BMRB Entry 19328

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PDB ID: 2ma5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19328
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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:

Solution NMR structure of PHD type Zinc finger domain of Lysine-specific demethylase 5B (PLU-1/JARID1B) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7375C

Deposition date:

2013-06-28

Original release date:

2013-08-02

Authors:

Hassan, Faizule; Ramelot, Theresa; Yang, Yunhuang; Cort, John; Janjua, Haleema; Kohan, Eitan; Lee, Dan; Xiao, Rong; Acton, Thomas; Everett, John; Montelione, Gaetano; Kennedy, Michael

Citation:

Citation: Hassan, Faizule; Ramelot, Theresa; Yang, Yunhuang; Cort, John; Janjua, Haleema; Kohan, Eitan; Lee, Dan; Xiao, Rong; Acton, Thomas; Everett, John; Montelione, Gaetano; Kennedy, Michael. "Solution NMR structure of PHD type Zinc finger domain of Lysine-specific demethylase 5B (PLU-1/JARID1B) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7375C" To be published ., .-..

Assembly members:

Assembly members:
HR7375C, polymer, 61 residues, 6934.479 Da.
entity_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: pET15Avi6HT_NESG

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HR7375C: SHMCPAVSCLQPEGDEVDWV QCDGSCNQWFHQVCVGVSPE MAEKEDYICVRCTVKDAPSR K

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list
- NUS_Nnoesy
- NUS_Cnoesy

Data type	Count
1H chemical shifts	390
13C chemical shifts	251
15N chemical shifts	62

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HR7375C	1
2	Zinc ion, 1	2
3	Zinc ion, 2	2

Entities:

Entity 1, HR7375C 61 residues - 6934.479 Da.

Three non-native residues at the N-terminus, SHM. Residues 1487 to 1544 from KDM5B.

1

SER

HIS

MET

CYS

PRO

ALA

VAL

SER

CYS

LEU

2

GLN

PRO

GLU

GLY

ASP

GLU

VAL

ASP

TRP

VAL

3

GLN

CYS

ASP

GLY

SER

CYS

ASN

GLN

TRP

PHE

4

HIS

GLN

VAL

CYS

VAL

GLY

VAL

SER

PRO

GLU

5

MET

ALA

GLU

LYS

GLU

ASP

TYR

ILE

CYS

VAL

6

ARG

CYS

THR

VAL

LYS

ASP

ALA

PRO

SER

ARG

7

LYS

Entity 2, Zinc ion, 1 - Zn - 65.409 Da.

1

ZN

Samples:

NC_HR7375C.005: HR7375C.005, [U-100% 13C; U-100% 15N], 1.04 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 10%; DSS 50 uM

NC_HR7375C.006: HR7375C.006, [U-100% 13C; U-100% 15N], 1.04 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 10%; DSS 50 uM

NC5_HR7375C.007: HR7375C.007, [U-100% 15N] 5% 13C fractionally labeled, 0.33 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 10%; DSS 50 uM

D2O_NC_HR7375C.005: HR7375C.005, [U-100% 13C; U-100% 15N], 1.04 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 100%; DSS 50 uM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC_HR7375C.005	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	NC_HR7375C.005	isotropic	sample_conditions_1
3D 1H-15N NOESY NUS	NC_HR7375C.005	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic NUS	NC_HR7375C.005	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic NUS	NC_HR7375C.005	isotropic	sample_conditions_1
2D 1H-15N HSQC	NC5_HR7375C.007	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	NC5_HR7375C.007	isotropic	sample_conditions_1
2D 1H-15N HSQC HIS	NC5_HR7375C.007	isotropic	sample_conditions_1
1D 1H-15N HSQC T1 array	NC_HR7375C.005	isotropic	sample_conditions_1
1D 1H-15N HSQC T2 array	NC_HR7375C.005	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	NC_HR7375C.005	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic ct	NC_HR7375C.005	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic noct	NC_HR7375C.005	isotropic	sample_conditions_1
3D HNCACB	NC_HR7375C.005	isotropic	sample_conditions_1
3D CBCA(CO)NH	NC_HR7375C.005	isotropic	sample_conditions_1
3D HN(CO)CA	NC_HR7375C.005	isotropic	sample_conditions_1
3D HNCO	NC_HR7375C.005	isotropic	sample_conditions_1
3D HBHA(CO)NH	NC_HR7375C.005	isotropic	sample_conditions_1
3D C(CO)NH	NC_HR7375C.005	isotropic	sample_conditions_1
3D H(CCO)NH	NC_HR7375C.005	isotropic	sample_conditions_1
3D HCCH-TOCSY	NC_HR7375C.005	isotropic	sample_conditions_1
3D CCH-TOCSY	NC_HR7375C.005	isotropic	sample_conditions_1
2D 1H-15N HSQC	D2O_NC_HR7375C.005	isotropic	sample_conditions_1
3D 1H-15N NOESY	NC_HR7375C.006	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	NC_HR7375C.006	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	NC_HR7375C.006	isotropic	sample_conditions_1

UNP	Q9UGL1
HUGO	KD5MB
PDB	2MA5
DBJ	BAG51084
EMBL	CAB43532 CAB61368 CAB61375 CAB61395 CAB63108
GB	AAD16061 AAI56050 AAI57032 EAW91433 EAW91435
REF	NP_001300971 NP_006609 XP_002807770 XP_002808303 XP_003792395
SP	Q9UGL1
AlphaFold	Q9Y3Q5 Q9UGL1

BMRB Entry 19328

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Entities:

Samples:

Experiments:

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