BMRB Entry 16271

Name: A PH domain within OCRL bridges clathrin mediated membrane trafficking to phosphoinositide metabolis
Published: 2009-06-25

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PDB ID: 2kie
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16271
MolProbity Validation Chart

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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:

A PH domain within OCRL bridges clathrin mediated membrane trafficking to phosphoinositide metabolis

Deposition date:

2009-05-03

Original release date:

2009-06-25

Authors:

Mao, Yuxin; Balkin, Daniel; Zoncu, Roberto; Erdmann, Kai; Tomasini, Livia; Hu, Fenghua; Jin, Moonsoon; Hodsdon, Michael; De Camilli, Pietro

Citation:

Citation: Mao, Yuxin; Balkin, Daniel; Zoncu, Roberto; Erdmann, Kai; Tomasini, Livia; Hu, Fenghua; Jin, Moonsoon; Hodsdon, Michael; De Camilli, Pietro. "A PH domain within OCRL bridges clathrin-mediated membrane trafficking to phosphoinositide metabolism" EMBO J. 28, 1831-1842 (2009).
PubMed: 19536138

Assembly members:

Assembly members:
PH domain, polymer, 372 residues, 41573.961 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: pGEX6p-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PH domain: GPLGSMEPPLPVGAQPLATV EGMEMKGPLREPCALTLAQR NGQYELIIQLHEKEQHVQDI IPINSHFRCVQEAEETLLID IASNSGCKIRVQGDWIRERR FEIPDEEHCLKFLSAVLAAQ KAQSGPLGSMEPPLPVGAQP LATVEGMEMKGPLREPCALT LAQRNGQYELIIQLHEKEQH VQDIIPINSHFRCVQEAEET LLIDIASNSGCKIRVQGDWI RERRFEIPDEEHCLKFLSAV LAAQKAQSGPLGSMEPPLPV GAQPLATVEGMEMKGPLREP CALTLAQRNGQYELIIQLHE KEQHVQDIIPINSHFRCVQE AEETLLIDIASNSGCKIRVQ GDWIRERRFEIPDEEHCLKF LSAVLAAQKAQS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	424
15N chemical shifts	131
1H chemical shifts	899

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 372 residues - 41573.961 Da.

1

GLY

PRO

LEU

GLY

SER

MET

GLU

PRO

LEU

2

PRO

VAL

GLY

ALA

GLN

PRO

LEU

ALA

THR

VAL

3

GLU

GLY

MET

GLU

MET

LYS

GLY

PRO

LEU

ARG

4

GLU

PRO

CYS

ALA

LEU

THR

LEU

ALA

GLN

ARG

5

ASN

GLY

GLN

TYR

GLU

LEU

ILE

GLN

LEU

6

HIS

GLU

LYS

GLU

GLN

HIS

VAL

GLN

ASP

ILE

7

ILE

PRO

ILE

ASN

SER

HIS

PHE

ARG

CYS

VAL

8

GLN

GLU

ALA

GLU

THR

LEU

ILE

ASP

9

ILE

ALA

SER

ASN

SER

GLY

CYS

LYS

ILE

ARG

10

VAL

GLN

GLY

ASP

TRP

ILE

ARG

GLU

ARG

11

PHE

GLU

ILE

PRO

ASP

GLU

HIS

CYS

LEU

12

LYS

PHE

LEU

SER

ALA

VAL

LEU

ALA

GLN

13

LYS

ALA

GLN

SER

GLY

PRO

LEU

GLY

SER

MET

14

GLU

PRO

LEU

PRO

VAL

GLY

ALA

GLN

PRO

15

LEU

ALA

THR

VAL

GLU

GLY

MET

GLU

MET

LYS

16

GLY

PRO

LEU

ARG

GLU

PRO

CYS

ALA

LEU

THR

17

LEU

ALA

GLN

ARG

ASN

GLY

GLN

TYR

GLU

LEU

18

ILE

GLN

LEU

HIS

GLU

LYS

GLU

GLN

HIS

19

VAL

GLN

ASP

ILE

PRO

ILE

ASN

SER

HIS

20

PHE

ARG

CYS

VAL

GLN

GLU

ALA

GLU

THR

21

LEU

ILE

ASP

ILE

ALA

SER

ASN

SER

GLY

22

CYS

LYS

ILE

ARG

VAL

GLN

GLY

ASP

TRP

ILE

23

ARG

GLU

ARG

PHE

GLU

ILE

PRO

ASP

GLU

24

GLU

HIS

CYS

LEU

LYS

PHE

LEU

SER

ALA

VAL

25

LEU

ALA

GLN

LYS

ALA

GLN

SER

GLY

PRO

26

LEU

GLY

SER

MET

GLU

PRO

LEU

PRO

VAL

27

GLY

ALA

GLN

PRO

LEU

ALA

THR

VAL

GLU

GLY

28

MET

GLU

MET

LYS

GLY

PRO

LEU

ARG

GLU

PRO

29

CYS

ALA

LEU

THR

LEU

ALA

GLN

ARG

ASN

GLY

30

GLN

TYR

GLU

LEU

ILE

GLN

LEU

HIS

GLU

31

LYS

GLU

GLN

HIS

VAL

GLN

ASP

ILE

PRO

32

ILE

ASN

SER

HIS

PHE

ARG

CYS

VAL

GLN

GLU

33

ALA

GLU

THR

LEU

ILE

ASP

ILE

ALA

34

SER

ASN

SER

GLY

CYS

LYS

ILE

ARG

VAL

GLN

35

GLY

ASP

TRP

ILE

ARG

GLU

ARG

PHE

GLU

36

ILE

PRO

ASP

GLU

HIS

CYS

LEU

LYS

PHE

37

LEU

SER

ALA

VAL

LEU

ALA

GLN

LYS

ALA

38

GLN

SER

Samples:

sample_1: entity 1 mM; potassium phosphate 20 mM

sample_conditions_1: pH: 6.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - chemical shift assignment

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

SPARKY, Goddard - peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization

NMR spectrometers:

Varian INOVA 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks