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 25559

Title: Structure of C-terminal domain of human polymerase Rev1 in complex with PolD3 RIR-motif   PubMed: 26982350

Deposition date: 2015-04-01 Original release date: 2016-04-12

Authors: Pustovalova, Yulia; Korzhnev, Dmitry

Citation: Pustovalova, Yulia; Magalhaes, Mariana; D'Souza, Sanjay; Rizzo, Alessandro; Korza, George; Walker, Graham; Korzhnev, Dmitry. "Interaction between the Rev1 C-terminal Domain and the PolD3 Subunit of Pol-zeta Suggests a Mechanism of Polymerase Exchange upon Rev1/Pol-zeta-Dependent Translesion Synthesis"  Biochemistry 55, 2043-2053 (2016).

Assembly members:
Rev1-CT, polymer, 94 residues, 10954.707 Da.
PolD3, polymer, 16 residues, 1779.138 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   Vector: pET28b+

Entity Sequences (FASTA):
Rev1-CT: NLAGAVEFNDVKTLLREWIT TISDPMEEDILQVVKYCTDL IEEKDLEKLDLVIKYMKRLM QQSVESVWNMAFDFILDNVQ VVLQQTYGSTLKVT
PolD3: KGNMMSNFFGKAAMNK

Data sets:
Data typeCount
13C chemical shifts338
15N chemical shifts103
1H chemical shifts731

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Rev1-CT1
2PolD32

Entities:

Entity 1, Rev1-CT 94 residues - 10954.707 Da.

C-terminal domain of human polymerase Rev1 (residues 1158-1251)

1   ASNLEUALAGLYALAVALGLUPHEASNASP
2   VALLYSTHRLEULEUARGGLUTRPILETHR
3   THRILESERASPPROMETGLUGLUASPILE
4   LEUGLNVALVALLYSTYRCYSTHRASPLEU
5   ILEGLUGLULYSASPLEUGLULYSLEUASP
6   LEUVALILELYSTYRMETLYSARGLEUMET
7   GLNGLNSERVALGLUSERVALTRPASNMET
8   ALAPHEASPPHEILELEUASPASNVALGLN
9   VALVALLEUGLNGLNTHRTYRGLYSERTHR
10   LEULYSVALTHR

Entity 2, PolD3 16 residues - 1779.138 Da.

RIR-motif of accessory subunit PolD3 of human polymerase delta (residues 233-246)

1   LYSGLYASNMETMETSERASNPHEPHEGLY
2   LYSALAALAMETASNLYS

Samples:

15N-13C_Rev1-CT-PolD3: Rev1-CT, [U-100% 13C; U-100% 15N], 0.5 mM; PolD30.5 – 0.8 mM; potassium phosphate 50 mM; sodium chloride 100 mM; DTT 2 mM; EDTA 0.5 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1.0 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
2D 1H-13C HSQC15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
3D HNCO15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
3D HNCACB15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
3D HBHA(CO)NH15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
3D HCCH-TOCSY15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
3D CCH-TOCSY15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
3D 1H-13C NOESY15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
3D 1H-15N NOESY15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
2D 1H-1H (filt.) TOCSY15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
2D 1H-1H (filt.) NOESY15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
3D 1H-13C (CNfilt.) NOESY15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1
3D 1H-15N (CNfilt.) NOESY15N-13C_Rev1-CT-PolD3isotropicsample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMRPipe v5.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CARA v1.9.0, Keller and Wuthrich - chemical shift assignment, chemical shift calculation, peak picking

ABACUS_(CNS), Brunger, Adams, Clore, Gros, Nilges and Read - refinement

TALOS v2.20, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

  • Varian Avance 500 MHz
  • Varian Avance 800 MHz

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