BMRB Entry 19473

Name: 1H, 13C, and 15N Chemical Shift Assignments for Sp140 PHD finger cis conformer
Published: 2013-09-19

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PDB ID: 2md8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19473
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

1H, 13C, and 15N Chemical Shift Assignments for Sp140 PHD finger cis conformer

Deposition date:

2013-08-29

Original release date:

2013-09-19

Authors:

Zucchelli, Chiara; Quilici, Giacomo; Musco, Giovanna

Citation:

Citation: Zucchelli, Chiara; Tamburri, Simone; Quilici, Giacomo; Palagano, Eleonora; Berardi, Andrea; Saare, Mario; Peterson, Part; Bachi, Angela; Musco, Giovanna. "Structure of human Sp140 PHD finger: an atypical fold interacting with Pin1." FEBS J. 281, 216-231 (2014).
PubMed: 24267382

Assembly members:

Assembly members:
Sp140_PHD_finger_cis_conformer, polymer, 56 residues, Formula weight is not available
ZINC ION, non-polymer, 65.409 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: pETM11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Sp140_PHD_finger_cis_conformer: GAMGMRNLDECEVCRDGGEL FCCDTCSRVFHEDCHIPPVE AERTPWNCIFCRMKES

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	159
15N chemical shifts	53
1H chemical shifts	354

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PHD finger	1
2	ZN1	2
3	ZN2	2

Entities:

Entity 1, PHD finger 56 residues - Formula weight is not available

1

GLY

ALA

MET

GLY

MET

ARG

ASN

LEU

ASP

GLU

2

CYS

GLU

VAL

CYS

ARG

ASP

GLY

GLU

LEU

3

PHE

CYS

ASP

THR

CYS

SER

ARG

VAL

PHE

4

HIS

GLU

ASP

CYS

HIS

ILE

PRO

VAL

GLU

5

ALA

GLU

ARG

THR

PRO

TRP

ASN

CYS

ILE

PHE

6

CYS

ARG

MET

LYS

GLU

SER

Entity 2, ZN1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: Sp140 PHD finger, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate buffer pH 6.3 20 mM; NaCl 150 mM; DTT 4 mM; ZnCl2 50 uM; DSS 0.3 mM; H2O 90%; D2O 10%

sample_2: Sp140 PHD finger, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate buffer pH 6.3 20 mM; NaCl 150 mM; DTT 4 mM; ZnCl2 50 uM; DSS 0.3 mM; H2O 90%; D2O 10%

sample_3: Sp140 PHD finger, [U-100% 15N], 1 mM; sodium phosphate buffer pH 6.3 20 mM; NaCl 150 mM; DTT 4 mM; ZnCl2 50 uM; DSS 0.3 mM; H2O 90%; D2O 10%

sample_4: Sp140 PHD finger 1 mM; sodium phosphate buffer pH 6.3 20 mM; NaCl 150 mM; DTT 4 mM; ZnCl2 50 uM; DSS 0.3 mM; H2O 90%; D2O 10%

sample_5: Sp140 PHD finger 1 mM; sodium phosphate buffer pH 6.3 20 mM; NaCl 150 mM; DTT 4 mM; ZnCl2 50 uM; DSS 0.3 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.3; temperature: 298 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
2D 1H-1H TOCSY	sample_4	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_5	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	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 HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_3	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

ANALYSIS, T. Stevens, R. Fogh, W. Boucher, J. Ionides, C. Spronk - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 900 MHz

BMRB	19472
PDB	2MD7 2MD8
DBJ	BAG62830
GB	AAB18617 AAC50817 AAI05744 AAI05745 AAI05961
REF	NP_001265380 NP_001265381 NP_001265382 NP_009168 XP_003274775
SP	Q13342
AlphaFold	Q13342