HEADER TRANSFERASE 25-AUG-10 2L2P TITLE FOLDING INTERMEDIATE OF THE FYN SH3 A39V/N53P/V55L FROM NMR RELAXATION TITLE 2 DISPERSION EXPERIMENTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE FYN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN (UNP RESIDUES 85-142); COMPND 5 SYNONYM: PROTO-ONCOGENE C-FYN, P59-FYN; COMPND 6 EC: 2.7.10.2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: BANTAM,CHICKENS; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: FYN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS AMYLOID FIBRIL, CHEMICAL EXCHANGE, CPMG NMR RELAXATION DISPERSION, KEYWDS 2 FYN SH3 DOMAIN, PROTEIN FOLDING INTERMEDIATE, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR P.NEUDECKER,P.ROBUSTELLI,A.CAVALLI,M.VENDRUSCOLO,L.E.KAY REVDAT 4 01-MAY-24 2L2P 1 REMARK REVDAT 3 05-FEB-20 2L2P 1 REMARK SEQADV REVDAT 2 16-MAY-12 2L2P 1 JRNL REMARK COMPND REVDAT 1 14-SEP-11 2L2P 0 JRNL AUTH P.NEUDECKER,P.ROBUSTELLI,A.CAVALLI,P.WALSH,P.LUNDSTROM, JRNL AUTH 2 A.ZARRINE-AFSAR,S.SHARPE,M.VENDRUSCOLO,L.E.KAY JRNL TITL STRUCTURE OF AN INTERMEDIATE STATE IN PROTEIN FOLDING AND JRNL TITL 2 AGGREGATION. JRNL REF SCIENCE V. 336 362 2012 JRNL REFN ISSN 0036-8075 JRNL PMID 22517863 JRNL DOI 10.1126/SCIENCE.1214203 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 3.0 REV 2007.068.09.07, ALMOST 1.0.4 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), CAVALLI (ALMOST) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REPLICA EXCHANGE MOLECULAR DYNAMICS REMARK 3 SIMULATION OF RESIDUES 1 TO 56 WITH CAMSHIFT CHEMICAL SHIFT REMARK 3 RESTRAINTS, DNH RDCS AND 13CO RCSAS. RESIDUES 57 TO 60 WERE REMARK 3 EXCLUDED BECAUSE THEY EXHIBIT RANDOM COIL CHEMICAL SHIFTS AND REMARK 3 ARE UNSTRUCTURED IN THE FOLDING INTERMEDIATE. REMARK 4 REMARK 4 2L2P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000101881. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.15 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-15N] FYN SH3 REMARK 210 A39V/N53P/V55L, 0.2 MM EDTA, REMARK 210 0.05 % SODIUM AZIDE, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O; 1.0 MM [U-15N; U-2H] FYN REMARK 210 SH3 A39V/N53P/V55L, 0.2 MM EDTA, REMARK 210 0.05 % SODIUM AZIDE-7, 50 MM REMARK 210 POTASSIUM PHOSPHATE-8, 90% H2O/ REMARK 210 10% D2O; 0.8 MM [U-15N; U-2H] REMARK 210 FYN SH3 A39V/N53P/V55L, 0.2 MM REMARK 210 EDTA-10, 0.05 % SODIUM AZIDE, 50 REMARK 210 MM POTASSIUM PHOSPHATE, 24 MG/ML REMARK 210 PF1 PHAGE, 90% H2O/10% D2O; 0.5 REMARK 210 MM [U-15N; U-2H] FYN SH3 A39V/ REMARK 210 N53P/V55L, 0.2 MM EDTA, 0.05 % REMARK 210 SODIUM AZIDE, 50 MM POTASSIUM REMARK 210 PHOSPHATE, UNCERTAIN V/V PEG/ REMARK 210 HEXANOL, 90% H2O/10% D2O; 1.2 MM REMARK 210 [U-13C; U-15N; U-2H] FYN SH3 REMARK 210 A39V/N53P/V55L, 0.2 MM EDTA, REMARK 210 0.05 % SODIUM AZIDE, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O; 0.8 MM [U-13C; U-15N; U-2H] REMARK 210 FYN SH3 A39V/N53P/V55L, 0.2 MM REMARK 210 EDTA, 0.05 % SODIUM AZIDE, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 36 MG/ML REMARK 210 PF1 PHAGE, 90% H2O/10% D2O; 1.0 REMARK 210 MM [U-13C; U-15N; U-50% 2H] FYN REMARK 210 SH3 A39V/N53P/V55L, 0.2 MM EDTA, REMARK 210 0.05 % SODIUM AZIDE, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O; 1.0 MM [U-13C; U-15N; U-50% REMARK 210 2H] FYN SH3 A39V/N53P/V55L, 0.2 REMARK 210 MM EDTA, 0.05 % SODIUM AZIDE, 50 REMARK 210 MM POTASSIUM PHOSPHATE, 100% D2O; REMARK 210 1.0 MM [2'-13C GLUCOSE; U-15N] REMARK 210 FYN SH3 A39V/N53P/V55L, 0.2 MM REMARK 210 EDTA, 0.05 % SODIUM AZIDE, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 100% D2O; REMARK 210 1.0 MM [1'-13C GLUCOSE; U-15N] REMARK 210 FYN SH3 A39V/N53P/V55L, 0.2 MM REMARK 210 EDTA, 0.05 % SODIUM AZIDE, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O; 1.2 MM [1'-13C GLUCOSE; U- REMARK 210 15N] FYN SH3 A39V/N53P/V55L, 0.2 REMARK 210 MM EDTA, 0.05 % SODIUM AZIDE, 50 REMARK 210 MM POTASSIUM PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY REMARK 210 -HSQC; 3D HNCO; 3D HNCA; 3D C(CO) REMARK 210 NH; 2D 1H-13C CTHSQC; 2D 1H-13C REMARK 210 HSQC; 15N SQ CPMG; 15N TROSY/ REMARK 210 ANTITROSY CPMG; 1HN SQ CPMG; REMARK 210 13CO SQ CPMG; 13CA SQ CPMG; 1HA REMARK 210 SQ CPMG; 13CH3 SQ CPMG REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEWJ 8.0.RC4, MUNIN 1.0, REMARK 210 CATIA 0.52P, ALMOST 1.0.4, REMARK 210 CAMSHIFT 1.2 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 6666 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE CPMG EXPERIMENTS WERE SUPPLEMENTED WITH SIGN REMARK 210 DETERMINATION EXPERIMENTS AS APPROPRIATE. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A -5 REMARK 465 ALA A -4 REMARK 465 MET A -3 REMARK 465 VAL A -2 REMARK 465 GLN A -1 REMARK 465 ILE A 0 REMARK 465 PRO A 57 REMARK 465 VAL A 58 REMARK 465 ASP A 59 REMARK 465 ARG A 60 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 4 ARG A 13 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 GLU A 15 -3.75 95.10 REMARK 500 2 GLU A 15 -15.49 105.21 REMARK 500 2 SER A 31 56.31 -95.01 REMARK 500 3 GLU A 15 -20.39 100.68 REMARK 500 3 SER A 31 54.04 -99.18 REMARK 500 4 GLU A 15 -8.96 98.21 REMARK 500 4 ASN A 30 130.21 -175.93 REMARK 500 5 GLU A 15 -9.33 98.43 REMARK 500 6 GLU A 15 -23.43 109.21 REMARK 500 6 ASN A 30 141.80 -172.48 REMARK 500 7 GLU A 15 -9.19 95.10 REMARK 500 7 SER A 31 55.78 -93.35 REMARK 500 8 THR A 14 -166.01 -114.38 REMARK 500 8 PHE A 20 -162.63 -163.30 REMARK 500 8 SER A 31 45.93 -97.59 REMARK 500 9 THR A 14 -146.71 -113.78 REMARK 500 9 SER A 31 48.20 -93.86 REMARK 500 10 GLU A 15 -7.78 96.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 31 SER A 32 2 -139.52 REMARK 500 SER A 31 SER A 32 3 -136.92 REMARK 500 SER A 31 SER A 32 8 -137.61 REMARK 500 SER A 31 SER A 32 9 -138.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SHF RELATED DB: PDB REMARK 900 STRUCTURE OF THE NATIVE FYN SH3 DOMAIN FROM H. SAPIENS REMARK 900 RELATED ID: 3CQT RELATED DB: PDB REMARK 900 STRUCTURE OF THE NATIVE FYN SH3 DOMAIN MUTANT N53I/V55L FROM G. REMARK 900 GALLUS REMARK 900 RELATED ID: 17149 RELATED DB: BMRB REMARK 900 RELATED ID: 2LP5 RELATED DB: PDB DBREF 2L2P A 2 59 UNP Q05876 FYN_CHICK 85 142 SEQADV 2L2P GLY A -5 UNP Q05876 EXPRESSION TAG SEQADV 2L2P ALA A -4 UNP Q05876 EXPRESSION TAG SEQADV 2L2P MET A -3 UNP Q05876 EXPRESSION TAG SEQADV 2L2P VAL A -2 UNP Q05876 EXPRESSION TAG SEQADV 2L2P GLN A -1 UNP Q05876 EXPRESSION TAG SEQADV 2L2P ILE A 0 UNP Q05876 EXPRESSION TAG SEQADV 2L2P SER A 1 UNP Q05876 EXPRESSION TAG SEQADV 2L2P VAL A 39 UNP Q05876 ALA 122 ENGINEERED MUTATION SEQADV 2L2P PRO A 53 UNP Q05876 ASN 136 ENGINEERED MUTATION SEQADV 2L2P LEU A 55 UNP Q05876 VAL 138 ENGINEERED MUTATION SEQADV 2L2P ARG A 60 UNP Q05876 EXPRESSION TAG SEQRES 1 A 66 GLY ALA MET VAL GLN ILE SER THR LEU PHE GLU ALA LEU SEQRES 2 A 66 TYR ASP TYR GLU ALA ARG THR GLU ASP ASP LEU SER PHE SEQRES 3 A 66 HIS LYS GLY GLU LYS PHE GLN ILE LEU ASN SER SER GLU SEQRES 4 A 66 GLY ASP TRP TRP GLU VAL ARG SER LEU THR THR GLY GLU SEQRES 5 A 66 THR GLY TYR ILE PRO SER PRO TYR LEU ALA PRO VAL ASP SEQRES 6 A 66 ARG HELIX 1 1 PRO A 51 LEU A 55 5 5 SHEET 1 A 4 THR A 2 ALA A 6 0 SHEET 2 A 4 LYS A 25 ASN A 30 -1 O PHE A 26 N PHE A 4 SHEET 3 A 4 TRP A 36 SER A 41 -1 O ARG A 40 N GLN A 27 SHEET 4 A 4 THR A 47 ILE A 50 -1 O ILE A 50 N TRP A 37 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1