BMRB Entry 17459

Name: Identification of the Binding Site for Acidic Phospholipids on the PH Domain of Dynamin: Implications for Stimulation of GTPase Activity
Published: 2012-06-06

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17459

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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:

Identification of the Binding Site for Acidic Phospholipids on the PH Domain of Dynamin: Implications for Stimulation of GTPase Activity

Deposition date:

2011-02-11

Original release date:

2012-06-06

Authors:

Zheng, Jie; Cahill, Sean; Lemmon, Mark; Fushman, David; Schlessinger, Joseph; Cowburn, David

Citation:

Citation: Zheng, Jie; Cahill, Sean; Lemmon, Mark; Fushman, David; Schlessinger, Joseph; Cowburn, David. "Identification of the Binding Site for Acidic Phospholipids on the PH Domain of Dynamin: Implications for Stimulation of GTPase Activity" J. Mol. Biol. 255, 14-21 (1996).

Assembly members:

Assembly members:
dynaminPHdomain, polymer, 125 residues, Formula weight is not available
IBS, non-polymer, 492.158 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: ns

Entity Sequences (FASTA):

Entity Sequences (FASTA):
dynaminPHdomain: MKTSGNQDEILVIRKGWLTI NNIGIMKGGSKEYWFVLTAE NLSWYKDDEEKEKKYMLSVD NLKLRDVEKGFMSSKHIFAL FNTEQRNVYKDYRQLELACE TQEEVDSWKASFLRAGVYPE RVGDK

Data sets:

binding_constants

Data type	Count
binding constants	1

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	dynaminPHdomain	1
2	IBS	2

Entities:

Entity 1, dynaminPHdomain 125 residues - Formula weight is not available

1

MET

LYS

THR

SER

GLY

ASN

GLN

ASP

GLU

ILE

2

LEU

VAL

ILE

ARG

LYS

GLY

TRP

LEU

THR

ILE

3

ASN

ILE

GLY

ILE

MET

LYS

GLY

SER

4

LYS

GLU

TYR

TRP

PHE

VAL

LEU

THR

ALA

GLU

5

ASN

LEU

SER

TRP

TYR

LYS

ASP

GLU

6

LYS

GLU

LYS

TYR

MET

LEU

SER

VAL

ASP

7

ASN

LEU

LYS

LEU

ARG

ASP

VAL

GLU

LYS

GLY

8

PHE

MET

SER

LYS

HIS

ILE

PHE

ALA

LEU

9

PHE

ASN

THR

GLU

GLN

ARG

ASN

VAL

TYR

LYS

10

ASP

TYR

ARG

GLN

LEU

GLU

LEU

ALA

CYS

GLU

11

THR

GLN

GLU

VAL

ASP

SER

TRP

LYS

ALA

12

SER

PHE

LEU

ARG

ALA

GLY

VAL

TYR

PRO

GLU

13

ARG

VAL

GLY

ASP

LYS

Entity 2, IBS - C9 H19 O17 P3 - 492.158 Da.

1

IBS

Samples:

sample_1: dynaminPHdomain, [U-15N], 1.9 mM; IBS0 – 13.74 mM; dithiothreitol, [U-2H], 4 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

InsightII, Biosym Technologies - figure generation

NMR spectrometers:

Bruker DMX 500 MHz

PDB	1DYN 2DYN 3SNH 3ZVR 3ZYS 4UUD 4UUK
DBJ	BAD90284 BAD92361 BAG53342 BAG58137 BAG59018
EMBL	CAA38397
GB	AAA02803 AAA37318 AAA37323 AAH34679 AAH50279
PIR	B40671
PRF	1614348A
REF	NP_001005336 NP_001070288 NP_001124521 NP_001275666 NP_001275667
SP	P21575 P39053 Q05193 Q08DF4
TPG	DAA24145
AlphaFold	Q08DF4 Q05193 P39053 P21575