BMRB Entry 10311

Name: Solution structure of the PH domain of PEPP-3 from human
Published: 2010-03-11

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PDB ID: 2d9y
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR10311
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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:

Solution structure of the PH domain of PEPP-3 from human

Deposition date:

2009-03-11

Original release date:

2010-03-11

Authors:

Li, H.; Tochio, N.; Koshiba, S.; Inoue, M.; Kigawa, T.; Yokoyama, S.

Citation:

Citation: Li, H.; Tochio, N.; Koshiba, S.; Inoue, M.; Kigawa, T.; Yokoyama, S.. "Solution structure of the PH domain of PEPP-3 from human" .

Assembly members:

Assembly members:
PH domain, polymer, 117 residues, Formula weight is not available

Natural source:

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: Cell-free synthesis Vector: P050711-08

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PH domain: GSSGSSGNAPVTKAGWLFKQ ASSGVKQWNKRWFVLVDRCL FYYKDEKEESILGSIPLLSF RVAAVQPSDNISRKHTFKAE HAGVRTYFFSAESPEEQEAW IQAMGEAARVQSGPSSG

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	502
15N chemical shifts	116
1H chemical shifts	774

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PH domain	1

Entities:

Entity 1, PH domain 117 residues - Formula weight is not available

1

GLY

SER

GLY

SER

GLY

ASN

ALA

PRO

2

VAL

THR

LYS

ALA

GLY

TRP

LEU

PHE

LYS

GLN

3

ALA

SER

GLY

VAL

LYS

GLN

TRP

ASN

LYS

4

ARG

TRP

PHE

VAL

LEU

VAL

ASP

ARG

CYS

LEU

5

PHE

TYR

LYS

ASP

GLU

LYS

GLU

SER

6

ILE

LEU

GLY

SER

ILE

PRO

LEU

SER

PHE

7

ARG

VAL

ALA

VAL

GLN

PRO

SER

ASP

ASN

8

ILE

SER

ARG

LYS

HIS

THR

PHE

LYS

ALA

GLU

9

HIS

ALA

GLY

VAL

ARG

THR

TYR

PHE

SER

10

ALA

GLU

SER

PRO

GLU

GLN

GLU

ALA

TRP

11

ILE

GLN

ALA

MET

GLY

GLU

ALA

ARG

VAL

12

GLN

SER

GLY

PRO

SER

GLY

Samples:

sample_1: PH domain, [U-13C; U-15N], 1.14 mM; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%; H2O 90%; D2O 10%

condition_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 296 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-separated NOESY	sample_1	isotropic	condition_1
3D 13C-separated NOESY	sample_1	isotropic	condition_1

Software:

xwinnmr v3.5, Bruker - collection

NMRPipe v20030801, Delaglio, F. - processing

NMRView v5.0.4, Johnson, B.A. - data analysis

Kujira v0.932, Kobayashi, N. - data analysis

CYANA v2.0.17, Guntert, P. - refinement, structure solution

NMR spectrometers:

Bruker AVANCE 900 MHz

PDB	2D9Y
DBJ	BAA76813 BAG09923
GB	AAI52476 AAI67845 EAW91509 EAW91510
REF	NP_055750 XP_002808300 XP_002918242 XP_003474853 XP_003505811
SP	Q9Y2H5
AlphaFold	Q9Y2H5