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Found 1 Document (1.418 seconds)

BMRB: 30035

5IRT

Dimerization interface of the noncrystalline HIV-1 capsid protein lattice from solid state NMR spectroscopy of tubular assemblies

Authors

Bayro, M.J., Tycko, R.

Assembly

Capsid protein p24

Entity

1. Capsid protein p24 (polymer), 231 monomers, 25602.16 × 2 Da Detail

PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAGP IAPGQMREPR GSDIAGTTST LQEQIGWMTH NPPIPVGEIY KRWIILGLNK IVRMYSPTSI LDIRQGPKEP FRDYVDRFYK TLRAEQASQE VKNWMTETLL VQNANPDCKT ILKALGPGAT LEEMMTACQG VGGPGHKARV L

Total weight

51204.32 Da

Max. entity weight

25602.16 Da

Source organism

Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 85.7 %, Completeness: 62.9 %, Completeness (bb): 80.6 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	62.9 % (806 of 1281)	60.4 % (627 of 1038)	73.7 % (179 of 243)
Backbone	80.6 % (716 of 888)	79.7 % (538 of 675)	83.6 % (178 of 213)
Sidechain	41.6 % (252 of 606)	43.6 % (251 of 576)	3.3 % (1 of 30)
Aromatic	0.0 % (0 of 78)	0.0 % (0 of 73)	0.0 % (0 of 5)
Methyl	40.5 % (53 of 131)	40.5 % (53 of 131)

1. Capsid protein p24

Show sample condition

Sample #1

Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM U-15N,13C-Met and U-15N Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
1	Capsid protein	[U-15N; 13C-Met and U-15N]		15 mM
2	H2O	natural abundance		100 %

Sample #2

Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM 2-13C-glycerol and U-15N Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
3	Capsid protein	[2-13C-glycerol; U-15N]		15 mM
4	H2O	natural abundance		100 %

Sample #3

Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM 2-13C-glycerol, U-15N, unlabeled Tyr and Phe Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
5	Capsid protein	[2-13C-glycerol, U-15N; unlabeled Tyr and Phe]		15 mM
6	H2O	natural abundance		100 %

Sample #4

Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 7.5 mM Methyl-13C-Met Capsid protein-1, 7.5 mM 15N-indole Capsid protein-2, water

#	Name	Isotope labeling	Concentration
7	Capsid protein-1	[Methyl-13C-Met]	7.5 mM
8	Capsid protein-2	[15N-indole]	7.5 mM
9	H2O	natural abundance	100 %

Sample #5

Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM Methyl-13C-Met, 2-13C-indole, U-15N Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
10	Capsid protein	[Methyl-13C-Met, 2-13C-indole, U-15N]		15 mM
11	H2O	natural abundance		100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	external	indirect	0.2514495
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 0.25 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	external	indirect	0.2514495
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 0.25 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	external	indirect	0.2514495
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: -0.42 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5IRT, Strand ID: A, B Detail

Release date

2016-06-19

Citation

Structure of the Dimerization Interface in the Mature HIV-1 Capsid Protein Lattice from Solid State NMR of Tubular Assemblies
Bayro, M.J., Tycko, R.
J. Am. Chem. Soc. (2016), 138, 8538-8546, PubMed 27298207 , DOI 10.1021/jacs.6b03983 , Abstract

Related entities 1. Capsid protein p24, : 1 : 30 : 2 : 66 : 124 entities Detail

Interaction partners 1. Capsid protein p24, : 4 interactors Detail

More details for 4 interactors identified by 3 citations

Experiments performed 12 experiments Detail

1 13C-13C 2D correlation

Instrument

Varian Infinity - 600 MHz 3.2 mm BioMAS Varian probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM U-15N,13C-Met and U-15N Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
1	Capsid protein	[U-15N; 13C-Met and U-15N]		15 mM
2	H2O	natural abundance		100 %

2 NCACX 2D correlation

Instrument

Varian Infinity - 600 MHz 3.2 mm BioMAS Varian probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM U-15N,13C-Met and U-15N Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
1	Capsid protein	[U-15N; 13C-Met and U-15N]		15 mM
2	H2O	natural abundance		100 %

3 NCOCX 2D correlation

Instrument

Varian Infinity - 600 MHz 3.2 mm BioMAS Varian probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM U-15N,13C-Met and U-15N Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
1	Capsid protein	[U-15N; 13C-Met and U-15N]		15 mM
2	H2O	natural abundance		100 %

4 13C-13C 2D correlation

Instrument

Varian Infinity - 600 MHz 3.2 mm BioMAS Varian probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM 2-13C-glycerol and U-15N Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
3	Capsid protein	[2-13C-glycerol; U-15N]		15 mM
4	H2O	natural abundance		100 %

5 13C-13C 2D correlation

Instrument

Varian Infinity - 600 MHz 3.2 mm BioMAS Varian probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM 2-13C-glycerol, U-15N, unlabeled Tyr and Phe Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
5	Capsid protein	[2-13C-glycerol, U-15N; unlabeled Tyr and Phe]		15 mM
6	H2O	natural abundance		100 %

6 NCACX 2D correlation

Instrument

Varian Infinity - 600 MHz 3.2 mm BioMAS Varian probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM 2-13C-glycerol, U-15N, unlabeled Tyr and Phe Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
5	Capsid protein	[2-13C-glycerol, U-15N; unlabeled Tyr and Phe]		15 mM
6	H2O	natural abundance		100 %

7 LGCP 1H-13C 1D buildup

Instrument

Varian Infinity - 750 MHz 3.2 mm E-free Bruker probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 7.5 mM Methyl-13C-Met Capsid protein-1, 7.5 mM 15N-indole Capsid protein-2, water

