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BMRB: 34544

6ZXP

Solution structure of the C-terminal domain of the vaccinia virus DNA polymerase processivity factor component A20 fused to a short peptide from the viral DNA polymerase E9.

Authors

Bersch, B., Tarbouriech, N., Burmeister, W., Iseni, F.

Assembly

DNA polymerase processivity factor component A20,DNA polymerase processivity factor component E9

Entity

1. DNA polymerase processivity factor component A20,DNA polymerase processivity factor component E9 (polymer), 151 monomers, 16863.76 Da Detail

GNGKYFSKVG SAGLKQLTNK LDINECATVD ELVDEINKSG TVKRKIKNQS AFDLSRECLG YPEADFITLV NNMRFKIENC KVVNFNIENT NCLNNPSIET IYRNFNQFVS IFNVVTDVKK RLFENASGNG SGGGSNRLEE EINNQLALQK S

Formula weight

16863.76 Da

Source organism

Vaccinia virus Copenhagen

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.4 %, Completeness (bb): 98.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.4 % (1605 of 1776)	91.9 % (851 of 926)	87.4 % (584 of 668)	93.4 % (170 of 182)
Backbone	98.4 % (888 of 902)	98.1 % (305 of 311)	98.4 % (435 of 442)	99.3 % (148 of 149)
Sidechain	84.3 % (855 of 1014)	88.8 % (546 of 615)	78.4 % (287 of 366)	66.7 % (22 of 33)
Aromatic	47.4 % (54 of 114)	94.7 % (54 of 57)	0.0 % (0 of 57)
Methyl	100.0 % (158 of 158)	100.0 % (79 of 79)	100.0 % (79 of 79)

1. entity 1

GNGKYFSKVG SAGLKQLTNK LDINECATVD ELVDEINKSG TVKRKIKNQS AFDLSRECLG YPEADFITLV NNMRFKIENC KVVNFNIENT NCLNNPSIET IYRNFNQFVS IFNVVTDVKK RLFENASGNG SGGGSNRLEE EINNQLALQK S

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 6 (±0.1), Details 1 mM [U-15N] A20-i3, 50 mM potassium phosphate, 300 mM NaCl, 1.2 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	A20-i3	[U-15N]	1 mM
2	potassium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	300 mM
4	TCEP	natural abundance	1.2 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 6 (±0.1), Details 0.8 mM [U-15N13C] A20-i3, 50 mM potassium phosphate, 300 mM NaCl, 1.2 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	A20-i3	[U-15N; U-13C]	0.8 mM
6	potassium phosphate	natural abundance	50 mM
7	NaCl	natural abundance	300 mM
8	TCEP	natural abundance	1.2 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 6 (±0.1), Details 1 mM [U-15N13C] A20-i3, 50 mM potassium phosphate, 300 mM NaCl, 1.2 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	A20-i3	[U-15N; U-13C]	1 mM
10	potassium phosphate	natural abundance	50 mM
11	NaCl	natural abundance	300 mM
12	TCEP	natural abundance	1.2 mM

Heteronucl. T₁

116 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 700.2533 MHz, Pressure 1 atm, Temperature 298 (±0.5) K, pH 6 (±0.1) Detail

Heteronucl. T₂

116 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 700.2533 MHz, Pressure 1 atm, Temperature 298 (±0.5) K, pH 6 (±0.1) Detail

Heteronucl. NOE

118 NOE values in 1 lists
Value type peak height, Field strength (¹H) 700 MHz, Pressure 1 atm, Temperature 298 (±0.5) K, pH 6 (±0.1) Detail

Heteronucl. T₁/T₂

116 T₁/T₂ values in 1 lists
Field strength (¹H) 700.2533 MHz, Pressure 1 atm, Temperature 298 (±0.5) K, pH 6 (±0.1) Detail

Release date

2020-08-27

Citation 1

The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding
Tarbouriech, N., Ducournau, C., Hutin, S., Mas, P.J., Man, P., Forest, E., Hart, D.J., Peyrefitte, C.N., Burmeister, W., Iseni, F.
Nat. Commun. (2017), 8, 1455-1455, PubMed 29129932 , DOI 10.1038/s41467-017-01542-z , Abstract

Show more 1 citaion

Citation 2

Solution Structure of the C-terminal Domain of A20, the Missing Brick for the Characterization of the Interface between Vaccinia Virus DNA Polymerase and its Processivity Factor
Bersch, B., Tarbouriech, N., Burmeister, W., Iseni, F.
J. Mol. Biol. (2021), 433, 167009-167009, PubMed 33901538 , DOI 10.1016/j.jmb.2021.167009 , Abstract

Hide non-primary 1 citaion

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34545 released on 2020-08-27
Title Solution structure of the C-terminal domain of the vaccinia virus DNA polymerase processivity factor component A20.

