Entry STF0026
RNase H domain from HIV-1 reverse transcriptase
Protein information
| Name of the protein: | Gag-Pol polyprotein |
| Organism: | Human immunodeficiency virus type 1 group M subtype B (isolate BH10) |
| Number of residues: | 136 |
| Related UniProt entry: | P03366 (Fragment: 1026 - 1161) |
| Related PDB entry: | 1HRH |
Visualize the data
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Experiment sets
EARLY
Method: Pulse labeling HDX NMR
Conditions: pH 5.5; 25.0 Celsius; Probes: 23
Related publication:
PMID 9792104
Experiment details: "The pulse-labeling hydrogen exchange was carried out in a Bio- Logic SFM4/Q quench flow machine. Continuous flow mode was used for time points at 12, 22, 36, 74, 136, 363, and 636 ms, while the 1, 1.5, and 6 s time points were collected using an interrupted flow technique. Refolding of completely denatured and deuterated RNaseH was initiated by a 1:10 dilution into a protonated folding buffer (20 mM sodium acetate, 50 mM potassium chloride buffer, pHread 5.5). At the specified refolding time points, labeling of amide protons was achieved by a 1:2 dilution with pulse buffer (200 mM tridacetate for a final pHread of 8.0, 8.4, 8.5, 9.0, and also 200 mM glycine for a final PHread of 9.0). After 20 ms, the labeling pulse was quenched by a twofold dilution with 300 mM sodium acetate, pHread 4.5. The sample was immediately put on ice, concentrated in Amicon cells to ~5 mL and the buffer exchanged to 3 mM deuterated sodium acetate in H2O, pHread 4.5."
Protection threshold: P > 10 at 74 ms
Sequence:
YQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPXXXXXGGNEQVDKLVSAGI
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EARLY residues
15: Y;
54: Q;
55: A;
57: Y;
59: A;
68: N;
69: I;
94: Q;
95: I;
98: Q;
99: L;
106: Y;
108: A;
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INTERMEDIATE
Method: Pulse labeling HDX NMR
Conditions: pH 5.5; 25.0 Celsius; Probes: 23
Related publication:
PMID 9792104
Experiment details: "The pulse-labeling hydrogen exchange was carried out in a Bio- Logic SFM4/Q quench flow machine. Continuous flow mode was used for time points at 12, 22, 36, 74, 136, 363, and 636 ms, while the 1, 1.5, and 6 s time points were collected using an interrupted flow technique. Refolding of completely denatured and deuterated RNaseH was initiated by a 1:10 dilution into a protonated folding buffer (20 mM sodium acetate, 50 mM potassium chloride buffer, pHread 5.5). At the specified refolding time points, labeling of amide protons was achieved by a 1:2 dilution with pulse buffer (200 mM tridacetate for a final pHread of 8.0, 8.4, 8.5, 9.0, and also 200 mM glycine for a final PHread of 9.0). After 20 ms, the labeling pulse was quenched by a twofold dilution with 300 mM sodium acetate, pHread 4.5. The sample was immediately put on ice, concentrated in Amicon cells to ~5 mL and the buffer exchanged to 3 mM deuterated sodium acetate in H2O, pHread 4.5."
Protection threshold: 3 < P < 10 at 74 ms
Sequence:
YQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPXXXXXGGNEQVDKLVSAGI
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INTERMEDIATE residues
53: L;
56: I;
58: L;
60: L;
97: E;
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STRONG
Method: Native exchange NMR
Conditions: pH 5.5; 25.0 Celsius; Probes: 112
Related publication:
PMID 9792104
Experiment details: "None"
Protection threshold: exchange less than 5% during the sample preparation and NMR data collection
Sequence:
YQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPXXXXXGGNEQVDKLVSAGI
CLICK TO DOWNLOAD SEQUENCE IN FASTA
STRONG residues
15: Y;
16: V;
53: L;
54: Q;
55: A;
56: I;
57: Y;
58: L;
59: A;
60: L;
67: V;
68: N;
69: I;
70: V;
94: Q;
95: I;
97: E;
98: Q;
99: L;
100: I;
106: Y;
108: A;
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