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Found 1 Document (1.237 seconds)

BMRB: 18042

4A54

Structure of EDC3:DCP2

Authors

Truffault, V.

Assembly

EDC3 DCP2

Entity

1. EDC3 (polymer, Thiol state: all free), 96 monomers, 10587.88 Da Detail

MGMSVADFYG SNVEVLLNND SKARGVITNF DSSNSILQLR LANDSTKSIV TKDIKDLRIL PKNEIMPKNG TKSPSTNSTK LKSAETYSSK NKWSMD

2. DCP2 (polymer, Thiol state: all free), 48 monomers, 4940.379 Da Detail

GATTKEKNIS VDVDADASSQ LLSLLKSSTA PSDLATPQPS TFPQPPVE

Total weight

15528.259 Da

Max. entity weight

10587.88 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

XPLOR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 78.5 %, Completeness: 68.2 %, Completeness (bb): 74.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	68.2 % (1106 of 1622)	65.7 % (555 of 845)	71.2 % (446 of 626)	69.5 % (105 of 151)
Backbone	74.2 % (628 of 846)	71.5 % (203 of 284)	76.1 % (325 of 427)	74.1 % (100 of 135)
Sidechain	64.2 % (587 of 915)	62.7 % (352 of 561)	68.0 % (230 of 338)	31.3 % (5 of 16)
Aromatic	34.5 % (20 of 58)	69.0 % (20 of 29)	0.0 % (0 of 28)	0.0 % (0 of 1)
Methyl	90.3 % (139 of 154)	88.3 % (68 of 77)	92.2 % (71 of 77)

1. EDC3

MGMSVADFYG SNVEVLLNND SKARGVITNF DSSNSILQLR LANDSTKSIV TKDIKDLRIL PKNEIMPKNG TKSPSTNSTK LKSAETYSSK NKWSMD

2. DCP2

GATTKEKNIS VDVDADASSQ LLSLLKSSTA PSDLATPQPS TFPQPPVE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	EDC3	[U-100% 15N]	0.7 mM
2	DCP2	[U-100% 15N]	0.7 mM
3	NaPO4	natural abundance	50 mM
4	imidazole	natural abundance	10 mM
5	NaCl	natural abundance	150 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	2.6 ppm	na	indirect	1.0
¹H	TMS	methyl protons	0.0 ppm	na	indirect	1.0
¹⁵N	TMS	nitrogen	0.0 ppm	na	indirect	1.0

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	2.6 ppm	na	indirect	1.0
¹H	TMS	methyl protons	0.0 ppm	na	indirect	1.0
¹⁵N	TMS	nitrogen	0.0 ppm	na	indirect	1.0

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	2.6 ppm	na	indirect	1.0
¹H	TMS	methyl protons	0.0 ppm	na	indirect	1.0
¹⁵N	TMS	nitrogen	0.0 ppm	na	indirect	1.0

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	2.6 ppm	na	indirect	1.0
¹H	TMS	methyl protons	0.0 ppm	na	indirect	1.0
¹⁵N	TMS	nitrogen	0.0 ppm	na	indirect	1.0

Referencing offset: 0.29 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 22 models in PDB: 4A54, Strand ID: A, B Detail

Release date

2012-01-22

Citation

The structural basis of Edc3- and Scd6-mediated activation of the Dcp1:Dcp2 mRNA decapping complex
Fromm, S.A., Truffault, V., Kamenz, J., Braun, J.E., Hoffmann, N.A., Izaurralde, E., Sprangers, R.
EMBO J. (2012), 31, 279-290, PubMed 22085934 , DOI 10.1038/emboj.2011.408 , Abstract

Entries sharing articles BMRB: 1, Swiss-Prot: 2 entries Detail

  BMRB: 18041 released on 2012-01-22
    Title Solution structure of the EDC3-LSm domain
  Swiss-Prot: O13828 released on 2009-05-05
    Title DCP2_SCHPO Entity mRNA decapping complex subunit 2
  Swiss-Prot: O94752 released on 2005-11-22
    Title EDC3_SCHPO Entity Enhancer of mRNA-decapping protein 3

Related entities 1. EDC3, : 1 : 1 : 2 : 1 entities Detail

Related entities 2. DCP2, : 1 : 2 : 4 entities Detail

Interaction partners 1. EDC3, : 1 : 1 interactors Detail

More details for 2 interactors identified by 1 citations

Interaction partners 2. DCP2, : 3 : 1 interactors Detail

More details for 4 interactors identified by 3 citations

Experiments performed 1 experiments Detail

NMR combined restraints 9 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18042_4a54.nef
Input source #2: Coordindates	4a54.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

-0--------10--------20--------30--------40--------50--------60--------70--------80--------90----
MGMSVADFYGSNVEVLLNNDSKARGVITNFDSSNSILQLRLANDSTKSIVTKDIKDLRILPKNEIMPKNGTKSPSTNSTKLKSAETYSSKNKWSMD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGMSVADFYGSNVEVLLNNDSKARGVITNFDSSNSILQLRLANDSTKSIVTKDIKDLRILPKNEIMPKNGTKSPSTNSTKLKSAETYSSKNKWSMD
--------10--------20--------30--------40--------50--------60--------70--------80--------90------

