

GLN

ARG

LYS

ASP

GLU

LEU

GLN

ALA

3

ARG

LYS

ARG

PHE

LEU

ASN

LYS

Entity 3, entity_3 58 residues - 6473.385 Da.

1

ALA

VAL

ALA

THR

PRO

GLU

LEU

ALA

VAL

2

ASN

ASP

CYS

ALA

ILE

CYS

TRP

ASP

3

SER

MET

GLN

ALA

ARG

LYS

LEU

PRO

CYS

4

GLY

HIS

LEU

PHE

HIS

ASN

SER

CYS

LEU

ARG

5

SER

TRP

LEU

GLU

GLN

ASP

THR

SER

CYS

PRO

6

THR

CYS

ARG

MET

SER

LEU

ASN

ILE

Entity 4, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: gp78RING, [U-100% 13C; U-100% 15N], 0.7 – 1 mM; TRIS 50 mM; TCEP 2 mM; sodium azide 0.2 mM

sample_conditions_1: ionic strength: 0 M; pH: 7.2; 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-13C HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

SPARKY, Goddard - chemical shift assignment, data analysis

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

CNS, Alexandre Bonvin - structure solution

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 500 MHz

REF	XP_007486190 NP_001135 NP_001267243 XP_001091030 XP_002761010 XP_003263117 NP_001039439 NP_001135 NP_001267243 NP_001271666 NP_035917
PDB	2LXP 3FSH 3H8K 4LAD 2LXH 2LXP 4LAD
DBJ	BAE01277 BAK63135 BAE01277 BAE34049 BAE41974 BAE87377 BAK63135
GB	AAA36671 AAA79362 AAD56722 AAH17043 AAH56869 AAD56721 AAD56722 AAH17043 AAH34538 AAH40338
SP	Q9UKV5 Q9R049 Q9UKV5
BMRB	18677
TPG	DAA20037
AlphaFold	Q9UKV5 Q9R049 Q9UKV5