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BMRB: 19716

2MJC

Zn-binding domain of eukaryotic translation initiation factor 3, subunit G

Authors

Al-Abdul-Wahid, M., Menade, M., Xie, J., Kozlov, G., Gehring, K.

Assembly

Zn-binding domain of eukaryotic translation initiation factor 3, subunit G

Entity

1. eif3G Zn (polymer, Thiol state: all free), 24 monomers, 2781.239 Da Detail

KIVSCRICKG DHWTTRCPYK DTLG

2. ZINC ION (non-polymer), 65.409 Da

Total weight

2846.648 Da

Max. entity weight

2781.239 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.9 %, Completeness (bb): 82.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.9 % (233 of 281)	88.4 % (130 of 147)	71.8 % (79 of 110)	100.0 % (24 of 24)
Backbone	82.4 % (117 of 142)	98.0 % (48 of 49)	65.7 % (46 of 70)	100.0 % (23 of 23)
Sidechain	85.1 % (137 of 161)	83.7 % (82 of 98)	87.1 % (54 of 62)	100.0 % (1 of 1)
Aromatic	83.3 % (20 of 24)	83.3 % (10 of 12)	81.8 % (9 of 11)	100.0 % (1 of 1)
Methyl	100.0 % (22 of 22)	100.0 % (11 of 11)	100.0 % (11 of 11)

1. eif3G Zn

KIVSCRICKG DHWTTRCPYK DTLG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±.2) K, pH 6.3 (±1)

#	Name	Isotope labeling	Type	Concentration
1	eif3G_Zn	natural abundance		10 mM
2	HEPES	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	zinc chloride	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2MJC, Strand ID: A Detail

Release date

2015-01-04

Citation

Solution NMR structure of the Zn-binding domain of eukaryotic translation initiation factor 3, subunit G
Al-Abdul-Wahid, M., Menade, M., Xie, J., Kozlov, G., Gehring, K.
Proteins: Struct. Funct. Genet.

Related entities 1. eif3G Zn, : 1 : 12 : 71 entities Detail

Interaction partners 1. eif3G Zn, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±.2) K, pH 6.3 (±1)

#	Name	Isotope labeling	Type	Concentration
1	eif3G_Zn	natural abundance		10 mM
2	HEPES	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	zinc chloride	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±.2) K, pH 6.3 (±1)

#	Name	Isotope labeling	Type	Concentration
1	eif3G_Zn	natural abundance		10 mM
2	HEPES	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	zinc chloride	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±.2) K, pH 6.3 (±1)

#	Name	Isotope labeling	Type	Concentration
1	eif3G_Zn	natural abundance		10 mM
2	HEPES	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	zinc chloride	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±.2) K, pH 6.3 (±1)

#	Name	Isotope labeling	Type	Concentration
1	eif3G_Zn	natural abundance		10 mM
2	HEPES	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	zinc chloride	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D HNHB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±.2) K, pH 6.3 (±1)

#	Name	Isotope labeling	Type	Concentration
1	eif3G_Zn	natural abundance		10 mM
2	HEPES	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	zinc chloride	natural abundance		1 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 (±.2) K, pH 6.3 (±1)

#	Name	Isotope labeling	Type	Concentration
1	eif3G_Zn	natural abundance		10 mM
2	HEPES	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	zinc chloride	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±.2) K, pH 6.3 (±1)

#	Name	Isotope labeling	Type	Concentration
1	eif3G_Zn	natural abundance		10 mM
2	HEPES	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	zinc chloride	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±.2) K, pH 6.3 (±1)

#	Name	Isotope labeling	Type	Concentration
1	eif3G_Zn	natural abundance		10 mM
2	HEPES	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	zinc chloride	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19716_2mjc.nef
Input source #2: Coordindates	2mjc.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:15:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:19:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:24:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:12:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

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

-------10--------20--------30-----
PLGSKGQKIVSCRICKGDHWTTRCPYKDTLGPMQ
||||||||||||||||||||||||||||||||||
PLGSKGQKIVSCRICKGDHWTTRCPYKDTLGPMQ
--------10--------20--------30----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	34	0	0	100.0

Content subtype: combined_19716_2mjc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	213		64.7 (chain: A, length: 34)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	823 (1)	noe	64.7 (chain: A, length: 34)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	6 (1)	undefined	11.8 (chain: A, length: 34)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	22 (22)	.	55.9 (chain: A, length: 34)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 64.7%
- Total number of assignments
  - ¹H chemical shifts: 119
  - ¹³C chemical shifts: 72
  - ¹⁵N chemical shifts: 22
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 64.7%
- Total number of restraints: 797
- Weight of restraints: 1.0 (797)
- Potential type of restraints: square-well-parabolic (797)
- Range of distance target values: 2.4, 3.65 (Å)
- Histogram of distance target values
- Histogram of discrepancy in 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: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 11.8%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: square-well-parabolic (6)
  - Range of distance target values: 3.85, 3.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - 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: 34, Sequence coverage: 55.9%
- Total number of restraints: 22
- Total number of restraints per polymer type: 22
- Weight of restraints: 1.0 (22)
- Potential type of restraints: square-well-parabolic (22)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords eif3, eukaryotic translation initiation factor, zinc-binding domain