#	Name	Isotope labeling	Concentration
7	Capsid protein-1	[Methyl-13C-Met]	7.5 mM
8	Capsid protein-2	[15N-indole]	7.5 mM
9	H2O	natural abundance	100 %

8 LGCP 1H-15N 1D buildup

Instrument

Varian Infinity - 750 MHz 3.2 mm E-free Bruker probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 7.5 mM Methyl-13C-Met Capsid protein-1, 7.5 mM 15N-indole Capsid protein-2, water

#	Name	Isotope labeling	Concentration
7	Capsid protein-1	[Methyl-13C-Met]	7.5 mM
8	Capsid protein-2	[15N-indole]	7.5 mM
9	H2O	natural abundance	100 %

9 Intermolecular REDOR

Instrument

Varian Infinity - 600 MHz 3.2 mm BioMAS Varian probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 7.5 mM Methyl-13C-Met Capsid protein-1, 7.5 mM 15N-indole Capsid protein-2, water

#	Name	Isotope labeling	Concentration
7	Capsid protein-1	[Methyl-13C-Met]	7.5 mM
8	Capsid protein-2	[15N-indole]	7.5 mM
9	H2O	natural abundance	100 %

10 Side-chain/backbone REDOR

Instrument

Varian Infinity - 600 MHz 3.2 mm BioMAS Varian probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM Methyl-13C-Met, 2-13C-indole, U-15N Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
10	Capsid protein	[Methyl-13C-Met, 2-13C-indole, U-15N]		15 mM
11	H2O	natural abundance		100 %

11 BroBaRR 13C-13C buildup

Instrument

Varian Infinity - 750 MHz 3.2 mm E-free Bruker probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM U-15N,13C-Met and U-15N Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
1	Capsid protein	[U-15N; 13C-Met and U-15N]		15 mM
2	H2O	natural abundance		100 %

12 Vector angle Trp Ca-N/Cd1-Ne1

Instrument

Varian Infinity - 600 MHz 3.2 mm BioMAS Varian probe

Sample

State isotropic, Solvent system water, Pressure 1 atm, Temperature 278 K, pH 8.0, Details 15 mM 2-13C-glycerol, U-15N, unlabeled Tyr and Phe Capsid protein, water

#	Name	Isotope labeling	Type	Concentration
5	Capsid protein	[2-13C-glycerol, U-15N; unlabeled Tyr and Phe]		15 mM
6	H2O	natural abundance		100 %

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_30035_5irt.nef
Input source #2: Coordindates	5irt.cif
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	Error

Disulfide bonds

None

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

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPR

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
GSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKT

-------210-------220-------230-
ILKALGPGATLEEMMTACQGVGGPGHKARVL
|||||||||||||||||||||||||||||||
ILKALGPGATLEEMMTACQGVGGPGHKARVL

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPR

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
GSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKT

-------210-------220-------230-
ILKALGPGATLEEMMTACQGVGGPGHKARVL
|||||||||||||||||||||||||||||||
ILKALGPGATLEEMMTACQGVGGPGHKARVL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	231	0	0	100.0
B	B	231	0	0	100.0

Content subtype: combined_30035_5irt.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	791		84.0 (chain: A, length: 231)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 231, Sequence coverage: 84.0%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPR
||||||       |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||  |||
PIVQNL.......AISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQ.LKETINEEAAEWDRLHPVHAGPIAPGQ..EPR
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
GSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKT
||||||||||||||||||||||||||||||| ||||||||     |||||||||||||||||||| |||||    |||    ||||||||||||||||||
GSDIAGTTSTLQEQIGWMTHNPPIPVGEIYK.WIILGLNK.....SPTSILDIRQGPKEPFRDYV.RFYKT....QAS....NWMTETLLVQNANPDCKT
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

-------210-------220-------230-
ILKALGPGATLEEMMTACQGVGGPGHKARVL
|||||||||||||||||||            
ILKALGPGATLEEMMTACQ            
-------210---------

Total number of assignments
- ¹³C chemical shifts: 603
- ¹⁵N chemical shifts: 188

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	PRO	N	49.48
17	PRO	N	137.68
23	TRP	CG	110.85
34	PRO	N	134.58
38	PRO	N	134.58
49	PRO	N	132.68
80	TRP	CG	109.95
85	PRO	N	137.78
90	PRO	N	136.18
93	PRO	N	133.98
99	PRO	N	134.08
117	TRP	CG	112.45
121	ASN	CG	177.15
122	PRO	N	138.48
123	PRO	N	134.18
125	PRO	N	136.48
133	TRP	CG	112.15
147	PRO	N	133.78
157	PRO	N	136.88
160	PRO	N	143.58
164	TYR	CG	126.75
184	TRP	CG	111.15
196	PRO	N	132.38
207	PRO	N	132.48

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	1038	596	57.4
¹⁵N chemical shifts	254	171	67.3

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	462	363	78.6
¹⁵N chemical shifts	213	171	80.3

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	576	233	40.5
¹⁵N chemical shifts	41	0	0.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	142	43	30.3

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	73	0	0.0
¹⁵N chemical shifts	5	0	0.0

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: A

Keywords VIRAL PROTEIN, noncrystalline lattice, supramolecular structure, symmetric dimer, tubular assembly

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Found 1 Document (1.418 seconds)

BMRB: 30035

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Capsid protein p24, : 1 : 30 : 2 : 66 : 124 entities Detail

Interaction partners 1. Capsid protein p24, : 4 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 2 contents Detail