BMRBj - BMREntryMaster

Found 1 Document (3.42 seconds)

BMRB: 18663

4B6V

The third member of the eIF4E family represses gene expression via a novel mode of recognition of the methyl-7 guanosine cap moiety

Authors

Osborne, M.J., Volpon, L., Kornblatt, J.A., Culjkovic-kraljcic, B., Baguet, A., Borden, K.L.B., Borden, A.

Assembly

The third member of the eIF4E family represses gene expression via a novel mode of recognition of the methyl-7 guanosine cap mo

Entity

1. The third member of the eIF4E family represses gene expression via a novel mode of recognition of the methyl-7 guanosine cap mo (polymer, Thiol state: all free), 207 monomers, 22835.81 Da Detail

MALPPAAAPP GANEPLDKAL SALPPEPGGV PLHSPWTFWL DRSLPGATAA ECASNLKKIY TVQTVQIFWS VYNNIPPVTS LPLRCSYHLM RGERRPLWEE ESNAKGGVWK MKVPKDSTST VWKELLLATI GEQFTDCAAA DDEIIGVSVS VRDREDVVQV WNVNASLVGE ATVLEKIHQL LPHIAFKAVF YKPHEEHHAF EGGRGKH

Formula weight

22835.81 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

XPLOR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.5 %, Completeness: 81.8 %, Completeness (bb): 82.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.8 % (1957 of 2393)	88.2 % (1092 of 1238)	69.5 % (658 of 947)	99.5 % (207 of 208)
Backbone	82.6 % (996 of 1206)	97.3 % (398 of 409)	67.4 % (410 of 608)	99.5 % (188 of 189)
Sidechain	82.8 % (1143 of 1381)	83.7 % (694 of 829)	80.7 % (430 of 533)	100.0 % (19 of 19)
Aromatic	63.0 % (131 of 208)	72.1 % (75 of 104)	50.5 % (49 of 97)	100.0 % (7 of 7)
Methyl	97.5 % (236 of 242)	99.2 % (120 of 121)	95.9 % (116 of 121)

1. EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TYPE

Show sample condition

Sample

Solvent system 50mM Phosphate, 100mM NaCl, 100uM TCEP, NaN3, 7% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 7.300, Details eIF4E3 0.2mM

#	Name	Isotope labeling	Concentration
1	EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TYPE	[U-13C; U-15N]	0.2 mM
2	Phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	TCEP	natural abundance	100 uM
5	D2O	[U-100% 2H]	7 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	external	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	external	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	external	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: -0.1 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 4B6V, Strand ID: A Detail

Release date

2013-02-27

Citation

eIF4E3 acts as a tumor suppressor by utilizing an atypical mode of methyl-7-guanosine cap recognition
Osborne, M.J., Volpon, L., Kornblatt, J.A., Culjkovic-Kraljacic, B., Baguet, A., Borden, K.L.B.
Proc. Natl. Acad. Sci. U. S. A. (2013), 110, 3877-3882, PubMed 23431134 , DOI 10.1073/pnas.1216862110 , Abstract

Related entities 1. The third member of the eIF4E family represses gene expression via a novel mode of recognition of the methyl-7 guanosine cap mo, : 1 : 3 : 65 entities Detail

Interaction partners 1. The third member of the eIF4E family represses gene expression via a novel mode of recognition of the methyl-7 guanosine cap mo, : 6 interactors Detail

More details for 6 interactors identified by 1 citations

Experiments performed 1 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18663_4b6v.nef
Input source #2: Coordindates	4b6v.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-------100
MALPPAAAPPGANEPLDKALSALPPEPGGVPLHSPWTFWLDRSLPGATAAECASNLKKIYTVQTVQIFWSVYNNIPPVTSLPLRCSYHLMRGERRPLWEE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MALPPAAAPPGANEPLDKALSALPPEPGGVPLHSPWTFWLDRSLPGATAAECASNLKKIYTVQTVQIFWSVYNNIPPVTSLPLRCSYHLMRGERRPLWEE

