BMRB Entry 18002

Name: Structural Basis of Phosphoinositide Binding to Kindlin-2 Pleckstrin Homology Domain in Regulating Integrin Activation
Published: 2011-11-21

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PDB ID: 2lko
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18002
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structural Basis of Phosphoinositide Binding to Kindlin-2 Pleckstrin Homology Domain in Regulating Integrin Activation

Deposition date:

2011-10-17

Original release date:

2011-11-21

Authors:

Liu, Jianmin; Fukuda, Koichi; Xu, Zhen

Citation:

Citation: Liu, Jianmin; Fukuda, Koichi; Xu, Zhen; Ma, Yan-Qing; Hirbawi, Jamila; Mao, Xian; Wu, Chuanyue; Plow, Edward; Qin, Jun. "Structural basis of phosphoinositide binding to kindlin-2 protein pleckstrin homology domain in regulating integrin activation." J. Biol. Chem. 286, 43334-43342 (2011).
PubMed: 22030399

Assembly members:

Assembly members:
Kindlin-2, polymer, 138 residues, 15722.256 Da.
4IP, non-polymer, 500.075 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):
Kindlin-2: GSHMGDITSIPELADYIKVF KPKKLTLKGYKQYWCTFKDT SISCYKSKEESSGTPAHQMN LRGCEVTPDVNISGQKFNIK LLIPVAEGMNEIWLRCDNEK QYAHWMAACRLASKGKTMAD SSYNLEVQNILSFLKMQH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	377
15N chemical shifts	129
1H chemical shifts	669

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Kindlin-2	1
2	4IP	2

Entities:

Entity 1, Kindlin-2 138 residues - 15722.256 Da.

1

GLY

SER

HIS

MET

GLY

ASP

ILE

THR

SER

ILE

2

PRO

GLU

LEU

ALA

ASP

TYR

ILE

LYS

VAL

PHE

3

LYS

PRO

LYS

LEU

THR

LEU

LYS

GLY

TYR

4

LYS

GLN

TYR

TRP

CYS

THR

PHE

LYS

ASP

THR

5

SER

ILE

SER

CYS

TYR

LYS

SER

LYS

GLU

6

SER

GLY

THR

PRO

ALA

HIS

GLN

MET

ASN

7

LEU

ARG

GLY

CYS

GLU

VAL

THR

PRO

ASP

VAL

8

ASN

ILE

SER

GLY

GLN

LYS

PHE

ASN

ILE

LYS

9

LEU

ILE

PRO

VAL

ALA

GLU

GLY

MET

ASN

10

GLU

ILE

TRP

LEU

ARG

CYS

ASP

ASN

GLU

LYS

11

GLN

TYR

ALA

HIS

TRP

MET

ALA

CYS

ARG

12

LEU

ALA

SER

LYS

GLY

LYS

THR

MET

ALA

ASP

13

SER

TYR

ASN

LEU

GLU

VAL

GLN

ASN

ILE

14

LEU

SER

PHE

LEU

LYS

MET

GLN

HIS

Entity 2, 4IP - C6 H16 O18 P4 - 500.075 Da.

1

4IP

Samples:

sample_1: Kindlin-2, [U-100% 13C; U-100% 15N], 1 mM; 4IP 2 mM; H2O 90%; D2O 10%

sample_2: Kindlin2-PH, [U-100% 13C; U-100% 15N], 1 mM; 4IP 2 mM; D2O 100%

sample_conditions_1: ionic strength: 0.05 M; pH: 6.8; 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 CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	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 HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D 15N/13C filtered (F1) [1H-13C]-NOESY-HSQC	sample_2	isotropic	sample_conditions_1
1D 15N/13C filtered (F1) NOESY	sample_2	isotropic	sample_conditions_1
2D 15N/13C filtered (F1) TOCSY	sample_2	isotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment, peak picking

xwinnmr, Bruker Biospin - collection

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

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

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

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 900 MHz

PDB	2LKO 4F7H
DBJ	BAE38850 BAF84427
EMBL	CAA80852 CAD61925
GB	AAH17327 AAH33436 AAH83876 AAI51293 AAN75823
REF	NP_001011915 NP_001094734 NP_001128471 NP_001128472 NP_001253248
SP	Q8CIB5 Q96AC1
TPG	DAA25234
AlphaFold	Q8CIB5 Q96AC1