BMRBj - BMREntryMaster

Found 1 Document (0.528 seconds)

BMRB: 16907

2KXA

The hemagglutinin fusion peptide (H1 subtype) at pH 7.4

Authors

Lorieau, J.L., Louis, J.M., Bax, A.

Assembly

HAfp

Entity

1. HAfp (polymer, Thiol state: not present), 30 monomers, 3147.561 Da Detail

GLFGAIAGFI EGGWTGMIDG WYGSGKKKKD

Formula weight

3147.561 Da

Source organism

Influenza A virus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation, H_exch_rates

Chem. Shift Complete

Sequence coverage: 80.0 %, Completeness: 65.7 %, Completeness (bb): 75.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	65.7 % (224 of 341)	71.0 % (125 of 176)	57.1 % (76 of 133)	71.9 % (23 of 32)
Backbone	75.0 % (135 of 180)	76.8 % (53 of 69)	75.3 % (61 of 81)	70.0 % (21 of 30)
Sidechain	57.7 % (105 of 182)	67.3 % (72 of 107)	42.5 % (31 of 73)	100.0 % (2 of 2)
Aromatic	53.8 % (28 of 52)	100.0 % (26 of 26)	0.0 % (0 of 24)	100.0 % (2 of 2)
Methyl	100.0 % (22 of 22)	100.0 % (11 of 11)	100.0 % (11 of 11)

1. HAfp

GLFGAIAGFI EGGWTGMIDG WYGSGKKKKD

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
1	HAfp	[U-13C; U-15N; U-2H]	0.6 ~ 0.8 mM
2	D2O	[U-2H]	7 %
3	TRIS	[U-99% 2H]	25 mM
4	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
5	HAfp	[U-13C; U-15N]	0.6 ~ 0.8 mM
6	TRIS	[U-99% 2H]	25 mM
7	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

Sample #3

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
8	HAfp	[U-13C; U-15N]	0.6 ~ 0.8 mM
9	D2O	[U-2H]	7 %
10	TRIS	[U-99% 2H]	25 mM
11	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

Sample #4

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
12	HAfp	[U-15N]	0.6 ~ 0.8 mM
13	D2O	[U-2H]	7 %
14	TRIS	[U-99% 2H]	25 mM
15	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
16	HAfp	[U-15N]	0.6 ~ 0.8 mM
17	TRIS	[U-99% 2H]	25 mM
18	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2KXA, Strand ID: A Detail

Heteronucl. T₁

43 T₁ values in 2 lists
Coherence Sz, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 305 K, pH 4.0, 7.4 Detail

Heteronucl. T₂

43 T₂ values in 2 lists
Coherence S(+,-), Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 305 K, pH 4.0, 7.4 Detail

Heteronucl. NOE

43 NOE values in 2 lists
Value type peak height, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 305 K, pH 7.4 Detail

Heteronucl. T₁/T₂

43 T₁/T₂ values in 2 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 305 K, pH 4.0, 7.4 Detail

¹H exchange rate

22 k_ex values in 1 lists
Pressure 1 atm, Temperature 305 K, pH 7.4 Detail

Release date

2010-07-27

Citation

The complete influenza hemagglutinin fusion domain adopts a tight helical hairpin arrangement at the lipid:water interface
Lorieau, J.L., Louis, J.M., Bax, A.
Proc. Natl. Acad. Sci. U. S. A. (2010), 107, 11341-11346, PubMed 20534508 , DOI 10.1073/pnas.1006142107 , Abstract

Related entities 1. HAfp, : 1 : 1 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
1	HAfp	[U-13C; U-15N; U-2H]	0.6 ~ 0.8 mM
2	D2O	[U-2H]	7 %
3	TRIS	[U-99% 2H]	25 mM
4	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
5	HAfp	[U-13C; U-15N]	0.6 ~ 0.8 mM
6	TRIS	[U-99% 2H]	25 mM
7	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
5	HAfp	[U-13C; U-15N]	0.6 ~ 0.8 mM
6	TRIS	[U-99% 2H]	25 mM
7	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