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
ESNAKGGVWKMKVPKDSTSTVWKELLLATIGEQFTDCAAADDEIIGVSVSVRDREDVVQVWNVNASLVGEATVLEKIHQLLPHIAFKAVFYKPHEEHHAF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ESNAKGGVWKMKVPKDSTSTVWKELLLATIGEQFTDCAAADDEIIGVSVSVRDREDVVQVWNVNASLVGEATVLEKIHQLLPHIAFKAVFYKPHEEHHAF

-------
EGGRGKH
|||||||
EGGRGKH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	207	0	0	100.0

Content subtype: combined_18663_4b6v.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	1910		99.5 (chain: A, length: 207)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3869 (1)	noe	92.8 (chain: A, length: 207)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	124 (1)	hbond	38.2 (chain: A, length: 207)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	303 (303)	.	85.5 (chain: A, length: 207)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	112 (112)	.	54.1 (chain: A, length: 207)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 207, Sequence coverage: 99.5%
- Total number of assignments
  - ¹H chemical shifts: 1083
  - ¹³C chemical shifts: 620
  - ¹⁵N chemical shifts: 207
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1238	1083	87.5
¹³C chemical shifts	947	620	65.5
¹⁵N chemical shifts	216	207	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	409	399	97.6
¹³C chemical shifts	414	197	47.6
¹⁵N chemical shifts	189	188	99.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	829	684	82.5
¹³C chemical shifts	533	423	79.4
¹⁵N chemical shifts	27	19	70.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	122	98.4
¹³C chemical shifts	124	117	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	104	66	63.5
¹³C chemical shifts	97	44	45.4
¹⁵N chemical shifts	7	7	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 207, Sequence coverage: 92.8%
- Total number of restraints: 3858
- Weight of restraints: 1.0 (3858)
- Potential type of restraints: square-well-parabolic (3858)
- Range of distance target values: 2.75, 4.83 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 207, Sequence coverage: 38.2%
  - Total number of restraints: 124
  - Weight of restraints: 1.0 (124)
  - Potential type of restraints: square-well-parabolic (124)
  - Range of distance target values: 1.9, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 207, Sequence coverage: 85.5%
- Total number of restraints: 303
- Total number of restraints per polymer type: 303
- Weight of restraints: 1.0 (303)
- Potential type of restraints: square-well-parabolic (303)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 207, Sequence coverage: 54.1%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MALPPAAAPPGANEPLDKALSALPPEPGGVPLHSPWTFWLDRSLPGATAAECASNLKKIYTVQTVQIFWSVYNNIPPVTSLPLRCSYHLMRGERRPLWEE
                               ||| || |||  | ||||||||  ||||| | |||      |||   |||  | | |||| ||| ||  
...............................LHS.WT.WLD..L.GATAAECA..LKKIY.V.TVQ......NNI...TSL..R.S.HLMR.ERR.LW..
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
ESNAKGGVWKMKVPKDSTSTVWKELLLATIGEQFTDCAAADDEIIGVSVSVRDREDVVQVWNVNASLVGEATVLEKIHQLLPHIAFKAVFYKPHEEHHAF
||| || ||||   |||||| | ||||| || | | |||||||||||||| |||| ||   ||||||||| ||||| || | ||  |  |||  |     
ESN.KG.VWKM...KDSTST.W.ELLLA.IG.Q.T.CAAADDEIIGVSVS.RDRE.VV...NVNASLVGE.TVLEK.HQ.L.HI..K..FYK..E     
-------110-------120-------130-------140-------150-------160-------170-------180-------190-----     

-------
EGGRGKH

Total number of restraints: 112
Potential type of restraints: undefined (112)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords eIF4E3, m7G cap, NMR, TRANSLATION

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Found 1 Document (3.42 seconds)

BMRB: 18663

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. The third member of the eIF4E family represses gene expression via a novel mode of recognition of the methyl-7 guanosine cap mo, : 1 : 3 : 65 entities Detail

Interaction partners 1. The third member of the eIF4E family represses gene expression via a novel mode of recognition of the methyl-7 guanosine cap mo, : 6 interactors Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 6 contents Detail