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 25985

Title: NMR Structure of the C-Terminal Domain of human APOBEC3B   PubMed: 27163633

Authors: Byeon, In-Ja; Byeon, Chang-Hyeock; Gronenborn, Angela

Citation: Byeon, In-Ja; Byeon, Chang-Hyeock; Wu, Tiyun; Mitra, Mithun; Singer, Dustin; Levin, Judith; Gronenborn, Angela. "Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity"  Biochemistry 55, 2944-2959 (2016).

Assembly members:
A3B-CTD, polymer, 205 residues, 24409.651 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):
A3B-CTD: MEILRYLMDPDTFTFNFNND PLVLRRRQTYLCYEVERLDN GTWVLMDQHMGFLCNEAKNL LCGFYGRHAELRFLDLVPSL QLDPAQIYRVTWFISWSPCF SWGCAGEVRAFLQENTHVRL RIFAARIYDYDPLYKEALQM LRDAGAQVSIMTYDEFEYCW DTFVYRQGCPFQPWDGLEEH SQALSGRLRAILQNQGNLEH HHHHH

Data sets:
Data typeCount
13C chemical shifts481
15N chemical shifts388
1H chemical shifts1359

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1A3B CTD1

Entities:

Entity 1, A3B CTD 205 residues - 24409.651 Da.

1   METGLUILELEUARGTYRLEUMETASPPRO
2   ASPTHRPHETHRPHEASNPHEASNASNASP
3   PROLEUVALLEUARGARGARGGLNTHRTYR
4   LEUCYSTYRGLUVALGLUARGLEUASPASN
5   GLYTHRTRPVALLEUMETASPGLNHISMET
6   GLYPHELEUCYSASNGLUALALYSASNLEU
7   LEUCYSGLYPHETYRGLYARGHISALAGLU
8   LEUARGPHELEUASPLEUVALPROSERLEU
9   GLNLEUASPPROALAGLNILETYRARGVAL
10   THRTRPPHEILESERTRPSERPROCYSPHE
11   SERTRPGLYCYSALAGLYGLUVALARGALA
12   PHELEUGLNGLUASNTHRHISVALARGLEU
13   ARGILEPHEALAALAARGILETYRASPTYR
14   ASPPROLEUTYRLYSGLUALALEUGLNMET
15   LEUARGASPALAGLYALAGLNVALSERILE
16   METTHRTYRASPGLUPHEGLUTYRCYSTRP
17   ASPTHRPHEVALTYRARGGLNGLYCYSPRO
18   PHEGLNPROTRPASPGLYLEUGLUGLUHIS
19   SERGLNALALEUSERGLYARGLEUARGALA
20   ILELEUGLNASNGLNGLYASNLEUGLUHIS
21   HISHISHISHISHIS

Samples:

2H_13C_15N_A3B-CTD: A3B-CTD, [U-13C; U-15N; U-2H], 0.08 mM; Zinc 0.08 mM; D2O, [U-100% 2H], 7%; H2O 93%; DTT 10 mM; sodium phosphate 25 mM

13C_15N_A3B-CTD: A3B-CTD, [U-100% 13C; U-100% 15N], 0.08 mM; Zinc 0;08 mM; D2O, [U-100% 2H], 7%; H2O 93%; DTT 10 mM; sodium phosphate 25 mM

A3B-CTD_3: A3B-CTD 0.05 mM; Zinc 0.05 mM; D2O, [U-100% 2H], 7%; H2O 93%; DTT 10 mM; sodium phosphate 25 mM

H2O: ionic strength: 25 mM; pH: 6.9; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC2H_13C_15N_A3B-CTDisotropicH2O
3D HNCA13C_15N_A3B-CTDisotropicH2O
3D HNCACB2H_13C_15N_A3B-CTDisotropicH2O
3D HN(CO)CACB2H_13C_15N_A3B-CTDisotropicH2O
2D 1H-15N HSQC13C_15N_A3B-CTDisotropicH2O
3D simultaneous 13C- and 15N-edited NOESY13C_15N_A3B-CTDisotropicH2O
3D TROSY-HNCACB2H_13C_15N_A3B-CTDisotropicH2O
3D TROSY-HN(CO)CACB2H_13C_15N_A3B-CTDisotropicH2O
2D 1H-1H NOESYA3B-CTD_3isotropicH2O
3D HCCH-TOCSY13C_15N_A3B-CTDisotropicH2O
2D 1H-13C HSQC13C_15N_A3B-CTDisotropicH2O

Software:

CcpNmr_Analysis v2.2, CCPN - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 900 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 600 MHz

Related Database Links: