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
3Dmol.js: molecular visualization with WebGL
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

Software:

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinemen,structure solution,geometry optimization

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - refinement,geometry optimization,structure solution

AutoStructure v2.1, Huang, Tejero, Powers and Montelione - data analysis,refinement

NMRPipe vNMRPipe-2008//nmrbin.linux9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TOPSPIN v2.4, Bruker Biospin - collection

VNMRJ, Varian - collection

PINE, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment

SPARKY v3.113, Goddard - data analysis

TALOS+ vVersion 1.2009.0721.18, Shen, Cornilescu, Delaglio and Bax - geometry optimization

PSVS v1.4, Bhattacharya, Montelione - structure validation

FMCGUI vfmcgui2.1_linux, Alex Lemak, Cheryl Arrowmith - refinement

NMR spectrometers:

Bruker Avance II 850 MHz
Varian INOVA 600 MHz
Varian INOVA 750 MHz

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