BMRB Entry 18092

Name: Solution structure of the N-terminal domain of human polypeptide chain release factor eRF1
Published: 2012-05-22

Click here to enlarge.

PDB ID: 2llx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18092
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title: Solution structure of the N-terminal domain of human polypeptide chain release factor eRF1 PubMed: 22517631

Deposition date: 2011-11-21 Original release date: 2012-05-22

Authors: Polshakov, Vladimir; Eliseev, Boris; Birdsall, Berry; Frolova, Ludmila

Citation: Polshakov, Vladimir; Eliseev, Boris; Birdsall, Berry; Frolova, Ludmila Yu. "Structure and dynamics in solution of the stop codon decoding N-terminal domain of the human polypeptide chain release factor eRF1." Protein Sci. 21, 896-903 (2012).

Assembly members:
NeRF1, polymer, 150 residues, 15698.317 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
NeRF1: MADDPSAADRNVEIWKIKKL IKSLEAARGNGTSMISLIIP PKDQISRVAKMLADEFGTAS NIKSRVNRLSVLGAITSVQQ RLKLYNKVPPNGLVVYCGTI VTEEGKEKKVNIDFEPFKPI NTSLYLCDNKFHTEALTALL SDLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1

Data type	Count
13C chemical shifts	522
15N chemical shifts	152
1H chemical shifts	1023
heteronuclear NOE values	123
T1 relaxation values	125
T2 relaxation values	125

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	NeRF1	1

Entities:

Entity 1, NeRF1 150 residues - 15698.317 Da.

1	MET	ALA	ASP	ASP	PRO	SER	ALA	ALA	ASP	ARG
2	ASN	VAL	GLU	ILE	TRP	LYS	ILE	LYS	LYS	LEU
3	ILE	LYS	SER	LEU	GLU	ALA	ALA	ARG	GLY	ASN
4	GLY	THR	SER	MET	ILE	SER	LEU	ILE	ILE	PRO
5	PRO	LYS	ASP	GLN	ILE	SER	ARG	VAL	ALA	LYS
6	MET	LEU	ALA	ASP	GLU	PHE	GLY	THR	ALA	SER
7	ASN	ILE	LYS	SER	ARG	VAL	ASN	ARG	LEU	SER
8	VAL	LEU	GLY	ALA	ILE	THR	SER	VAL	GLN	GLN
9	ARG	LEU	LYS	LEU	TYR	ASN	LYS	VAL	PRO	PRO
10	ASN	GLY	LEU	VAL	VAL	TYR	CYS	GLY	THR	ILE
11	VAL	THR	GLU	GLU	GLY	LYS	GLU	LYS	LYS	VAL
12	ASN	ILE	ASP	PHE	GLU	PRO	PHE	LYS	PRO	ILE
13	ASN	THR	SER	LEU	TYR	LEU	CYS	ASP	ASN	LYS
14	PHE	HIS	THR	GLU	ALA	LEU	THR	ALA	LEU	LEU
15	SER	ASP	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

Samples:

sample_13C15N_H2O: NeRF1, [U-99% 13C; U-99% 15N], 1 mM; sodium chloride 25 mM; sodium phosphate 10 mM; beta-mercaptoethanol 2 mM; sodium azide 0.01%; H2O 90%; D2O 10%

sample_13C15N_D2O: NeRF1, [U-99% 13C; U-99% 15N], 1 mM; sodium chloride 25 mM; sodium phosphate 10 mM; beta-mercaptoethanol 2 mM; sodium azide 0.01%; D2O 100%

sample_unl_D2O: NeRF1 1 mM; sodium chloride 25 mM; sodium phosphate 10 mM; beta-mercaptoethanol 2 mM; sodium azide 0.01%; D2O 100%

sample_15N_H2O: NeRF1, [U-99% 15N], 1 mM; sodium chloride 25 mM; sodium phosphate 10 mM; beta-mercaptoethanol 2 mM; sodium azide 0.01%; H2O 90%; D2O 10%

sample_15N_aniso: NeRF1, [U-99% 15N], 1 mM; sodium chloride 25 mM; sodium phosphate 10 mM; beta-mercaptoethanol 2 mM; sodium azide 0.01%; C12E5 5.00%; hexanol 1.068%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.035 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_15N_H2O	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_13C15N_H2O	isotropic	sample_conditions_1
2D DQF-COSY	sample_unl_D2O	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_unl_D2O	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_13C15N_H2O	isotropic	sample_conditions_1
3D HNCO	sample_13C15N_H2O	isotropic	sample_conditions_1
3D HNCACB	sample_13C15N_H2O	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_13C15N_H2O	isotropic	sample_conditions_1
3D HNHA	sample_15N_H2O	isotropic	sample_conditions_1
3D HNHB	sample_15N_H2O	isotropic	sample_conditions_1
3D H(CCO)NH	sample_13C15N_H2O	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_13C15N_D2O	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_15N_H2O	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_13C15N_D2O	isotropic	sample_conditions_1
2D IPAP	sample_15N_aniso	anisotropic	sample_conditions_1
2D J-modulated 1H-15N HSQC	sample_15N_H2O	isotropic	sample_conditions_1
15N{1H} NOE	sample_15N_H2O	isotropic	sample_conditions_1
15N T1	sample_15N_H2O	isotropic	sample_conditions_1
15N T2	sample_15N_H2O	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

VNMR, Varian - collection

NMRPipe v5.99, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.114, Goddard - data analysis

TALOS, Cornilescu, Delaglio and Bax - data analysis

AngleSearch v2.10, Polshakov, Feeney - data analysis

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMRest v0.99, Polshakov - data analysis

Relax v0.99, Polshakov - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

InsightII v2000, Accelrys Software Inc. - data analysis

NMR spectrometers:

Varian INOVA 800 MHz
Varian INOVA 600 MHz
Bruker Avance 600 MHz
Bruker Avance 600 MHz

BMRB	17822 19506 25016 25020
PDB	1DT9 2LGT 2LLX 2MQ6 2MQ9 3E1Y 3J5Y 4D5N 4D61
DBJ	BAA85489 BAC33839 BAE31210 BAE31619 BAE37589
EMBL	CAA37987 CAA57281 CAA57282 CAA78620 CAF90786
GB	AAA36665 AAB49726 AAD43966 AAH13717 AAH14269
REF	NP_001008345 NP_001069722 NP_001076236 NP_001084363 NP_001126989
SP	P35615 P62495 P62496 P62497 P62498
TPG	DAA27419

Biological Magnetic Resonance Data Bank