BMRB Entry 18080

Name: structure of amyloid precursor protein&#039;s transmembrane domain
Published: 2012-01-25

Click here to enlarge.

PDB ID: 2llm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18080
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

structure of amyloid precursor protein's transmembrane domain

Deposition date:

2011-11-15

Original release date:

2012-01-25

Authors:

Nadezhdin, Kirill; Bocharova, Olga; Bocharov, Eduard; Arseniev, Alexander

Citation:

Citation: Nadezhdin, Kirill; Bocharova, Olga; Bocharov, Eduard; Arseniev, Alexander. "Structural and Dynamic Study of the Transmembrane Domain of the Amyloid Precursor Protein" Acta Naturae ., .-. (2010).

Assembly members:

Assembly members:
entity, polymer, 43 residues, 4450.500 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: pGEMEX-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GSQKLVFFAEDVGSNKGAII GLMVGGVVIATVIVITLVML KKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	138
15N chemical shifts	44
1H chemical shifts	273

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	amyloid precursor protein's transmembrane domain	1

Entities:

Entity 1, amyloid precursor protein's transmembrane domain 43 residues - 4450.500 Da.

1

GLY

SER

GLN

LYS

LEU

VAL

PHE

ALA

GLU

2

ASP

VAL

GLY

SER

ASN

LYS

GLY

ALA

ILE

3

GLY

LEU

MET

VAL

GLY

VAL

ILE

ALA

4

THR

VAL

ILE

VAL

ILE

THR

LEU

VAL

MET

LEU

5

LYS

Samples:

sample_1: APPjmtm, [U-100% 13C; U-100% 15N], 0.3 – 1 mM; DPC, [U-100% 2H], 21 – 70 mM; H2O 95%; D2O 5%

sample_2: APPjmtm, [U-100% 15N], 0.3 – 1 mM; DPC21 – 70 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 20 mM; pH: 4.6; pressure: 1 atm; temperature: 273 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 HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_2	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - geometry optimization, visualization

TALOS+, Cornilescu, Delaglio and Bax - refinement, structure solution

CARA, R.L.J.Keller - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

BMRB	15775 18649
PDB	2LLM 2LOH 2LP1 2LZ3 5AEF
DBJ	BAA22264 BAA84580 BAB71958 BAC34997 BAC36369
EMBL	CAA30050 CAA30488 CAA31830 CAA39589 CAA39590
GB	AAA35540 AAA36829 AAA37139 AAA51722 AAA51726
PIR	A60045 D60045 E60045 G60045 JH0773
PRF	1303338A 1403400A 1507304A 1507304B 1507304C
REF	NP_000475 NP_001005698 NP_001006601 NP_001013036 NP_001070264
SP	O73683 P05067 P08592 P12023 P53601
TPG	DAA33655
AlphaFold	O73683 P05067 P08592 P12023 P53601