Related entities 1. DNA polymerase processivity factor component A20,DNA polymerase processivity factor component E9, : 1 : 1 : 3 entities Detail

Interaction partners 1. DNA polymerase processivity factor component A20,DNA polymerase processivity factor component E9, : 4 interactors Detail

More details for 4 interactors identified by 2 citations

Experiments performed 14 experiments Detail

1 15N-Trosy

Instrument

Bruker AVANCE - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 6 (±0.1), Details 1 mM [U-15N] A20-i3, 50 mM potassium phosphate, 300 mM NaCl, 1.2 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	A20-i3	[U-15N]	1 mM
2	potassium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	300 mM
4	TCEP	natural abundance	1.2 mM

2 13C-HSQC

Instrument

Bruker AVANCE - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 6 (±0.1), Details 0.8 mM [U-15N13C] A20-i3, 50 mM potassium phosphate, 300 mM NaCl, 1.2 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	A20-i3	[U-15N; U-13C]	0.8 mM
6	potassium phosphate	natural abundance	50 mM
7	NaCl	natural abundance	300 mM
8	TCEP	natural abundance	1.2 mM

3 2D-Tocsy

Instrument

Bruker AVANCE - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.5) K, pH 6 (±0.1), Details 1 mM [U-15N13C] A20-i3, 50 mM potassium phosphate, 300 mM NaCl, 1.2 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	A20-i3	[U-15N; U-13C]	1 mM
10	potassium phosphate	natural abundance	50 mM
11	NaCl	natural abundance	300 mM
12	TCEP	natural abundance	1.2 mM

4 3D HNCO

Instrument

Bruker AVANCE - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
5	A20-i3	[U-15N; U-13C]	0.8 mM
6	potassium phosphate	natural abundance	50 mM
7	NaCl	natural abundance	300 mM
8	TCEP	natural abundance	1.2 mM

5 3D HNCACB

Instrument

Bruker AVANCE - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
5	A20-i3	[U-15N; U-13C]	0.8 mM
6	potassium phosphate	natural abundance	50 mM
7	NaCl	natural abundance	300 mM
8	TCEP	natural abundance	1.2 mM

6 2D NOESY

Instrument

Bruker AVANCE - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
9	A20-i3	[U-15N; U-13C]	1 mM
10	potassium phosphate	natural abundance	50 mM
11	NaCl	natural abundance	300 mM
12	TCEP	natural abundance	1.2 mM

7 3D-13C-13C methyl noesy

Instrument

Bruker AVANCE - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
5	A20-i3	[U-15N; U-13C]	0.8 mM
6	potassium phosphate	natural abundance	50 mM
7	NaCl	natural abundance	300 mM
8	TCEP	natural abundance	1.2 mM

8 3D-13C edited NOESY

Instrument

Bruker AVANCE - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
5	A20-i3	[U-15N; U-13C]	0.8 mM
6	potassium phosphate	natural abundance	50 mM
7	NaCl	natural abundance	300 mM
8	TCEP	natural abundance	1.2 mM

9 3D-15N-edited NOESY

Instrument

Bruker AVANCE - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	A20-i3	[U-15N]	1 mM
2	potassium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	300 mM
4	TCEP	natural abundance	1.2 mM

10 3D HCCH-TOCSY

Instrument

Bruker AVANCE - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
5	A20-i3	[U-15N; U-13C]	0.8 mM
6	potassium phosphate	natural abundance	50 mM
7	NaCl	natural abundance	300 mM
8	TCEP	natural abundance	1.2 mM

11 3D HN(COCA)CB

Instrument

Bruker AVANCE - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
5	A20-i3	[U-15N; U-13C]	0.8 mM
6	potassium phosphate	natural abundance	50 mM
7	NaCl	natural abundance	300 mM
8	TCEP	natural abundance	1.2 mM

12 15N hetNOE

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	A20-i3	[U-15N]	1 mM
2	potassium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	300 mM
4	TCEP	natural abundance	1.2 mM

13 15N-R2

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	A20-i3	[U-15N]	1 mM
2	potassium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	300 mM
4	TCEP	natural abundance	1.2 mM

14 15N-R1

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	A20-i3	[U-15N]	1 mM
2	potassium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	300 mM
4	TCEP	natural abundance	1.2 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts, Heteronucl NOE exptl data, Heteronucl T1 relaxation data, Heteronucl T2 relaxation data	bmr34544_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr34544_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1760		100.0 (chain: 1, length: 151)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 151, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 583
  - ¹H chemical shifts: 1008
  - ¹⁵N chemical shifts: 169
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	668	583	87.3
¹H chemical shifts	926	848	91.6
¹⁵N chemical shifts	182	169	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	302	296	98.0
¹H chemical shifts	311	302	97.1
¹⁵N chemical shifts	149	147	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	366	287	78.4
¹H chemical shifts	615	546	88.8
¹⁵N chemical shifts	33	22	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	80	80	100.0
¹H chemical shifts	80	80	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	57	0	0.0
¹H chemical shifts	57	54	94.7

Keywords DNA polymerase holoenzyme, Poxviridae, REPLICATION, processivity factor binding

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Found 1 Document (0.656 seconds)

BMRB: 34544

Sample #1

Sample #2

Sample #3

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. DNA polymerase processivity factor component A20,DNA polymerase processivity factor component E9, : 1 : 1 : 3 entities Detail

Interaction partners 1. DNA polymerase processivity factor component A20,DNA polymerase processivity factor component E9, : 4 interactors Detail

Experiments performed 14 experiments Detail

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Chemical shift validation 3 contents Detail