BMRB Entry 16744

Name: Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response
Published: 2010-05-18

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PDB ID: 2kuo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16744
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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:

Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response

Deposition date:

2010-02-23

Original release date:

2010-05-18

Authors:

Li, Guang-Yao; McCulloch, Richard; Fenton, Amanda; Cheung, Melissa; Meng, Li; Ikura, Mitsuhiko; Koch, C. Anne

Citation:

Citation: Li, Guang-Yao; McCulloch, Richard; Fenton, Amanda; Cheung, Melissa; Meng, Li; Ikura, Mitsuhiko; Koch, C. Anne. "Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response." Proc. Natl. Acad. Sci. U.S.A. 107, 9129-9134 (2010).
PubMed: 20439749

Assembly members:

Assembly members:
APLF_Tandem_ZF, polymer, 91 residues, 10272.400 Da.
ZN, 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: pGEX4T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
APLF_Tandem_ZF: GSKATDSVLQGSEGNKVKRT SCMYGANCYRKNPVHFQHFS HPGDSDYGGVQIVGQDETDD RPECPYGPSCYRKNPQHKIE YRHNTLPVRNV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	302
15N chemical shifts	95
1H chemical shifts	608

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, entity_1 91 residues - 10272.400 Da.

The first two residues (GS)are from the experssion vector.The sequence of APLF used in this study is from K360 to V448.

1

GLY

SER

LYS

ALA

THR

ASP

SER

VAL

LEU

GLN

2

GLY

SER

GLU

GLY

ASN

LYS

VAL

LYS

ARG

THR

3

SER

CYS

MET

TYR

GLY

ALA

ASN

CYS

TYR

ARG

4

LYS

ASN

PRO

VAL

HIS

PHE

GLN

HIS

PHE

SER

5

HIS

PRO

GLY

ASP

SER

ASP

TYR

GLY

VAL

6

GLN

ILE

VAL

GLY

GLN

ASP

GLU

THR

ASP

7

ARG

PRO

GLU

CYS

PRO

TYR

GLY

PRO

SER

CYS

8

TYR

ARG

LYS

ASN

PRO

GLN

HIS

LYS

ILE

GLU

9

TYR

ARG

HIS

ASN

THR

LEU

PRO

VAL

ARG

ASN

10

VAL

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1_h2o: APLF Tandem ZF, [U-100% 13C; U-100% 15N], 0.5 – 0.8 mM; Bis-tris 20 mM; sodium chloride 50 mM; sodium azide 1 mM; zinc chloride 0.05 mM; H2O 93%; D2O 7%

sample_1_d2o: APLF Tandem ZF, [U-100% 13C; U-100% 15N], 0.5 – 0.8 mM; Bis-tris 20 mM; sodium chloride 50 mM; sodium azide 1 mM; zinc chloride 0.05 mM; D2O 99%

sample_2_h2o: APLF Tandem ZF, [U-100% 15N], 0.1 mM; Bis-tris 20 mM; sodium chloride 50 mM; sodium azide 1 mM; zinc chloride 0.05 mM; H2O 93%; D2O 7%

sample_3_h2o: APLF Tandem ZF, [U-100% 15N], 0.1 mM; sodium phosphate 20 mM; potassium chloride 150 mM; sodium azide 1 mM; zinc chloride 0.05 mM; magnesium chloride 2 mM; H2O 93%; D2O 7%

sample_4_high_salt: APLF Tandem ZF, [U-100% 15N], 0.5 mM; Bis-tris 20 mM; sodium chloride 500 mM; sodium azide 1 mM; zinc chloride 0.05 mM; Pf1 phage 10 mg/ml; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 50 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 150 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 500 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1_h2o	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1_d2o	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1_d2o	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1_h2o	isotropic	sample_conditions_1
3D HNCACB	sample_1_h2o	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1_h2o	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1_h2o	isotropic	sample_conditions_1
3D C(CO)NH	sample_1_h2o	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1_d2o	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1_h2o	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1_h2o	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1_d2o	isotropic	sample_conditions_1
2D 1H-15N IPAP HSQC	sample_4_high_salt	isotropic	sample_conditions_3
2D 1H-15N HSQC	sample_2_h2o	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3_h2o	isotropic	sample_conditions_2

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

Molmol v2k, Koradi, Billeter and Wuthrich - data analysis

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

TALOS, Cornilescu, Delaglio and Bax - chemical shift based dihedral angle calculation

TOPSPIN, Bruker Biospin - collection

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

BMRB	16596
PDB	2KQB 2KQC 2KQD 2KQE 2KUO
DBJ	BAF83530
GB	AAH41144 AAY24113 ADZ15607 AIC53375 EAW99871
REF	NP_775816 XP_003830966 XP_005575759 XP_009235504 XP_009440878
SP	Q8IW19
AlphaFold	Q8IW19