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BMRB: 19333

2MA9

HIV-1 Vif SOCS-box and Elongin BC solution structure

Authors

LU, Z., Bergeron, J., Atkinson, A., Schaller, T., Veselkov, D., Oregioni, A., Yang, Y., Matthews, S., Malim, M., Sanderson, M.

Assembly

HIV-1 Vif SOCS-box with Elongin BC

Entity

1. Vif SOCS (polymer, Thiol state: not present), 36 monomers, 4109.856 Da Detail

HNKVGSLQYL ALAALIKPKQ IKPPLPSVRK LTEDRW

2. Elongin B (polymer, Thiol state: all free), 118 monomers, 13132.66 Da Detail

MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALCI EPFSSPPELP DVMKPQDSGS SANEQAVQ

3. Elongin C (polymer, Thiol state: all free), 91 monomers, 10206.57 Da Detail

VKLISSDGHE FIVKREHALT SGTIKAMLSG PGQFAENETN EVNFREIPSH VLSKVCMYFT YKVRYTNSST EIPEFPIAPE IALELLMAAN F

Total weight

27449.086 Da

Max. entity weight

13132.66 Da

Source organism

Human immunodeficiency virus 1 , Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 23.7 %, Completeness: 10.7 %, Completeness (bb): 18.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	10.7 % (308 of 2881)	8.2 % (123 of 1504)	11.9 % (135 of 1132)	20.4 % (50 of 245)
Backbone	18.8 % (269 of 1434)	19.5 % (94 of 483)	17.5 % (127 of 724)	21.1 % (48 of 227)
Sidechain	5.4 % (91 of 1681)	2.8 % (29 of 1021)	9.3 % (60 of 642)	11.1 % (2 of 18)
Aromatic	0.0 % (0 of 202)	0.0 % (0 of 101)	0.0 % (0 of 100)	0.0 % (0 of 1)
Methyl	4.4 % (12 of 274)	2.9 % (4 of 137)	5.8 % (8 of 137)

1. Vif SOCS

HNKVGSLQYL ALAALIKPKQ IKPPLPSVRK LTEDRW

2. Elongin B

MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALCI EPFSSPPELP DVMKPQDSGS SANEQAVQ

3. Elongin C

VKLISSDGHE FIVKREHALT SGTIKAMLSG PGQFAENETN EVNFREIPSH VLSKVCMYFT YKVRYTNSST EIPEFPIAPE IALELLMAAN F

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details labeled SOCS in the presence of unlabeled EloBC

#	Name	Isotope labeling	Concentration
1	Vif SOCS	[U-99% 13C; U-99% 15N]	0.2 mM
2	Elongin B	natural abundance	0.2 mM
3	Elongin C	natural abundance	0.2 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	Na-phosphate buffer	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details labeled EloBC in the presence of unlabeled SOCS

#	Name	Isotope labeling	Concentration
7	Vif SOCS	natural abundance	0.2 mM
8	Elongin B	[U-99% 13C; U-99% 15N]	0.2 mM
9	Elongin C	[U-99% 13C; U-99% 15N]	0.2 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	Na-phosphate buffer	natural abundance	50 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 100% Deuterated labeled EloBC in the presence of unlabeled SOCS

#	Name	Isotope labeling	Concentration
13	Vif SOCS	natural abundance	0.2 mM
14	Elongin B	[U-99% 13C; U-99% 15N]	0.2 mM
15	Elongin C	[U-99% 13C; U-99% 15N]	0.2 mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %
18	Na-phosphate buffer	natural abundance	50 mM

Chem. Shift Complete2

Sequence coverage: 47.8 %, Completeness: 14.3 %, Completeness (bb): 26.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	14.3 % (826 of 5762)	9.3 % (281 of 3008)	17.6 % (398 of 2264)	30.0 % (147 of 490)
Backbone	26.8 % (768 of 2868)	24.5 % (237 of 966)	26.7 % (386 of 1448)	31.9 % (145 of 454)
Sidechain	4.7 % (158 of 3362)	2.2 % (44 of 2042)	8.7 % (112 of 1284)	5.6 % (2 of 36)
Aromatic	0.0 % (0 of 404)	0.0 % (0 of 202)	0.0 % (0 of 200)	0.0 % (0 of 2)
Methyl	3.8 % (21 of 548)	2.6 % (7 of 274)	5.1 % (14 of 274)

1. Vif SOCS

HNKVGSLQYL ALAALIKPKQ IKPPLPSVRK LTEDRW

2. Elongin B

MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALCI EPFSSPPELP DVMKPQDSGS SANEQAVQ

