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BMRB: 18720

2LYD

The solution structure of the Dm DCP1 EVH1 domain in complex with the XRN1 DBM peptide

Authors

Assembly

Dm DCP1 EVH1 domain in complex with the XRN1 DBM peptide

Entity

1. Dm DCP1 EVH1 domain (polymer, Thiol state: all free), 134 monomers, 15456.17 Da Detail

GPHMADLMAD ESITRMNLAA IKKIDPYAKE IVDSSSHVAF YTFNSSQNEW EKTDVEGAFF IYHRNAEPFH SIFINNRLNT TSFVEPITGS LELQSQPPFL LYRNERSRIR GFWFYNSEEC DRISGLVNGL LKSK

2. XRN1 DBM (polymer, Thiol state: not present), 38 monomers, 4352.917 Da Detail

GPQDPLLQQQ RAPFPGQMPN LPKPPLFWQQ EAQKQEAL

Total weight

19809.086 Da

Max. entity weight

15456.17 Da

Source organism

Drosophila melanogaster

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 81.4 %, Completeness: 36.8 %, Completeness (bb): 55.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	36.8 % (768 of 2087)	9.8 % (108 of 1098)	66.1 % (532 of 805)	69.6 % (128 of 184)
Backbone	55.6 % (558 of 1004)	12.7 % (43 of 338)	76.6 % (389 of 508)	79.7 % (126 of 158)
Sidechain	27.4 % (342 of 1247)	8.6 % (65 of 760)	59.7 % (275 of 461)	7.7 % (2 of 26)
Aromatic	10.4 % (22 of 212)	18.9 % (20 of 106)	1.9 % (2 of 103)	0.0 % (0 of 3)
Methyl	47.4 % (73 of 154)	10.4 % (8 of 77)	84.4 % (65 of 77)

1. Dm DCP1 EVH1 domain

GPHMADLMAD ESITRMNLAA IKKIDPYAKE IVDSSSHVAF YTFNSSQNEW EKTDVEGAFF IYHRNAEPFH SIFINNRLNT TSFVEPITGS LELQSQPPFL LYRNERSRIR GFWFYNSEEC DRISGLVNGL LKSK

2. XRN1 DBM

GPQDPLLQQQ RAPFPGQMPN LPKPPLFWQQ EAQKQEAL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 21 models in PDB: 2LYD, Strand ID: A, B Detail

Release date

2012-10-14

Citation

A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5' exonucleolytic degradation
Braun, J.E., Truffault, V., Boland, A., Huntzinger, E., Chang, C., Haas, G., Weichenrieder, O., Coles, M., Izaurralde, E.
Nat. Struct. Mol. Biol. (2012), 19, 1324-1331, PubMed 23142987 , DOI 10.1038/nsmb.2413 , Abstract

Related entities 1. Dm DCP1 EVH1 domain, : 1 : 33 entities Detail

Related entities 2. XRN1 DBM, : 1 : 12 entities Detail

Experiments performed 14 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 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D HNHB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 2D NOESYnoN

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

10 2D PLUSH-TACSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

11 3D NNH NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

12 3D CNH NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

13 3D CCH NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

14 4D CCANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	Dm_DCP1_EVH1_domain	[U-100% 15N]		0.4 mM
2	Dm_DCP1_EVH1_domain	[U-100% 13C; U-100% 15N]		0.7 mM
3	XRN1_DBM	[U-100% 15N]		0.4 mM
4	XRN1_DBM	[U-100% 13C; U-100% 15N]		0.7 mM
5	H2O	natural abundance		90 %
6	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_18720_2lyd.nef
Input source #2: Coordindates	2lyd.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--------40--------50--------60--------70--------80--------90---
GPHMADLMADESITRMNLAAIKKIDPYAKEIVDSSSHVAFYTFNSSQNEWEKTDVEGAFFIYHRNAEPFHSIFINNRLNTTSFVEPITGSLELQSQPPFL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPHMADLMADESITRMNLAAIKKIDPYAKEIVDSSSHVAFYTFNSSQNEWEKTDVEGAFFIYHRNAEPFHSIFINNRLNTTSFVEPITGSLELQSQPPFL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----100-------110-------120-------
LYRNERSRIRGFWFYNSEECDRISGLVNGLLKSK
||||||||||||||||||||||||||||||||||
LYRNERSRIRGFWFYNSEECDRISGLVNGLLKSK
-------110-------120-------130----

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

--1320---1330------1340------1350-----
GPQDPLLQQQRAPFPGQMPNLPKPPLFWQQEAQKQEAL
||||||||||||||||||||||||||||||||||||||
GPQDPLLQQQRAPFPGQMPNLPKPPLFWQQEAQKQEAL
--------10--------20--------30--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	134	0	0	100.0
B	B	38	0	0	100.0

Content subtype: combined_18720_2lyd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	665		88.1 (chain: A, length: 134), 55.3 (chain: B, length: 38)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	714 (1)	noe	92.5 (chain: A, length: 134), 73.7 (chain: B, length: 38)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	392 (392)	.	93.3 (chain: A, length: 134), 81.6 (chain: B, length: 38)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 88.1%
  - Entity_assembly_ID: B, Chain length: 38, Sequence coverage: 55.3%
- Total number of assignments
  - ¹³C chemical shifts: 524
  - ¹⁵N chemical shifts: 123
  - ¹H chemical shifts: 18
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 92.5%
  - Entity_assembly_ID: B, Chain length: 38, Sequence coverage: 73.7%
- Total number of restraints: 714
- Weight of restraints: 1.0 (714)
- Potential type of restraints: square-well-parabolic (714)
- Range of distance target values: 1.35, 6.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 134, Sequence coverage: 93.3%
  - Entity_assembly_ID: B, Chain length: 38, Sequence coverage: 81.6%
- Total number of restraints: 392
- Total number of restraints per polymer type: 392
- Weight of restraints: 1.0 (392)
- Potential type of restraints: square-well-parabolic (392)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords DCP1/XRN1