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BMRB: 18391

2LRR

Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate

Authors

Jaudzems, K., Zhulenkovs, D., Otting, G., Liepinsh, E.

Assembly

R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate

Entity

1. Smubp2 R3H (polymer, Thiol state: not present), 86 monomers, 9684.663 Da Detail

MGSLNGGSPE GVESQDGVDH FRAMIVEFMA SKKMQLEFPP SLNSHDRLRV HQIAEEHGLR HDSSGEGKRR FITVSKRAGS HHHHHH

2. 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE (non-polymer), 347.221 Da

Total weight

10031.884 Da

Max. entity weight

9684.663 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 83.7 %, Completeness: 72.7 %, Completeness (bb): 62.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	72.7 % (436 of 600)	81.4 % (417 of 512)	21.6 % (19 of 88)
Backbone	62.5 % (163 of 261)	80.9 % (144 of 178)	22.9 % (19 of 83)
Sidechain	80.5 % (273 of 339)	81.7 % (273 of 334)	0.0 % (0 of 5)
Aromatic	71.4 % (30 of 42)	71.4 % (30 of 42)
Methyl	100.0 % (31 of 31)	100.0 % (31 of 31)

1. Smubp2 R3H

MGSLNGGSPE GVESQDGVDH FRAMIVEFMA SKKMQLEFPP SLNSHDRLRV HQIAEEHGLR HDSSGEGKRR FITVSKRAGS HHHHHH

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.3 (±0.1)

#	Name	Isotope labeling	Concentration
1	Smubp2_R3H	[U-99% 15N]	0.9 (±0.1) mM
2	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE	natural abundance	5.5 (±0.1) mM
3	D2O	[U-100% 2H]	5 (±0.1) %
4	sodium phosphate	natural abundance	10 (±1.0) mM
5	sodium chloride	natural abundance	100 (±5.0) mM
6	sodium azide	natural abundance	0.03 (±0.005) %
7	H2O	natural abundance	95 %

Chem. Shift Complete2

Sequence coverage: 82.6 %, Completeness: 74.3 %, Completeness (bb): 71.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	74.3 % (892 of 1200)	78.3 % (802 of 1024)	51.1 % (90 of 176)
Backbone	71.5 % (373 of 522)	80.6 % (287 of 356)	51.8 % (86 of 166)
Sidechain	76.5 % (519 of 678)	77.1 % (515 of 668)	40.0 % (4 of 10)
Aromatic	65.5 % (55 of 84)	65.5 % (55 of 84)
Methyl	96.8 % (60 of 62)	96.8 % (60 of 62)

1. Smubp2 R3H

MGSLNGGSPE GVESQDGVDH FRAMIVEFMA SKKMQLEFPP SLNSHDRLRV HQIAEEHGLR HDSSGEGKRR FITVSKRAGS HHHHHH

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.3 (±0.1)

#	Name	Isotope labeling	Concentration
1	Smubp2_R3H	[U-99% 15N]	0.9 (±0.1) mM
2	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE	natural abundance	5.5 (±0.1) mM
3	D2O	[U-100% 2H]	5 (±0.1) %
4	sodium phosphate	natural abundance	10 (±1.0) mM
5	sodium chloride	natural abundance	100 (±5.0) mM
6	sodium azide	natural abundance	0.03 (±0.005) %
7	H2O	natural abundance	95 %

Chem. Shift Complete3

Sequence coverage: 12.8 %, Completeness: 51.9 %, Completeness (bb): 51.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	51.9 % (935 of 1800)	54.4 % (836 of 1536)	37.5 % (99 of 264)
Backbone	51.0 % (399 of 783)	56.9 % (304 of 534)	38.2 % (95 of 249)
Sidechain	52.7 % (536 of 1017)	53.1 % (532 of 1002)	26.7 % (4 of 15)
Aromatic	43.7 % (55 of 126)	43.7 % (55 of 126)
Methyl	66.7 % (62 of 93)	66.7 % (62 of 93)

1. Smubp2 R3H

MGSLNGGSPE GVESQDGVDH FRAMIVEFMA SKKMQLEFPP SLNSHDRLRV HQIAEEHGLR HDSSGEGKRR FITVSKRAGS HHHHHH

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.2) K, pH 6.3 (±0.1)

#	Name	Isotope labeling	Concentration
1	Smubp2_R3H	[U-99% 15N]	0.9 (±0.1) mM
2	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE	natural abundance	5.5 (±0.1) mM
3	D2O	[U-100% 2H]	5 (±0.1) %
4	sodium phosphate	natural abundance	10 (±1.0) mM
5	sodium chloride	natural abundance	100 (±5.0) mM
6	sodium azide	natural abundance	0.03 (±0.005) %
7	H2O	natural abundance	95 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LRR, Strand ID: A Detail

Release date

2012-10-21

Citation

Structural basis for 5'-end-specific recognition of single-stranded DNA by the R3H domain from human Sμbp-2
Jaudzems, K., Jia, X., Yagi, H., Zhulenkovs, D., Graham, B., Otting, G., Liepinsh, E.
J. Mol. Biol. (2012), 424, 42-53, PubMed 22999958 , DOI 10.1016/j.jmb.2012.09.010 , Abstract

Related entities 1. Smubp2 R3H, : 1 : 1 : 2 : 1 entities Detail

Interaction partners 1. Smubp2 R3H, : 5 interactors Detail

More details for 5 interactors identified by 2 citations

Experiments performed 5 experiments Detail

1 2D 1H-15N HSQC