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

240-----250-------260-------270-------280-------290-
GATTKEKNISVDVDADASSQLLSLLKSSTAPSDLATPQPSTFPQPPVESHSS
||||||||||||||||||||||||||||||||||||||||||||||||||||
GATTKEKNISVDVDADASSQLLSLLKSSTAPSDLATPQPSTFPQPPVESHSS
--------10--------20--------30--------40--------50--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	96	0	0	100.0
B	B	52	0	0	100.0

Content subtype: combined_18042_4a54.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1077		82.3 (chain: A, length: 96), 59.6 (chain: B, length: 52)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	67 (1)	noe	54.2 (chain: A, length: 96), 19.2 (chain: B, length: 52)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	49 (1)	noe	27.1 (chain: A, length: 96), 19.2 (chain: B, length: 52)
3	Distance restraints	CNS/XPLOR_distance_constraints_8	Warning	132 (1)	noe	60.4 (chain: A, length: 96), 25.0 (chain: B, length: 52)
4	Distance restraints	CNS/XPLOR_distance_constraints_10	OK	144 (1)	noe	43.8 (chain: A, length: 96)
5	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	44 (1)	hbond	36.5 (chain: A, length: 96), 21.2 (chain: B, length: 52)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	Warning	134 (134)	.	61.5 (chain: A, length: 96), 26.9 (chain: B, length: 52)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_9	Warning	62 (62)	.	42.7 (chain: A, length: 96), 9.6 (chain: B, length: 52)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 82.3%
  - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 59.6%
- Total number of assignments
  - ¹H chemical shifts: 540
  - ¹³C chemical shifts: 436
  - ¹⁵N chemical shifts: 101
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	579	414	71.5
¹³C chemical shifts	423	319	75.4
¹⁵N chemical shifts	108	76	70.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	193	145	75.1
¹³C chemical shifts	192	154	80.2
¹⁵N chemical shifts	93	71	76.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	386	269	69.7
¹³C chemical shifts	231	165	71.4
¹⁵N chemical shifts	15	5	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	46	86.8
¹³C chemical shifts	53	48	90.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	20	83.3
¹³C chemical shifts	23	0	0.0
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	284	126	44.4
¹³C chemical shifts	217	117	53.9
¹⁵N chemical shifts	50	25	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	99	52	52.5
¹³C chemical shifts	104	56	53.8
¹⁵N chemical shifts	46	25	54.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	185	74	40.0
¹³C chemical shifts	113	61	54.0
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	23	82.1
¹³C chemical shifts	28	24	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	0	0.0
¹³C chemical shifts	7	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 54.2%
  - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 19.2%
- Total number of restraints: 67
- Weight of restraints: 1.0 (67)
- Potential type of restraints: square-well-parabolic (67)
- Range of distance target values: 1.6, 6.75 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 27.1%
    - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 19.2%
  - Total number of restraints: 49
  - Weight of restraints: 1.0 (49)
  - Potential type of restraints: square-well-parabolic (49)
  - Range of distance target values: 1.35, 6.75 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_8
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 60.4%
      - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 25.0%
    - Total number of restraints: 131
    - Weight of restraints: 1.0 (131)
    - Potential type of restraints: square-well-parabolic (131)
    - Range of distance target values: 1.35, 7.75 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_10
      - Status: OK
      - Experiment type: noe
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 43.8%
      - Total number of restraints: 144
        Long range restraints, | i - j | >= 5 : 144
      - Weight of restraints: 1.0 (144)
        Long range restraints, | i - j | >= 5 : 1.0 (144)
      - Potential type of restraints: square-well-parabolic (144)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (144)
      - Range of distance target values: 1.35, 7.75 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
      - Distance restraints on contact map
      - Saveframe: CNS/XPLOR_distance_constraints_3
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 36.5%
        Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 21.2%
        Total number of restraints: 44
        Total hydrogen bond restraints: 44
        O...H-x: 16
        O...h-N: 7
        Long range: 21
        O...H-x: 21
        Weight of restraints: 1.0 (44)
        Total hydrogen bond restraints: 1.0 (44)
        O...H-x: 1.0 (16)
        O...h-N: 1.0 (7)
        Long range: 1.0 (21)
        O...H-x: 1.0 (21)
        Potential type of restraints: square-well-parabolic (44)
        Total hydrogen bond restraints: square-well-parabolic (44)
        O...H-x: square-well-parabolic (16)
        O...h-N: square-well-parabolic (7)
        Long range: square-well-parabolic (21)
        O...H-x: square-well-parabolic (21)
        Range of distance target values: 2.2, 3.05 (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_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 61.5%
  - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 26.9%
- Total number of restraints: 134
- Total number of restraints per polymer type: 134
- Weight of restraints: 1.0 (134)
- Potential type of restraints: square-well-parabolic (134)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_9
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 42.7%
    - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 9.6%
  - Total number of restraints: 62
  - Total number of restraints per polymer type: 62
  - Weight of restraints: 1.0 (62)
  - Potential type of restraints: square-well-parabolic (62)
  - Plot of Chi1-Chi2 angle restraints
  - Dihedral angle restraints per residue

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Found 1 Document (1.237 seconds)

BMRB: 18042

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1, Swiss-Prot: 2 entries Detail

Related entities 1. EDC3, : 1 : 1 : 2 : 1 entities Detail

Related entities 2. DCP2, : 1 : 2 : 4 entities Detail

Interaction partners 1. EDC3, : 1 : 1 interactors Detail

Interaction partners 2. DCP2, : 3 : 1 interactors Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 9 contents Detail