BMRB Entry 18521

Name: The NMR structure of the Vta1-Vps60 complex
Published: 2012-11-05

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PDB ID: 2luh
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18521
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

The NMR structure of the Vta1-Vps60 complex

Deposition date:

2012-06-13

Original release date:

2012-11-05

Authors:

Yang, Zhongzheng; Vild, Cody; Ju, Jiaying; Zhang, Xu; Liu, Jianping; Shen, Jie; Zhao, Bin; Lan, Wenxian; Gong, Fuchun; Liu, Maili; Cao, Chunyang; Xu, Zhaohui

Citation:

Citation: Yang, Zhongzheng; Vild, Cody; Ju, Jiaying; Zhang, Xu; Liu, Jianping; Shen, Jie; Zhao, Bin; Lan, Wenxian; Gong, Fuchun; Liu, Maili; Cao, Chunyang; Xu, Zhaohui. "Structural basis of molecular recognition between ESCRT-III-like protein Vps60 and AAA-ATPase regulator Vta1 in the multivesicular body pathway." J. Biol. Chem. 287, 43899-43908 (2012).
PubMed: 23105107

Assembly members:

Assembly members:
entity_1, polymer, 167 residues, 19062.176 Da.
entity_2, polymer, 59 residues, 6609.143 Da.

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MASNAARVVATAKDFDKVGL GIIGYYLQLYAVELILSEED RSQEMTALATELLDTIEAFK KEIGGESEAEDSDKSLHVMN TLIHDQEKAKIYMLNFTMSL YNEKLKQLKDGPWDVMLKRS LWCCIDLFSCILHLWKENIS ETSTNSLQKRIKYCKIYLSK LAKGEIG
entity_2: INIDKLQDMQDEMLDLIEQG DELQEVLAMNNNSGELDDIS DAELDAELDALAQEDFTLP

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	926
15N chemical shifts	232
1H chemical shifts	1605

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_1 167 residues - 19062.176 Da.

1

MET

ALA

SER

ASN

ALA

ARG

VAL

ALA

2

THR

ALA

LYS

ASP

PHE

ASP

LYS

VAL

GLY

LEU

3

GLY

ILE

GLY

TYR

LEU

GLN

LEU

TYR

4

ALA

VAL

GLU

LEU

ILE

LEU

SER

GLU

ASP

5

ARG

SER

GLN

GLU

MET

THR

ALA

LEU

ALA

THR

6

GLU

LEU

ASP

THR

ILE

GLU

ALA

PHE

LYS

7

LYS

GLU

ILE

GLY

GLU

SER

GLU

ALA

GLU

8

ASP

SER

ASP

LYS

SER

LEU

HIS

VAL

MET

ASN

9

THR

LEU

ILE

HIS

ASP

GLN

GLU

LYS

ALA

LYS

10

ILE

TYR

MET

LEU

ASN

PHE

THR

MET

SER

LEU

11

TYR

ASN

GLU

LYS

LEU

LYS

GLN

LEU

LYS

ASP

12

GLY

PRO

TRP

ASP

VAL

MET

LEU

LYS

ARG

SER

13

LEU

TRP

CYS

ILE

ASP

LEU

PHE

SER

CYS

14

ILE

LEU

HIS

LEU

TRP

LYS

GLU

ASN

ILE

SER

15

GLU

THR

SER

THR

ASN

SER

LEU

GLN

LYS

ARG

16

ILE

LYS

TYR

CYS

LYS

ILE

TYR

LEU

SER

LYS

17

LEU

ALA

LYS

GLY

GLU

ILE

GLY

Entity 2, entity_2 59 residues - 6609.143 Da.

1

ILE

ASN

ILE

ASP

LYS

LEU

GLN

ASP

MET

GLN

2

ASP

GLU

MET

LEU

ASP

LEU

ILE

GLU

GLN

GLY

3

ASP

GLU

LEU

GLN

GLU

VAL

LEU

ALA

MET

ASN

4

ASN

SER

GLY

GLU

LEU

ASP

ILE

SER

5

ASP

ALA

GLU

LEU

ASP

ALA

GLU

LEU

ASP

ALA

6

LEU

ALA

GLN

GLU

ASP

PHE

THR

LEU

PRO

Samples:

sample_1: entity_1, [U-13C; U-15N], 1.0-1.2 mM; entity_2 1.0-1.2 mM

sample_2: entity_1, [U-13C; U-15N], 1.0-1.2 mM; entity_2 1.0-1.2 mM

sample_3: entity_1 1.0-1.2 mM; entity_2, [U-13C; U-15N], 1.0-1.2 mM

sample_4: entity_1 1.0-1.2 mM; entity_2, [U-13C; U-15N], 1.0-1.2 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 7.0; pressure: 1 atm; temperature: 293.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_4	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_3	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_3	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_3	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_3	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_3	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_4	isotropic	sample_conditions_1

Software:

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

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

SPARKY, Goddard - chemical shift assignment, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

VNMRJ, Varian - collection

ProcheckNMR, Laskowski and MacArthur - structure analysis

NMR spectrometers:

Varian INOVA 600 MHz
Bruker Avance 800 MHz

PDB	2LUH 2RKK 2LUH
DBJ	GAA25057 GAA22697
EMBL	CAY81418 CAY78983
GB	AAA66933 AAB67473 AHY78560 AJP40335 AJV46241 AAB64922 AAS56499 AHY75433 EDN60805 EDV07859
REF	NP_013282 NP_010774
SP	Q06263 Q03390
TPG	DAA09501 DAA12319
AlphaFold	Q06263 Q03390