Start2Fold

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

Entry STF0009

C-terminal domain of rat CD2 (CD2.D1)

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Protein information

Name of the protein: T-cell surface antigen CD2
Organism: Rattus norvegicus (Rat)
Number of residues: 98
Related UniProt entry:   P08921 (Fragment: 23 - 121)
Related PDB entry:   1A64

Visualize the data

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Experiment sets

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EARLY

Method: HDX-folding competition by NMR

Conditions: pH 6.0-10.0; 25.0 Celsius; Probes: 42

Related publication:
 PMID 9341233

Experiment details: "A 0.5 mL amount of a 2 mM sample of 15N-labeled CD2.D1 in H2O, containing 2.8 M GuHCl, was mixed against 8.3 vol of D2O, containing 25 mM sodium borate and 25 mM NaH2PO4, at the appropriate pH (not corrected), and 0.448 M Na2SO4, at 25C in a custom-built, rapid mixing device with a dead time of 2-3 ms (gives final concentrations of Na2SO4 and GuHCl of 0.4 and 0.3 M, respectively). Exchange was then quenched by the rapid addition (delay time = 2 s) of 6 mL of ice-cold D2O containing 100 mM sodium d3-acetate, pH 4.0."

Protection threshold: ln(P) > 1.0

Sequence: RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRK__PFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE
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EARLY residues

8: G; 28: D; 31: R; 34: R; 42: F; 55: F; 56: E; 61: G; 62: D; 65: I; 74: G; 76: Y; 77: N; 78: V; 79: T; 80: V; 82: S; 91: K; 94: D;
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INTERMEDIATE

Method: HDX-folding competition by NMR

Conditions: pH 6.0-10.0; 25.0 Celsius; Probes: 42

Related publication:
 PMID 9341233

Experiment details: "A 0.5 mL amount of a 2 mM sample of 15N-labeled CD2.D1 in H2O, containing 2.8 M GuHCl, was mixed against 8.3 vol of D2O, containing 25 mM sodium borate and 25 mM NaH2PO4, at the appropriate pH (not corrected), and 0.448 M Na2SO4, at 25C in a custom-built, rapid mixing device with a dead time of 2-3 ms (gives final concentrations of Na2SO4 and GuHCl of 0.4 and 0.3 M, respectively). Exchange was then quenched by the rapid addition (delay time = 2 s) of 6 mL of ice-cold D2O containing 100 mM sodium d3-acetate, pH 4.0."

Protection threshold: 0.5 < ln(P) < 1.0

Sequence: RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRK__PFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

INTERMEDIATE residues

14: I; 32: W; 40: A; 41: E; 58: L; 63: L; 64: K; 68: L; 72: D; 81: Y; 93: L;
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LATE

Method: HDX-folding competition by NMR

Conditions: pH 6.0-10.0; 25.0 Celsius; Probes: 42

Related publication:
 PMID 9341233

Experiment details: "A 0.5 mL amount of a 2 mM sample of 15N-labeled CD2.D1 in H2O, containing 2.8 M GuHCl, was mixed against 8.3 vol of D2O, containing 25 mM sodium borate and 25 mM NaH2PO4, at the appropriate pH (not corrected), and 0.448 M Na2SO4, at 25C in a custom-built, rapid mixing device with a dead time of 2-3 ms (gives final concentrations of Na2SO4 and GuHCl of 0.4 and 0.3 M, respectively). Exchange was then quenched by the rapid addition (delay time = 2 s) of 6 mL of ice-cold D2O containing 100 mM sodium d3-acetate, pH 4.0."

Protection threshold: 0 < ln(P) < 0.5

Sequence: RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRK__PFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE
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LATE residues

16: L; 30: V; 57: I; 88: I; 95: L;
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STRONG

Method: Native exchange NMR

Conditions: pH 5.5; 25.0 Celsius; Probes: 35

Related publication:
 PMID 11152615

Experiment details: "Freeze-dried 15N-labeled CD2.D1 was dissolved to a concentration of 0.5 mM in D2O, containing 25 mM KH2PO4 (pH* 5.5), 0.2 M Na2SO4, 0.02% sodium azide and the appropriate concentration of Gu2HCl. For each concentration of Gu2HCl, a series of 1H-15N heteronuclear single quantum coherence (HSQC) spectra were acquired at appropriate time intervals in a 500 MHz spectrometer at 25 °C."

Protection threshold: ΔG1 > 6.5

Sequence: RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRK__PFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

STRONG residues

14: I; 16: L; 30: V; 31: R; 32: W; 33: E; 62: D; 63: L; 64: K; 65: I; 76: Y; 77: N; 78: V; 79: T; 80: V; 81: Y; 93: L; 95: L;
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MEDIUM

Method: Native exchange NMR

Conditions: pH 5.5; 25.0 Celsius; Probes: 35

Related publication:
 PMID 11152615

Experiment details: "Freeze-dried 15N-labeled CD2.D1 was dissolved to a concentration of 0.5 mM in D2O, containing 25 mM KH2PO4 (pH* 5.5), 0.2 M Na2SO4, 0.02% sodium azide and the appropriate concentration of Gu2HCl. For each concentration of Gu2HCl, a series of 1H-15N heteronuclear single quantum coherence (HSQC) spectra were acquired at appropriate time intervals in a 500 MHz spectrometer at 25 °C."

Protection threshold: 4 < ΔG1 < 6.5

Sequence: RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRK__PFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

MEDIUM residues

8: G; 29: E; 34: R; 37: T; 40: A; 42: F; 56: E; 58: L; 61: G; 74: G; 94: D;
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