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BMRB: 19383

2MB1

NMR Structure of the Complete Internal Fusion Loop mutant I544A from Ebolavirus GP2 at pH 5.5

Authors

Tamm, L.K., Gregory, S.M.

Assembly

Complete Internal Fusion Loop mutant I544A from Ebolavirus GP2

Entity

1. Complete Internal Fusion Loop mutant I544A from Ebolavirus GP2 (polymer, Thiol state: all disulfide bound), 54 monomers, 5901.577 Da Detail

AQPKCNPNLH YWTTQDEGAA IGLAWIPYFG PAAEGIYAEG LMHNQDGLIC GLRQ

Formula weight

5901.577 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS5:SG	1:CYS50:SG

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 84.6 %, Completeness (bb): 95.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.6 % (518 of 612)	88.9 % (281 of 316)	80.2 % (190 of 237)	79.7 % (47 of 59)
Backbone	95.6 % (302 of 316)	97.3 % (108 of 111)	94.8 % (147 of 155)	94.0 % (47 of 50)
Sidechain	76.4 % (262 of 343)	84.4 % (173 of 205)	69.0 % (89 of 129)	0.0 % (0 of 9)
Aromatic	21.2 % (14 of 66)	42.4 % (14 of 33)	0.0 % (0 of 31)	0.0 % (0 of 2)
Methyl	90.7 % (49 of 54)	96.3 % (26 of 27)	85.2 % (23 of 27)

1. entity

AQPKCNPNLH YWTTQDEGAA IGLAWIPYFG PAAEGIYAEG LMHNQDGLIC GLRQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	I544A Ebov FL	[U-99% 13C; U-99% 15N]		600 uM
2	potassium phosphate	natural abundance		30 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.12 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -1.84 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MB1, Strand ID: A Detail

Release date

2014-04-06

Citation

Ebolavirus entry requires a compact hydrophobic fist at the tip of the fusion loop
Gregory, S.M., Larsson, P., Nelson, E.A., Kasson, P.M., White, J.M., Tamm, L.K.
J. Virol. (2014), 88, 6636-6649, PubMed 24696482 , DOI 10.1128/JVI.00396-14 , Abstract

Related entities 1. Complete Internal Fusion Loop mutant I544A from Ebolavirus GP2, : 1 : 20 : 17 entities Detail

Interaction partners 1. Complete Internal Fusion Loop mutant I544A from Ebolavirus GP2, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	I544A Ebov FL	[U-99% 13C; U-99% 15N]		600 uM
2	potassium phosphate	natural abundance		30 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	I544A Ebov FL	[U-99% 13C; U-99% 15N]		600 uM
2	potassium phosphate	natural abundance		30 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	I544A Ebov FL	[U-99% 13C; U-99% 15N]		600 uM
2	potassium phosphate	natural abundance		30 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	I544A Ebov FL	[U-99% 13C; U-99% 15N]		600 uM
2	potassium phosphate	natural abundance		30 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	I544A Ebov FL	[U-99% 13C; U-99% 15N]		600 uM
2	potassium phosphate	natural abundance		30 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	I544A Ebov FL	[U-99% 13C; U-99% 15N]		600 uM
2	potassium phosphate	natural abundance		30 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	I544A Ebov FL	[U-99% 13C; U-99% 15N]		600 uM
2	potassium phosphate	natural abundance		30 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	I544A Ebov FL	[U-99% 13C; U-99% 15N]		600 uM
2	potassium phosphate	natural abundance		30 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19383_2mb1.nef
Input source #2: Coordindates	2mb1.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:511:CYS:SG	A:556:CYS:SG	oxidized, CA 55.085, CB 41.809 ppm	oxidized, CA 56.233, CB 41.438 ppm	2.033

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

---510-----520-------530-------540-------550-------560
AQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYAEGLMHNQDGLICGLRQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||
AQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYAEGLMHNQDGLICGLRQ
--------10--------20--------30--------40--------50----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	54	0	0	100.0

Content subtype: combined_19383_2mb1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	Warning	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	518		100.0 (chain: A, length: 54)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	514 (1)	noe	98.1 (chain: A, length: 54)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	65 (65)	.	94.4 (chain: A, length: 54)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 281
  - ¹³C chemical shifts: 190
  - ¹⁵N chemical shifts: 47
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Covalent bonds

Saveframe: assembly
- Status: Warning

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 98.1%
- Total number of restraints: 514
- Weight of restraints: 1.0 (514)
- Potential type of restraints: square-well-parabolic (514)
- Range of distance target values: 2.28, 3.51 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 94.4%
- Total number of restraints: 65
- Total number of restraints per polymer type: 65
- Weight of restraints: 1.0 (65)
- Potential type of restraints: square-well-parabolic (65)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ebolavirus, Fusion Loop, I544A, peptide