BMRB Entry 17494

Title:
Zinc knuckle in PRDM4
Deposition date:
2011-02-26
Original release date:
2011-06-01
Authors:
Briknarova, Klara; Atwater, Daniel; Glicken, Jessica; Maynard, Stacy; Ness, Tara
Citation:

Citation: Briknarova, Klara; Atwater, Daniel; Glicken, Jessica; Maynard, Stacy; Ness, Tara. "The PR/SET domain in PRDM4 is preceded by a zinc knuckle."  Proteins 79, 2341-2345 (2011).
PubMed: 21604305

Assembly members:

Assembly members:
PRDM4(366-402), polymer, 39 residues, 4316.912 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: pGEX-4T1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PRDM4(366-402): GSKENMATLFTIWCTLCDRA YPSDCPEHGPVTFVPDTPI

Data sets:
Data typeCount
15N chemical shifts36
1H chemical shifts258

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1PRDM4(366-402)1
2ZINC ION2

Entities:

Entity 1, PRDM4(366-402) 39 residues - 4316.912 Da.

G364 and S365 are cloning artefacts

1   GLYSERLYSGLUASNMETALATHRLEUPHE
2   THRILETRPCYSTHRLEUCYSASPARGALA
3   TYRPROSERASPCYSPROGLUHISGLYPRO
4   VALTHRPHEVALPROASPTHRPROILE

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

H2O_sample: PRDM4(366-402) 0.5 mM; ZINC ION 2.5 mM; H2O 90%; D2O 10%; d11-Tris 50 mM; d16-TCEP 2.5 mM

D2O_sample: PRDM4(366-402) 0.5 mM; ZINC ION 2.5 mM; D2O 100%; d11-Tris 50 mM; d16-TCEP 2.5 mM

15N_sample: PRDM4(366-402), [U-100% 15N], 0.25 mM; ZINC ION 1.6 mM; H2O 90%; D2O 10%; d11-Tris 50 mM; d16-TCEP 2.5 mM

sample_conditions_1: pH: 7.15; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D DQF-COSYH2O_sampleisotropicsample_conditions_1
2D 1H-1H TOCSYH2O_sampleisotropicsample_conditions_1
2D 1H-1H NOESYH2O_sampleisotropicsample_conditions_1
ECOSYD2O_sampleisotropicsample_conditions_1
2D 1H-15N HSQC15N_sampleisotropicsample_conditions_1
3D HNHA15N_sampleisotropicsample_conditions_1
3D HNHB15N_sampleisotropicsample_conditions_1
3D 1H-15N TOCSY15N_sampleisotropicsample_conditions_1
3D 1H-15N NOESY15N_sampleisotropicsample_conditions_1
2D 1H-15N HMQC15N_sampleisotropicsample_conditions_1

Software:

VNMRJ, Varian - collection

FELIX, Felix NMR Inc. - chemical shift assignment, data analysis, processing

ARIA v2.3, Linge, O'Donoghue and Nilges - refinement, structure solution

NMR spectrometers:

  • Varian Uniform NMR System 600 MHz

Related Database Links:

PDB
DBJ BAG10863 BAG51692
EMBL CAB61401 CAH92945
GB AAD55249 AAH35581 ABM82163 ABM85348 AIC50813
REF NP_001126735 NP_001244489 NP_036538 XP_001162965 XP_002807184
SP Q5R5M1 Q9UKN5
AlphaFold Q5R5M1 Q9UKN5

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks