Partial unfolding of diverse SH3 domains on a wide timescale.


Abstract

SH3 domains are small, modular domains that are found in many proteins, especially signal transduction proteins such as tyrosine kinases. While much is known about the sequences and tertiary structures of SH3 domains, far less is known about their solution dynamics. A slow, partial unfolding event that occurs under physiological conditions was previously identified in the Hck SH3 domain using hydrogen exchange (HX) mass spectrometry (MS). To determine if this unfolding was unique to Hck SH3, HX MS was used to analyze 11 other SH3 domains: seven SH3 domains from Src-family kinases and five SH3 domains from various proteins. A wide variety of unfolding rates were found, with unfolding half-lives ranging from 1s to 1h. The Lyn and alpha-spectrin SH3 domains exhibited slow, partial unfolding in beta strands D and E and part of the RT-loop. Hck SH3 also underwent partial unfolding in the same region, implying that a unique feature in this area of the domains is responsible for the partial unfolding. Partial unfolding was, however, not a function of sequence conservation. Although the Fyn and Yes SH3 domains are very similar to Hck SH3 in sequence, they exhibited no evidence of partial unfolding. Overall, the results suggest that while the tertiary structure of SH3 domains is highly conserved, the dynamics of SH3 domains are variable. Study holds ProTherm entries: 22139, 22140, 22141 Extra Details: SH3 domain hydrogen exchange; mass spectrometry; protein dynamics; Src-family kinases

Submission Details

ID: gdYd9VaR

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:53 p.m.

Version: 1

Publication Details
Wales TE;Engen JR,J. Mol. Biol. (2006) Partial unfolding of diverse SH3 domains on a wide timescale. PMID:16487539
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
2JMA 2007-04-24 R21A Spc-SH3:P41 complex
2ROT 2009-04-28 Structure of chimeric variant of SH3 domain- SHH
5HCK 1998-06-17 HUMAN HCK SH3 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE
2JMC 2007-04-24 Chimer between Spc-SH3 and P41
2JM8 2007-04-24 R21A Spc-SH3 free
1AEY 1997-05-15 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, SOLUTION NMR, 15 STRUCTURES
2JM9 2007-04-24 R21A Spc-SH3 bound
1AJ3 1997-07-07 SOLUTION STRUCTURE OF THE SPECTRIN REPEAT, NMR, 20 STRUCTURES
2KR3 2010-09-15 Solution structure of SHA-D
2RMO 2008-09-30 Solution structure of alpha-spectrin_SH3-bergerac from Chicken
2OI3 2007-02-20 NMR Structure Analysis of the Hematopoetic Cell Kinase SH3 Domain complexed with an artificial high affinity ligand (PD1)
2OJ2 2007-01-30 NMR Structure Analysis of the Hematopoetic Cell Kinase SH3 Domain complexed with an artificial high affinity ligand (PD1)
1W1F 2005-07-06 SH3 DOMAIN OF HUMAN LYN TYROSINE KINASE
4HCK 1998-06-17 HUMAN HCK SH3 DOMAIN, NMR, 25 STRUCTURES
2KXD 2011-04-20 The structure of SH3-F2
3HCK 1997-10-15 NMR ensemble of the uncomplexed human HCK SH2 domain, 20 structures
1WA7 2005-07-07 SH3 DOMAIN OF HUMAN LYN TYROSINE KINASE IN COMPLEX WITH A HERPESVIRAL LIGAND
2LJ3 2011-12-07 PFBD: High-throughput Strategy of Backbone fold Determination for small well-folded proteins in less than a day
1M8M 2002-11-20 SOLID-STATE MAS NMR STRUCTURE OF THE A-SPECTRIN SH3 DOMAIN
3NGP 2010-09-08 1.08 High resolution structure of alpha-spectrin SH3 domain mutant with a redesigned core
3M0U 2011-01-19 1.1 Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Hexagonal crystal obtained in sodium formate at pH 6.5.
3M0R 2011-01-19 1.1 Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Crystal obtained in ammonium sulphate at pH 6.
1G2B 2000-11-01 1.12 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT N47-D48
6NMW 2019-04-17 1.2 Crystal structure of the human Lyn SH3 domain
5IHK 2017-03-29 1.35 Crystal Structure of the alpha spectrin SH3 domain mutant N47A
5FWC 2016-12-28 1.4 Human Spectrin SH3 domain D48G, E7A, K60A
3I9Q 2009-12-15 1.45 Crystal Structure of the triple mutant S19G-P20D-R21S of alpha spectrin SH3 domain
5IHI 2017-03-29 1.45 Crystal Structure of the alpha spectrin SH3 domain double mutant V46G-D48G
1U06 2005-01-13 1.49 crystal structure of chicken alpha-spectrin SH3 domain
5IHN 2017-03-29 1.5 Crystal Structure of the alpha spectrin SH3 domain mutant N47G
5FWB 2016-12-28 1.5 Human Spectrin SH3 domain D48G, E7F, K60F
4F17 2013-05-08 1.55 Crystal Structure of the alpha spectrin SH3 domain at pH 9
5FW9 2016-12-28 1.55 Human Spectrin SH3 domain D48G, E7Y, K60Y
2F2X 2006-10-31 1.6 alpha-spectrin SH3 domain R21G mutant
3M0S 2011-01-19 1.6 Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Crystal obtained in ammonium sulphate at pH 7
5H0B 2017-10-11 1.65 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-4-methylpentanoic acid
3THK 2011-11-23 1.7 Structure of SH3 chimera with a type II ligand linked to the chain C-terminal
2F2W 2006-10-31 1.7 alpha-spectrin SH3 domain R21A mutant
3M0T 2011-01-19 1.7 Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Crystal obtained in ammonium sulphate at pH 9.
5ZJ6 2018-06-06 1.7 Crystal structure of HCK kinase complexed with a pyrrolo-pyrimidine inhibitor 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
5H0H 2017-10-04 1.72 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-N,N,4-trimethylpentanamide
3M0Q 2011-01-19 1.75 Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Crystal obtained in ammonium sulphate at pH 5.
1TUD 1996-08-01 1.77 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT N47-D48
1PWT 1999-05-11 1.77 THERMODYNAMIC ANALYSIS OF ALPHA-SPECTRIN SH3 AND TWO OF ITS CIRCULAR PERMUTANTS WITH DIFFERENT LOOP LENGTHS: DISCERNING THE REASONS FOR RAPID FOLDING IN PROTEINS
5H0G 2017-10-04 1.8 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-N,4-dimethylpentanamide
1SHG 1993-10-31 1.8 CRYSTAL STRUCTURE OF A SRC-HOMOLOGY 3 (SH3) DOMAIN
1QKX 2000-12-15 1.8 Alpha-spectrin Src Homology 3 domain, N47A mutant in the distal loop.
2NUZ 2007-05-15 1.85 crystal structure of alpha spectrin SH3 domain measured at room temperature
2F2V 2006-10-31 1.85 alpha-spectrin SH3 domain A56G mutant
4U5W 2014-08-20 1.86 Crystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains
2OAW 2008-04-08 1.9 Structure of SHH variant of 'Bergerac' chimera of spectrin SH3
4F16 2013-05-08 1.93 Crystal Structure of the alpha spectrin SH3 domain at pH 5
5H09 2017-10-04 1.95 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-ethyl2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-4-methylpentanoate
1HD3 2001-11-01 1.98 A-SPECTRIN SH3 DOMAIN F52Y MUTANT
4ORZ 2014-03-26 2.0 HIV-1 Nef protein in complex with single domain antibody sdAb19 and an engineered Hck SH3 domain
1U5P 2004-10-19 2.0 Crystal Structure of Repeats 15 and 16 of Chicken Brain Alpha Spectrin
1QCF 1999-06-08 2.0 CRYSTAL STRUCTURE OF HCK IN COMPLEX WITH A SRC FAMILY-SELECTIVE TYROSINE KINASE INHIBITOR
2HK5 2006-09-05 2.0 Hck Kinase in Complex with Lck targetted Inhibitor PG-1009247
3REA 2011-06-01 2.0 HIV-1 Nef protein in complex with engineered Hck-SH3 domain
1CUN 1999-10-06 2.0 CRYSTAL STRUCTURE OF REPEATS 16 AND 17 OF CHICKEN BRAIN ALPHA SPECTRIN
1QKW 2000-08-18 2.0 Alpha-spectrin Src Homology 3 domain, N47G mutant in the distal loop.
1BK2 1999-02-16 2.01 A-SPECTRIN SH3 DOMAIN D48G MUTANT
1E6H 2002-05-23 2.01 A-SPECTRIN SH3 DOMAIN A11V, M25I, V44I, V58L MUTANTS
1TUC 1996-08-01 2.02 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT S19-P20
4TZI 2015-01-21 2.1 Structure of unliganded Lyn SH2 domain
5H0E 2017-10-04 2.1 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-4-methylpentanamide
2C0T 2006-09-20 2.15 Src family kinase Hck with bound inhibitor A-641359
3VS3 2013-05-01 2.17 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
3VRZ 2013-05-01 2.22 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 1-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]-3-benzylurea
3F31 2009-10-13 2.3 Crystal Structure of the N-terminal region of AlphaII-spectrin Tetramerization Domain
1E6G 2002-05-23 2.3 A-SPECTRIN SH3 DOMAIN A11V, V23L, M25I, V53I, V58L MUTANT
1NEG 2003-01-14 2.3 Crystal Structure Analysis of N-and C-terminal labeled SH3-domain of alpha-Chicken Spectrin
2C0I 2006-09-20 2.3 Src family kinase Hck with bound inhibitor A-420983
3FB2 2008-11-25 2.3 Crystal structure of the human brain alpha spectrin repeats 15 and 16. Northeast Structural Genomics Consortium target HR5563a.
3RBB 2011-04-27 2.35 HIV-1 NEF protein in complex with engineered HCK SH3 domain
3VS6 2013-05-01 2.37 Crystal structure of HCK complexed with a pyrazolo-pyrimidine inhibitor tert-butyl {4-[4-amino-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]-2-methoxyphenyl}carbamate
2FOT 2006-09-05 2.45 Crystal structure of the complex between calmodulin and alphaII-spectrin
3VS1 2013-05-01 2.46 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 1-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]-3-phenylurea
3VRY 2013-05-01 2.48 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 4-Amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl-cyclopentane
1U4Q 2004-10-19 2.5 Crystal Structure of Repeats 15, 16 and 17 of Chicken Brain Alpha Spectrin
2ZV7 2008-11-11 2.5 Lyn Tyrosine Kinase Domain, apo form
2CDT 2007-02-20 2.54 alpha-SPECTRIN SH3 DOMAIN A56S MUTANT
2ZVA 2008-11-11 2.6 Lyn Tyrosine Kinase Domain-Dasatinib complex
1UUE 2004-02-19 2.6 a-SPECTRIN SH3 DOMAIN (V44T, D48G MUTANT)
1AD5 1997-05-15 2.6 SRC FAMILY KINASE HCK-AMP-PNP COMPLEX
3M0P 2011-01-19 2.6 Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Crystal obtained in ammonium sulphate at pH 4.
1BU1 1998-11-11 2.6 SRC FAMILY KINASE HCK SH3 DOMAIN
3VS2 2013-05-01 2.61 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 7-[cis-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
3NHN 2010-09-01 2.61 Crystal structure of the SRC-family kinase HCK SH3-SH2-linker regulatory region
5XY1 2017-08-02 2.7 Crystal structure of Lyn kinase domain in complex with N-(1H-indazol-6-yl)-8-(piperidin-4-yloxy)-6-propylquinazolin-2-amine
1H8K 2002-05-23 2.7 A-SPECTRIN SH3 DOMAIN A11V, V23L, M25V, V53I, V58L MUTANT
2ZV8 2008-11-11 2.7 Lyn Tyrosine Kinase Domain-AMP-PNP complex
3VS4 2013-05-01 2.75 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 5-(4-phenoxyphenyl)-7-(tetrahydro-2H-pyran-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
2ZV9 2008-11-11 2.76 Lyn Tyrosine Kinase Domain-PP2 complex
5NUH 2017-08-16 2.78 Crystal structure of SIVmac239 Nef bound to an engineered Hck SH3 domain
2C0O 2006-09-20 2.85 Src family kinase Hck with bound inhibitor A-770041
3VS5 2013-05-01 2.85 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor 7-(1-methylpiperidin-4-yl)-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
4LUD 2014-02-12 2.85 Crystal Structure of HCK in complex with the fluorescent compound SKF86002
3VS0 2013-05-01 2.93 Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor N-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]benzamide
3A4O 2009-12-08 3.0 Lyn kinase domain
2HCK 1997-08-20 3.0 SRC FAMILY KINASE HCK-QUERCETIN COMPLEX
3VS7 2013-05-01 3.0 Crystal structure of HCK complexed with a pyrazolo-pyrimidine inhibitor 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
4LUE 2014-02-12 3.04 Crystal Structure of HCK in complex with 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (resulting from displacement of SKF86002)
1E7O 2003-05-21 3.2 A-SPECTRIN SH3 DOMAIN A11V, V23L, M25V, V44I, V58L MUTATIONS
3REB 2011-06-01 3.45 HIV-1 Nef protein in complex with engineered Hck-SH3 domain
5M6S 2017-01-11 4.8 folding intermediate of spectrin R16

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Spectrin alpha chain, non-erythrocytic 1 P16546 SPTN1_MOUSE
100.0 Spectrin alpha chain, non-erythrocytic 1 P16086 SPTN1_RAT
100.0 Spectrin alpha chain, non-erythrocytic 1 Q13813 SPTN1_HUMAN
100.0 Spectrin alpha chain, non-erythrocytic 1 P07751 SPTN1_CHICK
98.2 Tyrosine-protein kinase HCK Q95M30 HCK_MACFA
100.0 Tyrosine-protein kinase HCK P08631 HCK_HUMAN
93.0 Tyrosine-protein kinase HCK P08103 HCK_MOUSE
93.3 Tyrosine-protein kinase HCK P50545 HCK_RAT
94.3 Tyrosine-protein kinase Lyn P25911 LYN_MOUSE
94.3 Tyrosine-protein kinase Lyn Q07014 LYN_RAT
100.0 Tyrosine-protein kinase Lyn P07948 LYN_HUMAN