BMRB Entry 34461

Name: Solution structure and 1H, 13C and 15N chemical shift assignments for the complex of VPS29 with VARP 687-747
Published: 2020-10-16

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PDB ID: 6tl0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34461
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:

Solution structure and 1H, 13C and 15N chemical shift assignments for the complex of VPS29 with VARP 687-747

Deposition date:

2019-11-29

Original release date:

2020-10-16

Authors:

Owen, D.; Neuhaus, D.; Yang, J.C.; Crawley-Snowdon, H.

Citation:

Citation: Crawley-Snowdon, Harriet; Yang, Ji-Chun; Zaccai, Nathan; Davis, Luther; Wartosch, Lena; Herman, Emily; Bright, Nicholas; Swarbrick, James; Collins, Brett; Jackson, Lauren; Seaman, Matthew; Luzio, J Paul; Dacks, Joel; Neuhaus, David; Owen, David. "Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29" Nat. Commun. 11, 5031-5031 (2020).
PubMed: 33024112

Assembly members:

Assembly members:
entity_1, polymer, 192 residues, 21626.832 Da.
entity_2, polymer, 61 residues, 6319.927 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21 Vector: pGEXVPS29

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSPEFGTRDRMLVLVLGDLH IPHRCNSLPAKFKKLLVPGK IQHILCTGNLCTKESYDYLK TLAGDVHIVRGDFDENLNYP EQKVVTVGQFKIGLIHGHQV IPWGDMASLALLQRQFDVDI LISGHTHKFEAFEHENKFYI NPGSATGAYNALETNIIPSF VLMDIQASTVVTYVYQLIGD DVKVERIEYKKS
entity_2: GPLGSTEEDLEDAEDTVSAA DPEFCHPLCQCPKCAPAQKR LAKVPASGLGVNVTSQDGSS W

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	749
15N chemical shifts	239
1H chemical shifts	1447

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

Entities:

Entity 1, entity_1 192 residues - 21626.832 Da.

1

GLY

SER

PRO

GLU

PHE

GLY

THR

ARG

ASP

ARG

2

MET

LEU

VAL

LEU

VAL

LEU

GLY

ASP

LEU

HIS

3

ILE

PRO

HIS

ARG

CYS

ASN

SER

LEU

PRO

ALA

4

LYS

PHE

LYS

LEU

VAL

PRO

GLY

LYS

5

ILE

GLN

HIS

ILE

LEU

CYS

THR

GLY

ASN

LEU

6

CYS

THR

LYS

GLU

SER

TYR

ASP

TYR

LEU

LYS

7

THR

LEU

ALA

GLY

ASP

VAL

HIS

ILE

VAL

ARG

8

GLY

ASP

PHE

ASP

GLU

ASN

LEU

ASN

TYR

PRO

9

GLU

GLN

LYS

VAL

THR

VAL

GLY

GLN

PHE

10

LYS

ILE

GLY

LEU

ILE

HIS

GLY

HIS

GLN

VAL

11

ILE

PRO

TRP

GLY

ASP

MET

ALA

SER

LEU

ALA

12

LEU

GLN

ARG

GLN

PHE

ASP

VAL

ASP

ILE

13

LEU

ILE

SER

GLY

HIS

THR

HIS

LYS

PHE

GLU

14

ALA

PHE

GLU

HIS

GLU

ASN

LYS

PHE

TYR

ILE

15

ASN

PRO

GLY

SER

ALA

THR

GLY

ALA

TYR

ASN

16

ALA

LEU

GLU

THR

ASN

ILE

PRO

SER

PHE

17

VAL

LEU

MET

ASP

ILE

GLN

ALA

SER

THR

VAL

18

VAL

THR

TYR

VAL

TYR

GLN

LEU

ILE

GLY

ASP

19

ASP

VAL

LYS

VAL

GLU

ARG

ILE

GLU

TYR

LYS

20

LYS

SER

Entity 2, entity_2 61 residues - 6319.927 Da.

1

GLY

PRO

LEU

GLY

SER

THR

GLU

ASP

LEU

2

GLU

ASP

ALA

GLU

ASP

THR

VAL

SER

ALA

3

ASP

PRO

GLU

PHE

CYS

HIS

PRO

LEU

CYS

GLN

4

CYS

PRO

LYS

CYS

ALA

PRO

ALA

GLN

LYS

ARG

5

LEU

ALA

LYS

VAL

PRO

ALA

SER

GLY

LEU

GLY

6

VAL

ASN

VAL

THR

SER

GLN

ASP

GLY

SER

7

TRP

Entity 3, entity_3 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: VPS29, [U-98% 13C; U-98% 15N], 0.45 ± 0.15 mM; VARP 692-746 0.45 ± 0.15 mM; TRIS, [U-2H], 20 mM; sodium chloride 200 mM; DTT, [U-2H], 1 mM

