BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 19328

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

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: 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:
HR7375C, polymer, 61 residues, 6934.479 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

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

Data sets:
Data typeCount
1H chemical shifts390
13C chemical shifts251
15N chemical shifts62

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1HR7375C1
2Zinc ion, 12
3Zinc ion, 22

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   SERHISMETCYSPROALAVALSERCYSLEU
2   GLNPROGLUGLYASPGLUVALASPTRPVAL
3   GLNCYSASPGLYSERCYSASNGLNTRPPHE
4   HISGLNVALCYSVALGLYVALSERPROGLU
5   METALAGLULYSGLUASPTYRILECYSVAL
6   ARGCYSTHRVALLYSASPALAPROSERARG
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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCNC_HR7375C.005isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticNC_HR7375C.005isotropicsample_conditions_1
3D 1H-15N NOESY NUSNC_HR7375C.005isotropicsample_conditions_1
3D 1H-13C NOESY aliphatic NUSNC_HR7375C.005isotropicsample_conditions_1
3D 1H-13C NOESY aromatic NUSNC_HR7375C.005isotropicsample_conditions_1
2D 1H-15N HSQCNC5_HR7375C.007isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticNC5_HR7375C.007isotropicsample_conditions_1
2D 1H-15N HSQC HISNC5_HR7375C.007isotropicsample_conditions_1
1D 1H-15N HSQC T1 arrayNC_HR7375C.005isotropicsample_conditions_1
1D 1H-15N HSQC T2 arrayNC_HR7375C.005isotropicsample_conditions_1
2D 1H-15N HSQC NH2 onlyNC_HR7375C.005isotropicsample_conditions_1
2D 1H-13C HSQC aromatic ctNC_HR7375C.005isotropicsample_conditions_1
2D 1H-13C HSQC aromatic noctNC_HR7375C.005isotropicsample_conditions_1
3D HNCACBNC_HR7375C.005isotropicsample_conditions_1
3D CBCA(CO)NHNC_HR7375C.005isotropicsample_conditions_1
3D HN(CO)CANC_HR7375C.005isotropicsample_conditions_1
3D HNCONC_HR7375C.005isotropicsample_conditions_1
3D HBHA(CO)NHNC_HR7375C.005isotropicsample_conditions_1
3D C(CO)NHNC_HR7375C.005isotropicsample_conditions_1
3D H(CCO)NHNC_HR7375C.005isotropicsample_conditions_1
3D HCCH-TOCSYNC_HR7375C.005isotropicsample_conditions_1
3D CCH-TOCSYNC_HR7375C.005isotropicsample_conditions_1
2D 1H-15N HSQCD2O_NC_HR7375C.005isotropicsample_conditions_1
3D 1H-15N NOESYNC_HR7375C.006isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticNC_HR7375C.006isotropicsample_conditions_1
3D 1H-13C NOESY aromaticNC_HR7375C.006isotropicsample_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

Related Database Links:

UNP Q9UGL1
HUGO KD5MB
PDB
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