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BMRB: 30010

5I22

Amphiphysin SH3 in complex with Chikungunya virus nsP3 peptide

Authors

Tossavainen, H., Aitio, O., Hellman, M., Saksela, K., Permi, P.

Assembly

Myc box-dependent-interacting protein 1, CHIKV nsP3 peptide

Entity

1. Myc box-dependent-interacting protein 1, CHIKV nsP3 peptide, entity 1 (polymer), 81 monomers, 9346.324 Da Detail

GRLDLPPGFM FKVQAQHDYT ATDTDELQLK AGDVVLVIPF QNPEEQDEGW LMGVKESDWN QHKELEKCRG VFPENFTERV P

2. Myc box-dependent-interacting protein 1, CHIKV nsP3 peptide, entity 2 (polymer, Thiol state: not present), 17 monomers, 1933.225 Da Detail

STVPVAPPRR RRGRNLT

Total weight

11279.549 Da

Max. entity weight

9346.324 Da

Source organism

Homo sapiens , Chikungunya virus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.7 %, Completeness (bb): 82.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.7 % (1045 of 1165)	99.0 % (609 of 615)	75.3 % (338 of 449)	97.0 % (98 of 101)
Backbone	82.5 % (470 of 570)	98.5 % (191 of 194)	67.2 % (193 of 287)	96.6 % (86 of 89)
Sidechain	97.1 % (666 of 686)	99.3 % (418 of 421)	93.3 % (236 of 253)	100.0 % (12 of 12)
Aromatic	84.4 % (76 of 90)	100.0 % (45 of 45)	67.4 % (29 of 43)	100.0 % (2 of 2)
Methyl	96.7 % (89 of 92)	97.8 % (45 of 46)	95.7 % (44 of 46)

1. entity 1

GRLDLPPGFM FKVQAQHDYT ATDTDELQLK AGDVVLVIPF QNPEEQDEGW LMGVKESDWN QHKELEKCRG VFPENFTERV P

2. entity 2

STVPVAPPRR RRGRNLT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] amphiphysin 2 SH3, 0.5 mM [U-13C; U-15N] CHIKV nsP3 peptide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5I22, Strand ID: A, B Detail

Release date

2016-06-12

Citation

Structural Basis of the High-Affinity Interaction Between the Alphavirus Nonstructural Protein-3 (nsP3) and the SH3 Domain of Amphiphysin-2
Tossavainen, H., Aitio, O., Hellman, M., Saksela, K., Permi, P.
J. Biol. Chem. (2016), 291, 16307-16317, PubMed 27268056 , DOI 10.1074/jbc.M116.732412 , Abstract

Related entities 1. Myc box-dependent-interacting protein 1, CHIKV nsP3 peptide, entity 1, : 2 : 4 : 193 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] amphiphysin 2 SH3, 0.5 mM [U-13C; U-15N] CHIKV nsP3 peptide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

2 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

4 3D H(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

5 3D C(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

6 3D HCCH-COSY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

9 2D (HB)CB(CGCDCE)HE

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

10 2D (HB)CB(CGCD)HD

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	CHIKV nsP3 peptide	[U-13C; U-15N]		0.5 mM
2	amphiphysin 2 SH3	[U-13C; U-15N]		0.5 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30010_5i22.nef
Input source #2: Coordindates	5i22.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

-----520-------530-------540-------550-------560-------570-------580-------590---
GRLDLPPGFMFKVQAQHDYTATDTDELQLKAGDVVLVIPFQNPEEQDEGWLMGVKESDWNQHKELEKCRGVFPENFTERVP
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GRLDLPPGFMFKVQAQHDYTATDTDELQLKAGDVVLVIPFQNPEEQDEGWLMGVKESDWNQHKELEKCRGVFPENFTERVP
--------10--------20--------30--------40--------50--------60--------70--------80-

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

--1730---1740----
STVPVAPPRRRRGRNLT
|||||||||||||||||
STVPVAPPRRRRGRNLT
--------10-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	81	0	0	100.0
B	B	17	0	0	100.0

Content subtype: combined_30010_5i22.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1049		100.0 (chain: A, length: 81), 100.0 (chain: B, length: 17)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3389 (1)	noe	100.0 (chain: A, length: 81), 94.1 (chain: B, length: 17)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	113 (113)	.	95.1 (chain: A, length: 81), 11.8 (chain: B, length: 17)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 17, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 610
  - ¹³C chemical shifts: 334
  - ¹⁵N chemical shifts: 105
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
589	THR	HG1	5.148

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	508	506	99.6
¹³C chemical shifts	374	278	74.3
¹⁵N chemical shifts	89	87	97.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	162	160	98.8
¹³C chemical shifts	162	81	50.0
¹⁵N chemical shifts	75	73	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	346	346	100.0
¹³C chemical shifts	212	197	92.9
¹⁵N chemical shifts	14	14	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	39	100.0
¹³C chemical shifts	39	39	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	45	100.0
¹³C chemical shifts	43	29	67.4
¹⁵N chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	103	96.3
¹³C chemical shifts	75	56	74.7
¹⁵N chemical shifts	20	18	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	31	96.9
¹³C chemical shifts	34	17	50.0
¹⁵N chemical shifts	14	13	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	75	72	96.0
¹³C chemical shifts	41	39	95.1
¹⁵N chemical shifts	6	5	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	8	88.9
¹³C chemical shifts	9	7	77.8

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 17, Sequence coverage: 94.1%
- Total number of restraints: 3389
- Weight of restraints: 1.0 (3389)
- Potential type of restraints: upper-bound-parabolic (3389)
- Range of distance target values: 2.6, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 95.1%
  - Entity_assembly_ID: B, Chain length: 17, Sequence coverage: 11.8%
- Total number of restraints: 113
- Total number of restraints per polymer type: 113
- Weight of restraints: 1.0 (113)
- Potential type of restraints: square-well-parabolic (113)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords SH3 domain, Transcription, function: protein binding Chikungunya virus nsP3 peptide, function: viral replication

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Found 1 Document (0.788 seconds)

BMRB: 30010

Sample

Related entities 1. Myc box-dependent-interacting protein 1, CHIKV nsP3 peptide, entity 1, : 2 : 4 : 193 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 4 contents Detail