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BMRB: 25985

2NBQ

NMR Structure of the C-Terminal Domain of human APOBEC3B

Authors

Byeon, I.L., Byeon, C., Gronenborn, A.M.

Assembly

A3B CTD

Entity

1. A3B CTD (polymer, Thiol state: all free), 205 monomers, 24407.42 Da Detail

MEILRYLMDP DTFTFNFNND PLVLRRRQTY LCYEVERLDN GTWVLMDQHM GFLCNEAKNL LCGFYGRHAE LRFLDLVPSL QLDPAQIYRV TWFISWSPCF SWGCAGEVRA FLQENTHVRL RIFAARIYDY DPLYKEALQM LRDAGAQVSI MTYDEFEYCW DTFVYRQGCP FQPWDGLEEH SQALSGRLRA ILQNQGNLEH HHHHH

Formula weight

24407.42 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 98.0 %, Completeness: 71.1 %, Completeness (bb): 80.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.1 % (1772 of 2493)	78.3 % (1012 of 1293)	57.1 % (557 of 976)	90.6 % (203 of 224)
Backbone	80.4 % (976 of 1214)	91.3 % (377 of 413)	68.9 % (416 of 604)	92.9 % (183 of 197)
Sidechain	65.9 % (970 of 1473)	71.9 % (633 of 880)	56.2 % (318 of 566)	70.4 % (19 of 27)
Aromatic	38.5 % (127 of 330)	69.7 % (115 of 165)	3.8 % (6 of 159)	100.0 % (6 of 6)
Methyl	91.7 % (187 of 204)	96.1 % (98 of 102)	87.3 % (89 of 102)

1. A3B-CTD

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
1	A3B-CTD	[U-13C; U-15N; U-2H]	0.08 mM
2	Zinc	natural abundance	0.08 mM
3	D2O	[U-100% 2H]	7 %
4	H2O	natural abundance	93 %
5	DTT	natural abundance	10 mM
6	sodium phosphate	natural abundance	25 mM

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	A3B-CTD	[U-100% 13C; U-100% 15N]	0.08 mM
8	Zinc	natural abundance	0;08 mM
9	D2O	[U-100% 2H]	7 %
10	H2O	natural abundance	93 %
11	DTT	natural abundance	10 mM
12	sodium phosphate	natural abundance	25 mM

Sample #3

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
13	A3B-CTD	natural abundance	0.05 mM
14	Zinc	natural abundance	0.05 mM
15	D2O	[U-100% 2H]	7 %
16	H2O	natural abundance	93 %
17	DTT	natural abundance	10 mM
18	sodium phosphate	natural abundance	25 mM

Chem. Shift Complete2

Sequence coverage: 88.8 %, Completeness: 50.0 %, Completeness (bb): 59.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	50.0 % (2491 of 4986)	53.7 % (1388 of 2586)	35.9 % (701 of 1952)	89.7 % (402 of 448)
Backbone	59.8 % (1453 of 2428)	71.1 % (587 of 826)	42.0 % (507 of 1208)	91.1 % (359 of 394)
Sidechain	41.8 % (1230 of 2946)	45.0 % (792 of 1760)	35.0 % (396 of 1132)	77.8 % (42 of 54)
Aromatic	25.3 % (167 of 660)	41.8 % (138 of 330)	5.3 % (17 of 318)	100.0 % (12 of 12)
Methyl	54.7 % (223 of 408)	56.9 % (116 of 204)	52.5 % (107 of 204)

1. A3B-CTD

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	A3B-CTD	[U-100% 13C; U-100% 15N]	0.08 mM
8	Zinc	natural abundance	0;08 mM
9	D2O	[U-100% 2H]	7 %
10	H2O	natural abundance	93 %
11	DTT	natural abundance	10 mM
12	sodium phosphate	natural abundance	25 mM

Protein Blocks Logo

Calculated from 30 models in PDB: 2NBQ, Strand ID: A Detail

Release date

2016-05-30

Citation

Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity
Byeon, I.L., Byeon, C., Wu, T., Mitra, M., Singer, D., Levin, J.G., Gronenborn, A.M.
Biochemistry (2016), 55, 2944-2959, PubMed 27163633 , DOI 10.1021/acs.biochem.6b00382 , Abstract

Related entities 1. A3B CTD, : 1 : 2 : 178 entities Detail

Interaction partners 1. A3B CTD, : 17 interactors Detail

More details for 17 interactors identified by 2 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC