BMRB Entry 17628

Name: NMR Structure of Alk1 extracellular domain
Published: 2012-08-30

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PDB ID: 2lcr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17628
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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 Structure of Alk1 extracellular domain

Deposition date:

2011-05-06

Original release date:

2012-08-30

Authors:

Ilangovan, Udayar

Citation:

Citation: Mahlawat, Pardeep; Ilangovan, Udayar; Biswas, Tanuka; Sun, Lu-Zhe; Hinck, Andrew. "Structure of the Alk1 extracellular domain and characterization of its bone morphogenetic protein (BMP) binding properties." Biochemistry 51, 6328-6341 (2012).
PubMed: 22799562

Assembly members:

Assembly members:
Alk1, polymer, 97 residues, 11148.615 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: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Alk1: DPVKPSRGPLVTCTCESPHC KGPTCRGAWCTVVLVREEGR HPQEHRGCGNLHRELCRGRP TEFVNHYCCDSHLCNHNVSL VLEATQPPSEQPGTDGQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	361
15N chemical shifts	84
1H chemical shifts	480

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Alk1	1

Entities:

Entity 1, Alk1 97 residues - 11148.615 Da.

1

ASP

PRO

VAL

LYS

PRO

SER

ARG

GLY

PRO

LEU

2

VAL

THR

CYS

THR

CYS

GLU

SER

PRO

HIS

CYS

3

LYS

GLY

PRO

THR

CYS

ARG

GLY

ALA

TRP

CYS

4

THR

VAL

LEU

VAL

ARG

GLU

GLY

ARG

5

HIS

PRO

GLN

GLU

HIS

ARG

GLY

CYS

GLY

ASN

6

LEU

HIS

ARG

GLU

LEU

CYS

ARG

GLY

ARG

PRO

7

THR

GLU

PHE

VAL

ASN

HIS

TYR

CYS

ASP

8

SER

HIS

LEU

CYS

ASN

HIS

ASN

VAL

SER

LEU

9

VAL

LEU

GLU

ALA

THR

GLN

PRO

SER

GLU

10

GLN

PRO

GLY

THR

ASP

GLY

GLN

Samples:

sample_1: Alk1, [U-100% 15N], 0.5 mM; sodium phosphate 25 mM; sodium azide 0.02%; H2O 95%; D2O 5%

sample_2: Alk1, [U-100% 13C; U-100% 15N], 0.5 mM; sodium phosphate 25 mM; sodium azide 0.02%; H2O 95%; D2O 5%

sample_3: Alk1, [U-100% 13C; U-100% 15N], 0.5 mM; sodium phosphate 25 mM; sodium azide 0.02%; Pf1 phage 5mg/mL mg; H2O 95%; D2O 5%

sample_conditions_1: pH: 5.5; pressure: 1 atm; temperature: 305 K

Experiments:

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

Software:

ARIA, Linge, O'Donoghue and Nilges - structure solution

CNSSOLVE, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

ModelFree, Palmer - realaxation

Molmol, Koradi, Billeter and Wuthrich - Structure Visualization

PECAN, Eghbalnia, Wang, Bahrami, Assadi, and Markley - chemical shift index calculation

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - Spectral Visualization

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

SPARKY, Goddard - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - dihedral angle determination

TOPSPIN, Bruker Biospin - data collection

NMR spectrometers:

Bruker Avance 700 MHz
Bruker DRX 600 MHz

PDB	2LCR 4FAO
EMBL	CAA80255 CAH91180
GB	AAA16160 AAB61900 AAH42637 AAQ02577 ADJ79922
REF	NP_000011 NP_001070869 NP_001125692 XP_001145609 XP_003831124
SP	P37023 Q5RAN0
AlphaFold	P37023 Q5RAN0