BMRB Entry 34419

Name: NMR solution structure of Hml-2 C-terminal dimer domain
Published: 2020-01-13

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PDB ID: 6sai
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34419
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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 solution structure of Hml-2 C-terminal dimer domain

Deposition date:

2019-07-16

Original release date:

2020-01-13

Authors:

Nicastro, G.; Taylor, I.; Ball, N.; Ramos, A.

Citation:

Citation: Acton, O.; Grant, T.; Nicastro, G.; Ball, N.; Goldstone, D.; Robertson, L.; Sader, K.; Nans, A.; Ramos, A.; Stoye, J.; Taylor, I.; Rosenthal, P.. "Structural basis for Fullerene geometry in a human endogenous retrovirus capsid." Nat. Commun. 10, 5822-5822 (2019).
PubMed: 31862888

Assembly members:

Assembly members:
entity_1, polymer, 93 residues, 10093.613 Da.

Natural source:

Natural source: Common Name: HERV-K Taxonomy ID: 45617 Superkingdom: Viruses Kingdom: not available Genus/species: Human endogenous retrovirus HERV-K

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: PSFNTVRQGSKEPYPDFVAR LQDVAQKSIADEKARKVIVE LMAYENANPECQSAIKPLKG KVPAGSDVISEYVKACDGIG GAMHKAMLMAQLE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	291
1H chemical shifts	621

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	1

Entities:

Entity 1, entity_1 93 residues - 10093.613 Da.

1

PRO

SER

PHE

ASN

THR

VAL

ARG

GLN

GLY

SER

2

LYS

GLU

PRO

TYR

PRO

ASP

PHE

VAL

ALA

ARG

3

LEU

GLN

ASP

VAL

ALA

GLN

LYS

SER

ILE

ALA

4

ASP

GLU

LYS

ALA

ARG

LYS

VAL

ILE

VAL

GLU

5

LEU

MET

ALA

TYR

GLU

ASN

ALA

ASN

PRO

GLU

6

CYS

GLN

SER

ALA

ILE

LYS

PRO

LEU

LYS

GLY

7

LYS

VAL

PRO

ALA

GLY

SER

ASP

VAL

ILE

SER

8

GLU

TYR

VAL

LYS

ALA

CYS

ASP

GLY

ILE

GLY

9

GLY

ALA

MET

HIS

LYS

ALA

MET

LEU

MET

ALA

10

GLN

LEU

GLU

Samples:

sample_1: Hml-2 Ctd, [U-13C; U-15N], 2.3 ± 0.2 mM; Tris 20 mM; NaCl 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 mmHg; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	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-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

ARIA, Linge, O'Donoghue and Nilges - refinement, structure calculation

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

NMR spectrometers:

Bruker AVANCE 800 MHz
Bruker AVANCE 700 MHz