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BMRB: 19052

2M5F

NMR Structure of the Complete Internal Fusion Loop mutant L529A/I544A from Ebolavirus GP2 at pH 5.5

Authors

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

Assembly

Ebolavirus Fusion Loop L529A/I544A

Entity

1. Ebolavirus Fusion Loop L529A/I544A (polymer, Thiol state: all disulfide bound), 54 monomers, 5859.497 Da Detail

AQPKCNPNLH YWTTQDEGAA IGAAWIPYFG PAAEGIYAEG LMHNQDGLIC GLRQ

Formula weight

5859.497 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

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.7 %, Completeness (bb): 98.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.7 % (555 of 605)	93.6 % (292 of 312)	91.0 % (213 of 234)	84.7 % (50 of 59)
Backbone	98.4 % (311 of 316)	100.0 % (111 of 111)	97.4 % (151 of 155)	98.0 % (49 of 50)
Sidechain	86.6 % (291 of 336)	90.0 % (181 of 201)	86.5 % (109 of 126)	11.1 % (1 of 9)
Aromatic	66.7 % (44 of 66)	78.8 % (26 of 33)	58.1 % (18 of 31)	0.0 % (0 of 2)
Methyl	98.1 % (51 of 52)	100.0 % (26 of 26)	96.2 % (25 of 26)

1. Ebolavirus Fusion Loop L529A/I544A

AQPKCNPNLH YWTTQDEGAA IGAAWIPYFG PAAEGIYAEG LMHNQDGLIC GLRQ

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	Ebolavirus Fusion Loop L529A/I544A	[U-15N]		600 uM
2	Phosphate buffer	natural abundance		30 mM
3	NaCl	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	Ebolavirus Fusion Loop L529A/I544A	[U-13C; U-15N]		600 uM
7	Phosphate buffer	natural abundance		30 mM
8	NaCl	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.26 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.26 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.13 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 1.9 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M5F, Strand ID: A Detail

Release date

2014-02-23

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. Ebolavirus Fusion Loop L529A/I544A, : 1 : 20 : 19 entities Detail

Interaction partners 1. Ebolavirus Fusion Loop L529A/I544A, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 10 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 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	Ebolavirus Fusion Loop L529A/I544A	[U-15N]		600 uM
2	Phosphate buffer	natural abundance		30 mM
3	NaCl	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	Ebolavirus Fusion Loop L529A/I544A	[U-13C; U-15N]		600 uM
7	Phosphate buffer	natural abundance		30 mM
8	NaCl	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	Ebolavirus Fusion Loop L529A/I544A	[U-13C; U-15N]		600 uM
7	Phosphate buffer	natural abundance		30 mM
8	NaCl	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	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 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	Ebolavirus Fusion Loop L529A/I544A	[U-13C; U-15N]		600 uM
7	Phosphate buffer	natural abundance		30 mM
8	NaCl	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

5 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	Ebolavirus Fusion Loop L529A/I544A	[U-13C; U-15N]		600 uM
7	Phosphate buffer	natural abundance		30 mM
8	NaCl	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	Ebolavirus Fusion Loop L529A/I544A	[U-13C; U-15N]		600 uM
7	Phosphate buffer	natural abundance		30 mM
8	NaCl	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	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 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	Ebolavirus Fusion Loop L529A/I544A	[U-13C; U-15N]		600 uM
7	Phosphate buffer	natural abundance		30 mM
8	NaCl	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

8 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	Ebolavirus Fusion Loop L529A/I544A	[U-13C; U-15N]		600 uM
7	Phosphate buffer	natural abundance		30 mM
8	NaCl	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	Ebolavirus Fusion Loop L529A/I544A	[U-13C; U-15N]		600 uM
7	Phosphate buffer	natural abundance		30 mM
8	NaCl	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 30 mM Phosphate buffer; 50 mM NaCl; pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	Ebolavirus Fusion Loop L529A/I544A	[U-13C; U-15N]		600 uM
7	Phosphate buffer	natural abundance		30 mM
8	NaCl	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	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_19052_2m5f.nef
Input source #2: Coordindates	2m5f.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 55.516, CB 41.836 ppm	oxidized, CA 55.915, CB 40.902 ppm	2.03

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
AQPKCNPNLHYWTTQDEGAAIGAAWIPYFGPAAEGIYAEGLMHNQDGLICGLRQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||
AQPKCNPNLHYWTTQDEGAAIGAAWIPYFGPAAEGIYAEGLMHNQDGLICGLRQ
--------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_19052_2m5f.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	550		100.0 (chain: A, length: 54)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	736 (1)	noe	100.0 (chain: A, length: 54)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	45 (45)	.	85.2 (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: 292
  - ¹³C chemical shifts: 209
  - ¹⁵N chemical shifts: 49
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: OK

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: 100.0%
- Total number of restraints: 735
- Weight of restraints: 1.0 (735)
- Potential type of restraints: square-well-parabolic (735)
- Range of distance target values: 2.21, 3.55 (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: 85.2%
- Total number of restraints: 45
- Total number of restraints per polymer type: 45
- Weight of restraints: 1.0 (45)
- Potential type of restraints: square-well-parabolic (45)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Double Mutant L529A/I544A, Ebolavirus, Fusion Loop