3. Elongin C

VKLISSDGHE FIVKREHALT SGTIKAMLSG PGQFAENETN EVNFREIPSH VLSKVCMYFT YKVRYTNSST EIPEFPIAPE IALELLMAAN F

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details labeled SOCS in the presence of unlabeled EloBC

#	Name	Isotope labeling	Concentration
1	Vif SOCS	[U-99% 13C; U-99% 15N]	0.2 mM
2	Elongin B	natural abundance	0.2 mM
3	Elongin C	natural abundance	0.2 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	Na-phosphate buffer	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details labeled EloBC in the presence of unlabeled SOCS

#	Name	Isotope labeling	Concentration
7	Vif SOCS	natural abundance	0.2 mM
8	Elongin B	[U-99% 13C; U-99% 15N]	0.2 mM
9	Elongin C	[U-99% 13C; U-99% 15N]	0.2 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	Na-phosphate buffer	natural abundance	50 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 100% Deuterated labeled EloBC in the presence of unlabeled SOCS

#	Name	Isotope labeling	Concentration
13	Vif SOCS	natural abundance	0.2 mM
14	Elongin B	[U-99% 13C; U-99% 15N]	0.2 mM
15	Elongin C	[U-99% 13C; U-99% 15N]	0.2 mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %
18	Na-phosphate buffer	natural abundance	50 mM

Chem. Shift Complete3

Sequence coverage: 28.6 %, Completeness: 12.7 %, Completeness (bb): 23.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	12.7 % (1101 of 8643)	8.3 % (374 of 4512)	15.7 % (532 of 3396)	26.5 % (195 of 735)
Backbone	23.6 % (1016 of 4302)	21.3 % (309 of 1449)	23.7 % (514 of 2172)	28.3 % (193 of 681)
Sidechain	4.2 % (211 of 5043)	2.1 % (65 of 3063)	7.5 % (144 of 1926)	3.7 % (2 of 54)
Aromatic	0.0 % (0 of 606)	0.0 % (0 of 303)	0.0 % (0 of 300)	0.0 % (0 of 3)
Methyl	4.1 % (34 of 822)	3.2 % (13 of 411)	5.1 % (21 of 411)

1. Vif SOCS

HNKVGSLQYL ALAALIKPKQ IKPPLPSVRK LTEDRW

2. Elongin B

MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALCI EPFSSPPELP DVMKPQDSGS SANEQAVQ

3. Elongin C

VKLISSDGHE FIVKREHALT SGTIKAMLSG PGQFAENETN EVNFREIPSH VLSKVCMYFT YKVRYTNSST EIPEFPIAPE IALELLMAAN F

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details labeled SOCS in the presence of unlabeled EloBC

#	Name	Isotope labeling	Concentration
1	Vif SOCS	[U-99% 13C; U-99% 15N]	0.2 mM
2	Elongin B	natural abundance	0.2 mM
3	Elongin C	natural abundance	0.2 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	Na-phosphate buffer	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details labeled EloBC in the presence of unlabeled SOCS

#	Name	Isotope labeling	Concentration
7	Vif SOCS	natural abundance	0.2 mM
8	Elongin B	[U-99% 13C; U-99% 15N]	0.2 mM
9	Elongin C	[U-99% 13C; U-99% 15N]	0.2 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	Na-phosphate buffer	natural abundance	50 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 100% Deuterated labeled EloBC in the presence of unlabeled SOCS

#	Name	Isotope labeling	Concentration
13	Vif SOCS	natural abundance	0.2 mM
14	Elongin B	[U-99% 13C; U-99% 15N]	0.2 mM
15	Elongin C	[U-99% 13C; U-99% 15N]	0.2 mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %
18	Na-phosphate buffer	natural abundance	50 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2MA9, Strand ID: A, B, C Detail

Release date

2013-12-08

Citation

Insight into the HIV-1 Vif SOCS-box-ElonginBC interaction
Lu, Z., Bergeron, J., Atkinson, A., Schaller, T., Veselkov, D., Oregioni, A., Yang, Y., Matthews, S., Malim, M., Sanderson, M.
Open Biol. (2013), 3, 130100-130100, PubMed 24225024 , DOI 10.1098/rsob.130100 , Abstract

Related entities 1. Vif SOCS, : 1 : 3 : 1 : 51 entities Detail

Related entities 2. Elongin B, : 4 : 4 : 18 entities Detail

Related entities 3. Elongin C, : 8 : 1 : 28 entities Detail

Interaction partners 1. Vif SOCS, : 20 : 1 interactors Detail

More details for 21 interactors identified by 5 citations

Interaction partners 2. Elongin B, : 55 : 1 interactors Detail

More details for 56 interactors identified by 24 citations

Experiments performed 22 experiments Detail

1 2D 1H-15N HSQC