BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18092

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

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:
Data typeCount
13C chemical shifts522
15N chemical shifts152
1H chemical shifts1023
heteronuclear NOE values123
T1 relaxation values125
T2 relaxation values125

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1NeRF11

Entities:

Entity 1, NeRF1 150 residues - 15698.317 Da.

1   METALAASPASPPROSERALAALAASPARG
2   ASNVALGLUILETRPLYSILELYSLYSLEU
3   ILELYSSERLEUGLUALAALAARGGLYASN
4   GLYTHRSERMETILESERLEUILEILEPRO
5   PROLYSASPGLNILESERARGVALALALYS
6   METLEUALAASPGLUPHEGLYTHRALASER
7   ASNILELYSSERARGVALASNARGLEUSER
8   VALLEUGLYALAILETHRSERVALGLNGLN
9   ARGLEULYSLEUTYRASNLYSVALPROPRO
10   ASNGLYLEUVALVALTYRCYSGLYTHRILE
11   VALTHRGLUGLUGLYLYSGLULYSLYSVAL
12   ASNILEASPPHEGLUPROPHELYSPROILE
13   ASNTHRSERLEUTYRLEUCYSASPASNLYS
14   PHEHISTHRGLUALALEUTHRALALEULEU
15   SERASPLEUGLUHISHISHISHISHISHIS

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_15N_H2Oisotropicsample_conditions_1
2D 1H-13C HSQCsample_13C15N_H2Oisotropicsample_conditions_1
2D DQF-COSYsample_unl_D2Oisotropicsample_conditions_1
2D 1H-1H NOESYsample_unl_D2Oisotropicsample_conditions_1
3D CBCA(CO)NHsample_13C15N_H2Oisotropicsample_conditions_1
3D HNCOsample_13C15N_H2Oisotropicsample_conditions_1
3D HNCACBsample_13C15N_H2Oisotropicsample_conditions_1
3D HBHA(CO)NHsample_13C15N_H2Oisotropicsample_conditions_1
3D HNHAsample_15N_H2Oisotropicsample_conditions_1
3D HNHBsample_15N_H2Oisotropicsample_conditions_1
3D H(CCO)NHsample_13C15N_H2Oisotropicsample_conditions_1
3D HCCH-TOCSYsample_13C15N_D2Oisotropicsample_conditions_1
3D 1H-15N NOESYsample_15N_H2Oisotropicsample_conditions_1
3D 1H-13C NOESYsample_13C15N_D2Oisotropicsample_conditions_1
2D IPAPsample_15N_anisoanisotropicsample_conditions_1
2D J-modulated 1H-15N HSQCsample_15N_H2Oisotropicsample_conditions_1
15N{1H} NOEsample_15N_H2Oisotropicsample_conditions_1
15N T1sample_15N_H2Oisotropicsample_conditions_1
15N T2sample_15N_H2Oisotropicsample_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

Related Database Links:

BMRB 17822 19506 25016 25020
PDB
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