sample_2: VPS29, [U-98% 13C; U-98% 15N], 0.45 ± 0.15 mM; VARP 692-746 0.45 ± 0.15 mM; TRIS, [U-2H], 20 mM; sodium chloride 200 mM; DTT, [U-2H], 1 mM

sample_3: VPS29 0.45 ± 0.15 mM; VARP 692-746, [U-98% 13C; U-98% 15N], 0.45 ± 0.15 mM; TRIS, [U-2H], 20 mM; sodium chloride 200 mM; DTT, [U-2H], 1 mM

sample_4: VPS29 0.45 ± 0.15 mM; VARP 692-746, [U-98% 13C; U-98% 15N], 0.45 ± 0.15 mM; TRIS, [U-2H], 20 mM; sodium chloride 200 mM; DTT, [U-2H], 1 mM

sample_conditions_1: ionic strength: 200 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 200 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

sample_conditions_3: ionic strength: 200 mM; pH: 7.0; pressure: 1 atm; temperature: 275 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic constant-time	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY (150ms mixing time) filtered to reject 13C-1 and 15N-coupled 1H in F1 and to accept 13C- and 15N-coupled 1H in F2	sample_1	isotropic	sample_conditions_1
3D 13C NOESY-HSQC aromatic (150ms mixing time)	sample_1	isotropic	sample_conditions_1
3D 13C NOESY-HSQC aliphatic (150ms mixing time)	sample_1	isotropic	sample_conditions_1
3D 15N NOESY-HSQC (150ms mixing time)	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY [13C-13C-1H]	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY [1H-13C-1H]	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCANH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY (150ms mixing time) filtered to reject 13C-1 and 15N-coupled 1H in F1 and to accept 13C- and 15N-coupled 1H in F2	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic constant-time	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY (70ms mixing time) filtered to reject 13C-1 and 15N-coupled 1H in F1 and to accept 13C- and 15N-coupled 1H in F2	sample_2	isotropic	sample_conditions_1
3D 13C NOESY-HSQC (120ms mixing time) aromatic, filtered to reject 13C-1 and 15N-coupled 1H in F1	sample_2	isotropic	sample_conditions_1
3D 13C NOESY-HSQC (50ms mixing time) aromatic, filtered to reject 13C-1 and 15N-coupled 1H in F1	sample_2	isotropic	sample_conditions_1
3D 13C NOESY-HSQC (120ms mixing time) aliphatic, filtered to reject 13C-1 and 15N-coupled 1H in F1	sample_2	isotropic	sample_conditions_1
3D 13C NOESY-HSQC (50ms mixing time) aliphatic, filtered to reject 13C-1 and 15N-coupled 1H in F1	sample_2	isotropic	sample_conditions_1
3D 13C NOESY-HSQC (120ms mixing time) aromatic	sample_2	isotropic	sample_conditions_1
3D 13C NOESY-HSQC (50ms mixing time) aromatic	sample_2	isotropic	sample_conditions_1
3D 13C NOESY-HSQC (120ms mixing time) aliphatic	sample_2	isotropic	sample_conditions_1
3D 13C NOESY-HSQC (50ms mixing time) aliphatic	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY [13C-13C-1H]	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_3	isotropic	sample_conditions_1
3D HNCA	sample_3	isotropic	sample_conditions_1
3D HN(CO)CA	sample_3	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_3	isotropic	sample_conditions_1
3D HNHA	sample_3	isotropic	sample_conditions_1
3D HCCH-TOCSY [1H-13C-1H]	sample_3	isotropic	sample_conditions_1
3D HCCH-TOCSY [13C-13C-1H]	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY-HSQC (70ms mixing time)	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY-HSQC (150ms mixing time)	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY-HSQC (50ms mixing time)	sample_3	isotropic	sample_conditions_2
3D 1H-15N NOESY-HSQC (50ms mixing time)	sample_3	isotropic	sample_conditions_3
3D 1H-13C NOESY (70ms mixing time) aliphatic	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_4	isotropic	sample_conditions_1
3D HCCH-TOCSY [1H-13C-1H]	sample_4	isotropic	sample_conditions_1
3D HCCH-TOCSY [13C-13C-1H]	sample_4	isotropic	sample_conditions_1
3D 13C NOESY-HSQC aliphatic (50ms mixing time)	sample_4	isotropic	sample_conditions_1
3D 13C NOESY-HSQC aliphatic (70ms mixing time)	sample_4	isotropic	sample_conditions_1
3D 13C NOESY-HSQC aliphatic (120ms mixing time)	sample_4	isotropic	sample_conditions_1
3D 13C NOESY-HSQC aromatic (70ms mixing time)	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic constant-time	sample_2	isotropic	sample_conditions_1

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