Start2Fold

The database of hydrogen/deuterium exchange data on protein folding and stability

Entry STF0027

Ubiquitin

 DOWNLOAD ENTRY IN XML

Protein information

Name of the protein: Polyubiquitin-C
Organism: Homo sapiens (Human)
Number of residues: 76
Related UniProt entry:   P0CG48 (Fragment: 609 - 684)
Related PDB entry:   1UBQ

Visualize the data

 Click here or on the image on the right to visualize the residues using JSmol. Warning: JSmol is known to load slowly on certain browsers, depending on the size of the macromolecule. The applet is optimized for Chrome, other browsers have limited support.

Experiment sets

 Show  Hide

EARLY

Method: Pulse labeling HDX NMR

Conditions: pH 5.0; 25.0 Celsius; Probes: 26

Related publication:
 PMID 1312711

Experiment details: "Refolding was initiated by rapid 6-fold dilution with 50 mM acetic acid at pH 5.5 in H2O (or D2O for folding times >1 s). The final pH of the mixture was 5.0, as determined in a separate control. The resulting GdnHCI concentration, 1.0 M, is well below the refolding transition. After the desired refolding time, the labeling pulse was initiated by mixing the protein with an equal volume of 100 mM glycine in H2O at pH 9.75, to give a final pH of 9.4. The pulse was terminated after 31 ms by mixing with an equal volume of 500 mM acetic acid at pH 2.6, yielding a final pH of 3.4."

Protection threshold: at least 80% protection in 8 ms

Sequence: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

EARLY residues

3: I; 4: F; 5: V; 6: K; 13: I; 16: E; 17: V; 21: D; 23: I; 26: V; 28: A; 29: K; 30: I; 41: Q; 42: R; 44: I; 45: F; 50: L; 55: T; 56: L; 65: S; 67: L; 70: V;
 CLICK TO DOWNLOAD LIST OF RESIDUES

 Show  Hide

LATE

Method: Pulse labeling HDX NMR

Conditions: pH 5.0; 25.0 Celsius; Probes: 26

Related publication:
 PMID 1312711

Experiment details: "Refolding was initiated by rapid 6-fold dilution with 50 mM acetic acid at pH 5.5 in H2O (or D2O for folding times >1 s). The final pH of the mixture was 5.0, as determined in a separate control. The resulting GdnHCI concentration, 1.0 M, is well below the refolding transition. After the desired refolding time, the labeling pulse was initiated by mixing the protein with an equal volume of 100 mM glycine in H2O at pH 9.75, to give a final pH of 9.4. The pulse was terminated after 31 ms by mixing with an equal volume of 500 mM acetic acid at pH 2.6, yielding a final pH of 3.4."

Protection threshold: 80% protection over 10 ms

Sequence: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

LATE residues

59: Y; 61: I; 69: L;
 CLICK TO DOWNLOAD LIST OF RESIDUES

 Show  Hide

STRONG

Method: Native exchange NMR

Conditions: pH 3.5; 22.0 Celsius; Probes: all

Related publication:
 PMID 1332757

Experiment details: "None"

Protection threshold: amides which persist exchange

Sequence: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

STRONG residues

3: I; 4: F; 5: V; 7: T; 17: V; 23: I; 26: V; 28: A; 29: K; 30: I; 44: I; 56: L; 59: Y;
 CLICK TO DOWNLOAD LIST OF RESIDUES