4 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
1	HAfp	[U-13C; U-15N; U-2H]	0.6 ~ 0.8 mM
2	D2O	[U-2H]	7 %
3	TRIS	[U-99% 2H]	25 mM
4	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

5 3D HNCA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
1	HAfp	[U-13C; U-15N; U-2H]	0.6 ~ 0.8 mM
2	D2O	[U-2H]	7 %
3	TRIS	[U-99% 2H]	25 mM
4	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

6 3D HN(CO)CA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
1	HAfp	[U-13C; U-15N; U-2H]	0.6 ~ 0.8 mM
2	D2O	[U-2H]	7 %
3	TRIS	[U-99% 2H]	25 mM
4	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 7.4, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
1	HAfp	[U-13C; U-15N; U-2H]	0.6 ~ 0.8 mM
2	D2O	[U-2H]	7 %
3	TRIS	[U-99% 2H]	25 mM
4	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

8 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 4.0, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
1	HAfp	[U-13C; U-15N; U-2H]	0.6 ~ 0.8 mM
2	D2O	[U-2H]	7 %
3	TRIS	[U-99% 2H]	25 mM
4	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

9 2D 1H-13C HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 4.0, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
1	HAfp	[U-13C; U-15N; U-2H]	0.6 ~ 0.8 mM
2	D2O	[U-2H]	7 %
3	TRIS	[U-99% 2H]	25 mM
4	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

10 3D HN(CO)CA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 305 K, pH 4.0, Details The hemagglutinin fusion peptide subtype H1 at pH 7.4 in DPC micelles

#	Name	Isotope labeling	Concentration
1	HAfp	[U-13C; U-15N; U-2H]	0.6 ~ 0.8 mM
2	D2O	[U-2H]	7 %
3	TRIS	[U-99% 2H]	25 mM
4	DPC	[U-99% 2H]	130.0 ~ 180.0 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16907_2kxa.nef
Input source #2: Coordindates	2kxa.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	Warning

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
GLFGAIAGFIEGGWTGMIDGWYGSGKKKKD
||||||||||||||||||||||||||||||
GLFGAIAGFIEGGWTGMIDGWYGSGKKKKD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	30	0	0	100.0

Content subtype: combined_16907_2kxa.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	224		80.0 (chain: A, length: 30)
1	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	743 (1)	noe	76.7 (chain: A, length: 30)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	4 (1)	hbond	20.0 (chain: A, length: 30)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	40 (40)	.	76.7 (chain: A, length: 30)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_2	Warning	147 (142)	.	76.7 (chain: A, length: 30)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 80.0%
- Total number of assignments
  - ¹H chemical shifts: 125
  - ¹³C chemical shifts: 76
  - ¹⁵N chemical shifts: 23
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	176	125	71.0
¹³C chemical shifts	133	76	57.1
¹⁵N chemical shifts	32	23	71.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	53	76.8
¹³C chemical shifts	60	45	75.0
¹⁵N chemical shifts	30	21	70.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	72	67.3
¹³C chemical shifts	73	31	42.5
¹⁵N chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	11	91.7
¹³C chemical shifts	12	11	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	26	100.0
¹³C chemical shifts	24	0	0.0
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_6
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 76.7%
- Total number of restraints: 741
- Weight of restraints: 1.0 (741)
- Potential type of restraints: square-well-parabolic (741)
- Range of distance target values: 1.85, 7.28 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 20.0%
  - Total number of restraints: 4
  - Weight of restraints: 1.0 (4)
  - Potential type of restraints: square-well-parabolic (4)
  - Range of distance target values: 1.35, 1.35 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 76.7%
- Total number of restraints: 40
- Total number of restraints per polymer type: 40
- Weight of restraints: 1.0 (40)
- Potential type of restraints: square-well-parabolic (40)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 76.7%
- Total number of restraints: 147
- Potential type of restraints: undefined (147)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords Fusion peptide, Hemagglutinin, Membrane protein, NMR, fusion peptide, hemagglutinin, influenza

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.528 seconds)

BMRB: 16907

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Related entities 1. HAfp, : 1 : 1 entities Detail

Experiments performed 10 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail