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NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element
Authors
Doucleff, M., Pelton, J.G., Lee, P.S., Wemmer, D.E.
Assembly
SIGMA-54 RPON DOMAIN-DNA COMPLEX
Entity
1. NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND (polymer, Thiol state: not present), 14 monomers, 4315.733 Da Detail

TTTTGGCACG TTTC


2. NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND (polymer, Thiol state: not present), 14 monomers, 4369.817 Da Detail

GAAACGTGCC AAAA


3. RNA POLYMERASE SIGMA FACTOR RPON (polymer, Thiol state: not present), 63 monomers, 7472.671 Da Detail

HMLTQGELMK LIKEIVENED KRKPYSDQEI ANILKEKGFK VARRTVAKYR EMLGIPSSRE RRI


Total weight
16158.221 Da
Max. entity weight
7472.671 Da
Source organism
Aquifex aeolicus
Exptl. method
solution NMR
Refine. method
docking, rigid-body minimization,
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 100.0 %, Completeness: 81.1 %, Completeness (bb): 79.4 % Detail

Polymer type: polydeoxyribonucleotide polypeptide(L)

Total1H13C15N
All81.1 % (865 of 1067)84.0 % (584 of 695)73.0 % (219 of 300)86.1 % (62 of 72)
Backbone79.4 % (450 of 567)81.6 % (261 of 320)68.8 % (128 of 186)100.0 % (61 of 61)
Sidechain85.4 % (478 of 560)87.2 % (327 of 375)86.2 % (150 of 174) 9.1 % (1 of 11)
Aromatic74.4 % (64 of 86)90.1 % (64 of 71) 0.0 % (0 of 15)
Methyl100.0 % (74 of 74)100.0 % (41 of 41)100.0 % (33 of 33)

1. NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND

TTTTGGCACG TTTC

2. NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND

GAAACGTGCC AAAA

3. RNA POLYMERASE SIGMA FACTOR RPON

HMLTQGELMK LIKEIVENED KRKPYSDQEI ANILKEKGFK VARRTVAKYR EMLGIPSSRE RRI

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA


#NameIsotope labelingTypeConcentration
1NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRANDnatural abundance1 (±0.2) mM
2NIRB SIGMA-54 BINDING SITE TEMPLATE STRANDnatural abundance1 (±0.2) mM
3RNA POLYMERASE SIGMA FACTOR RPON[U-100% 13C; U-100% 15N]1 (±0.2) mM
4HEPES[U-99% 2H]10 (±0.1) mM
5EDTAnatural abundance1 (±0.1) mM
6NaClnatural abundance250 (±0.1) mM
Sample #2

Solvent system 90% H2O; 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA


#NameIsotope labelingTypeConcentration
7NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRANDnatural abundance1 (±0.2) mM
8NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRANDnatural abundance1 (±0.2) mM
9RNA POLYMERASE SIGMA FACTOR RPON[U-100% 13C; U-100% 15N]1 (±0.2) mM
10HEPESnatural abundance10 (±0.1) mM
11EDTAnatural abundance1 (±0.1) mM
12NaClnatural abundance250 (±0.2) mM
Sample #3

Solvent system 90% H2O; 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA


#NameIsotope labelingTypeConcentration
13NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRANDnatural abundance1 (±0.2) mM
14NIRB SIGMA-54 BINDING SITE TEMPLATE STRANDnatural abundance1 (±0.2) mM
15RNA POLYMERASE SIGMA FACTOR RPONnatural abundance1 (±0.2) mM
16HEPESnatural abundance10 (±0.1) mM
17EDTAnatural abundance1 (±0.1) mM
18NaClnatural abundance250 (±0.1) mM

Protein Blocks Logo
Calculated from 20 models in PDB: 2O8K, Strand ID: A Detail


Release date
2007-10-16
Citation
Structural basis of DNA recognition by the alternative sigma-factor, sigma54
Doucleff, M., Pelton, J.G., Lee, P.S., Nixon, B.T., Wemmer, D.E.
J. Mol. Biol. (2007), 369, 1070-1078, PubMed 17481658 , DOI 10.1016/j.jmb.2007.04.019 ,
Related entities 3. RNA POLYMERASE SIGMA FACTOR RPON, : 1 : 1 : 2 : 52 entities Detail
Keywords HELIX-TURN-HELIX, PROTEIN-DNA COMPLEX, RNA POLYMERASE, SIGMA-54, TRANSCRIPTION FACTOR