BMRB Entry 25559

Name: Structure of C-terminal domain of human polymerase Rev1 in complex with PolD3 RIR-motif
Published: 2016-04-12

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PDB ID: 2n1g
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR25559
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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:

Structure of C-terminal domain of human polymerase Rev1 in complex with PolD3 RIR-motif

Deposition date:

2015-04-01

Original release date:

2016-04-12

Authors:

Pustovalova, Yulia; Korzhnev, Dmitry

Citation:

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).
PubMed: 26982350

Assembly members:

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

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	338
15N chemical shifts	103
1H chemical shifts	731

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Rev1-CT	1
2	PolD3	2

Entities:

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

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

1

ASN

LEU

ALA

GLY

ALA

VAL

GLU

PHE

ASN

ASP

2

VAL

LYS

THR

LEU

ARG

GLU

TRP

ILE

THR

3

THR

ILE

SER

ASP

PRO

MET

GLU

ASP

ILE

4

LEU

GLN

VAL

LYS

TYR

CYS

THR

ASP

LEU

5

ILE

GLU

LYS

ASP

LEU

GLU

LYS

LEU

ASP

6

LEU

VAL

ILE

LYS

TYR

MET

LYS

ARG

LEU

MET

7

GLN

SER

VAL

GLU

SER

VAL

TRP

ASN

MET

8

ALA

PHE

ASP

PHE

ILE

LEU

ASP

ASN

VAL

GLN

9

VAL

LEU

GLN

THR

TYR

GLY

SER

THR

10

LEU

LYS

VAL

THR

Entity 2, PolD3 16 residues - 1779.138 Da.

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

1

LYS

GLY

ASN

MET

SER

ASN

PHE

GLY

2

LYS

ALA

MET

ASN

LYS

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
2D 1H-13C HSQC	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
3D HNCO	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
3D HNCACB	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
3D HBHA(CO)NH	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
3D HCCH-TOCSY	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
3D CCH-TOCSY	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
3D 1H-13C NOESY	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
3D 1H-15N NOESY	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
2D 1H-1H (filt.) TOCSY	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
2D 1H-1H (filt.) NOESY	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
3D 1H-13C (CNfilt.) NOESY	15N-13C_Rev1-CT-PolD3	isotropic	sample_conditions_1
3D 1H-15N (CNfilt.) NOESY	15N-13C_Rev1-CT-PolD3	isotropic	sample_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 peaks
SPARKY: Backbone or all simulated peaks