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BMRB: 17738

2LF4

Structure of a monomeric mutant of the HIV-1 capsid protein

Authors

Shin, R.S., Tzou, Y., Krishna, N.

Assembly

HIV-1 CA

Entity

1. HIV-1 CA (polymer, Thiol state: all free), 240 monomers, 26609.18 Da Detail

MPIVQNLQGQ MVHQAISPRT LNAWVKVVEE KAFSPEVIPM FSALSEGATP QDLNTMLNTV GGHQAAMQML KETINEEAAE WDRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE PFRDYVDRFY KTLRAEQASQ EVKNAATETL LVQNANPDCK TILKALGPGA TLEEMMTACQ GVGGPGHKAR VLVEHHHHHH

Formula weight

26609.18 Da

Source organism

Human immunodeficiency virus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 86.2 %, Completeness (bb): 94.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.2 % (2388 of 2770)	85.7 % (1237 of 1444)	86.7 % (932 of 1075)	87.3 % (219 of 251)
Backbone	94.5 % (1327 of 1404)	96.0 % (461 of 480)	92.7 % (651 of 702)	96.8 % (215 of 222)
Sidechain	80.0 % (1271 of 1588)	80.5 % (776 of 964)	82.5 % (491 of 595)	13.8 % (4 of 29)
Aromatic	29.2 % (49 of 168)	44.0 % (37 of 84)	12.5 % (10 of 80)	50.0 % (2 of 4)
Methyl	99.3 % (268 of 270)	99.3 % (134 of 135)	99.3 % (134 of 135)

1. HIV-1 CA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 15N-labeled HIV-1 CA DM

#	Name	Isotope labeling	Concentration
1	HIV-1 CA	[U-98% 15N]	2 mM
2	sodium chloride	natural abundance	25 mM
3	sodium acetate	[U-99% 2H]	25 mM
4	DTT	[U-99% 2H]	10 mM
5	sodium azide	natural abundance	0.02 %
6	AEBSF protease inhibitor	natural abundance	0.1 mM
7	EDTA	[U-99% 2H]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 13C / 15N-labeled HIV-1 CA DM

#	Name	Isotope labeling	Concentration
10	HIV-1 CA	[U-98% 13C; U-98% 15N]	2 mM
11	sodium chloride	natural abundance	25 mM
12	sodium acetate	[U-99% 2H]	25 mM
13	DTT	[U-99% 2H]	10 mM
14	sodium azide	natural abundance	0.02 %
15	AEBSF protease inhibitor	natural abundance	0.1 mM
16	EDTA	[U-99% 2H]	1 mM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 13C / 15N-labeled HIV-1 CA DM

#	Name	Isotope labeling	Concentration
19	HIV-1 CA	[U-98% 13C; U-98% 15N]	2 mM
20	sodium chloride	natural abundance	25 mM
21	sodium acetate	[U-99% 2H]	25 mM
22	DTT	[U-99% 2H]	10 mM
23	sodium azide	natural abundance	0.02 %
24	AEBSF protease inhibitor	natural abundance	0.1 mM
25	EDTA	[U-99% 2H]	1 mM
26	D2O	natural abundance	100 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 13C / 15N / 2H-labeled HIV-1 CA DM

#	Name	Isotope labeling	Concentration
27	HIV-1 CA	[U-98% 13C; U-98% 15N]	2 mM
28	sodium chloride	natural abundance	25 mM
29	sodium acetate	[U-99% 2H]	25 mM
30	DTT	[U-99% 2H]	10 mM
31	sodium azide	natural abundance	0.02 %
32	AEBSF protease inhibitor	natural abundance	0.1 mM
33	EDTA	[U-99% 2H]	1 mM
34	H2O	natural abundance	90 %
35	D2O	natural abundance	10 %

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 13C / 15N / 2H-labeled HIV-1 CA DM

#	Name	Isotope labeling	Concentration
36	HIV-1 CA	[U-98% 13C; U-98% 15N]	2 mM
37	sodium chloride	natural abundance	25 mM
38	sodium acetate	[U-99% 2H]	25 mM
39	DTT	[U-99% 2H]	10 mM
40	sodium azide	natural abundance	0.02 %
41	AEBSF protease inhibitor	natural abundance	0.1 mM
42	EDTA	[U-99% 2H]	1 mM
43	D2O	natural abundance	100 %

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 15N HIV-1 CA DM

#	Name	Isotope labeling	Concentration
44	HIV-1 CA	[U-98% 13C; U-98% 15N]	2 mM
45	sodium chloride	natural abundance	25 mM
46	sodium acetate	[U-99% 2H]	25 mM
47	DTT	[U-99% 2H]	10 mM
48	sodium azide	natural abundance	0.02 %
49	AEBSF protease inhibitor	natural abundance	0.1 mM
50	EDTA	[U-99% 2H]	1 mM
51	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.54 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.54 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LF4, Strand ID: A Detail

Release date

2011-10-24

Citation

Structure of a monomeric mutant of the HIV-1 capsid protein
Shin, R., Tzou, Y., Krishna, N.
Biochemistry (2011), 50, 9457-9467, PubMed 21995733 , DOI 10.1021/bi2011493 , Abstract

Related entities 1. HIV-1 CA, : 1 : 97 : 129 entities Detail

Interaction partners 1. HIV-1 CA, : 4 interactors Detail

More details for 4 interactors identified by 3 citations