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BMRB: 30162

5T42

Structure of the Ebola virus envelope protein MPER/TM domain and its interaction with the fusion loop explains their fusion activity

Authors

Lee, J., Nyenhuis, D.A., Nelson, E.A., Cafiso, D.S., White, J.M., Tamm, L.K.

Assembly

Envelope glycoprotein

Entity

1. Envelope glycoprotein (polymer, Thiol state: not present), 47 monomers, 5131.793 Da Detail

GSDKTLPDQG DNDNWWTGWR QWIPAGIGVT GVVIAVIALF AIAKFVF

Formula weight

5131.793 Da

Source organism

Ebola virus - Zaire (1995)

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.8 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.8 % (470 of 548)	83.8 % (232 of 277)	86.7 % (189 of 218)	92.5 % (49 of 53)
Backbone	97.1 % (270 of 278)	96.9 % (95 of 98)	96.3 % (130 of 135)	100.0 % (45 of 45)
Sidechain	76.8 % (239 of 311)	76.5 % (137 of 179)	79.0 % (98 of 124)	50.0 % (4 of 8)
Aromatic	67.9 % (53 of 78)	69.2 % (27 of 39)	62.9 % (22 of 35)	100.0 % (4 of 4)
Methyl	82.8 % (53 of 64)	84.4 % (27 of 32)	81.3 % (26 of 32)

1. entity 1

GSDKTLPDQG DNDNWWTGWR QWIPAGIGVT GVVIAVIALF AIAKFVF

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	EBOV_MPER/TM	[U-99% 15N]		500 uM
2	Pi	natural abundance		30 mM
3	NaCl	natural abundance		100 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5T42, Strand ID: A Detail

Release date

2016-12-08

Citation

Structure of the Ebola virus envelope protein MPER/TM domain and its interaction with the fusion loop explains their fusion activity
Lee, J., Nyenhuis, D.A., Nelson, E.A., Cafiso, D.S., White, J.M., Tamm, L.K.
Proc. Natl. Acad. Sci. U. S. A. (2017), 114, E7987-E7996, PubMed 28874543 , DOI 10.1073/pnas.1708052114 , Abstract

Related entities 1. Envelope glycoprotein, : 1 : 15 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	EBOV_MPER/TM	[U-99% 15N]		500 uM
2	Pi	natural abundance		30 mM
3	NaCl	natural abundance		100 mM

2 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

3 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

4 3D HN(CO)CA

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

5 3D HN(CA)CO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

6 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

7 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

8 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

9 3D CBCANH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

10 HCCCONH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

11 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5, Details 500 uM [U-99% 13C; U-99% 15N] EBOV_MPER/TM, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	EBOV_MPER/TM	[U-99% 13C; U-99% 15N]		500 uM
5	Pi	natural abundance		30 mM
6	NaCl	natural abundance		100 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30162_5t42.nef
Input source #2: Coordindates	5t42.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

630-----640-------650-------660-------670------
GSDKTLPDQGDNDNWWTGWRQWIPAGIGVTGVVIAVIALFAIAKFVF
|||||||||||||||||||||||||||||||||||||||||||||||
GSDKTLPDQGDNDNWWTGWRQWIPAGIGVTGVVIAVIALFAIAKFVF
--------10--------20--------30--------40-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	47	0	0	100.0

Content subtype: combined_30162_5t42.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	468		100.0 (chain: A, length: 47)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	602 (1)	noe	100.0 (chain: A, length: 47)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	44 (44)	.	63.8 (chain: A, length: 47)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 232
  - ¹³C chemical shifts: 187
  - ¹⁵N chemical shifts: 49
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
- Total number of restraints: 594
- Weight of restraints: 1.0 (594)
- Potential type of restraints: square-well-parabolic (594)
- Range of distance target values: 1.39, 2.75 (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: 47, Sequence coverage: 63.8%
- Total number of restraints: 44
- Total number of restraints per polymer type: 44
- Weight of restraints: 1.0 (44)
- Potential type of restraints: square-well-parabolic (44)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ebola virus, VIRAL PROTEIN, membrane fusion, membrane protein, protein-protein interaction