PDB Short entry for 1JU5 HEADER PROTEIN BINDING/TRANSFERASE 23-AUG-01 1JU5 TITLE TERNARY COMPLEX OF AN CRK SH2 DOMAIN, CRK-DERIVED PHOPHOPEPTIDE, AND TITLE 2 ABL SH3 DOMAIN BY NMR SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRK; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CRK SH2 DOMAIN; COMPND 5 SYNONYM: PROTO-ONCOGENE C-CRK, ADAPTER MOLECULE CRK, P38; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CRK; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: CRK PHOSPHOPEPTIDE; COMPND 11 SYNONYM: PROTO-ONCOGENE C-CRK, ADAPTER MOLECULE CRK, P38; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: ABL; COMPND 15 CHAIN: C; COMPND 16 FRAGMENT: ABL SH3 DOMAIN; COMPND 17 SYNONYM: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE; COMPND 18 EC: 2.7.1.112; COMPND 19 ENGINEERED: YES; COMPND 20 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-2T; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PAED4-MMHB; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 ORGANISM_TAXID: 9606; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 25 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 27 EXPRESSION_SYSTEM_PLASMID: PET15 KEYWDS CRK, SH2, ABL, SH3, ADAPTOR PROTEIN, PHOSPHOPEPTIDE, PROTEIN BINDING- KEYWDS 2 TRANSFERASE COMPLEX EXPDTA SOLUTION NMR AUTHOR L.W.DONALDSON,T.PAWSON,L.E.KAY,J.D.FORMAN-KAY REVDAT 4 10-NOV-21 1JU5 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1JU5 1 VERSN REVDAT 2 12-AUG-03 1JU5 1 DBREF REVDAT 1 06-NOV-02 1JU5 0 JRNL AUTH L.W.DONALDSON,G.GISH,T.PAWSON,L.E.KAY,J.D.FORMAN-KAY JRNL TITL STRUCTURE OF A REGULATORY COMPLEX INVOLVING THE ABL SH3 JRNL TITL 2 DOMAIN, THE CRK SH2 DOMAIN, AND A CRK-DERIVED PHOSPHOPEPTIDE JRNL REF PROC.NATL.ACAD.SCI.USA V. 99 14053 2002 JRNL REFN ISSN 0027-8424 JRNL PMID 12384576 JRNL DOI 10.1073/PNAS.212518799 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 1.8, ARIA 1.0 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), BRUNGER (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THIS STRUCTURE REPRESENTS THE LOWEST ENERGY SOLUTION BASED ON 2406 REMARK 3 SH2 INTRAMOLECULAR RESTRAINTS, 1628 SH3 INTRAMOLECULAR RESTRAINTS, REMARK 3 37 SH2-SH3 INTERMOLECULAR RESTRAINTS, 64 SH2-PHOSPHOPEPTIDE REMARK 3 INTERMOLECULAR RESTRAINTS, 50 HYDROGEN BONDS, 54 DIRECT 3J-HNHA REMARK 3 COUPLINGS AND 166 DIHEDRAL ANGLE RESTRAINTS FROM TALOS REMARK 3 REMARK 3 RESIDUES 217-220 AND 225-229 OF THE CRK PHOSPHOPEPTIDE (CHAIN B) REMARK 3 ARE DISORDERED. AS INTERMOLECULAR CONTACTS BETWEEN THE SH2 DOMAIN REMARK 3 (CHAIN A) AND THE SH3 DOMAIN (CHAIN C) LIMITED TO AMINO ACIDS 67- REMARK 3 75 IN DE-LOOP OF THE SH2 DOMAIN, THERE IS NO UNIQUE ORIENTATION REMARK 3 BETWEEN THE SH2 DOMAIN AND SH3 DOMAIN. REMARK 4 REMARK 4 1JU5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014188. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 50MM SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6-1.5MM CRK SH2 DOMAIN U-15N, REMARK 210 13C; 50MM SODIUM PHOSPHATE PH6.8, REMARK 210 0.02% SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C_F1-FILTERED_F3-EDITED_NOESY; J-HNHA; REMARK 210 IPAP-15N_HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP 4.3.2, CNS 1.0, ARIA 1.0 REMARK 210 METHOD USED : ARIA 1.0, CNS 1.0 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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: INTERMOLECULAR DISTANCE RESTRAINTS WERE OBTAINED FROM REMARK 210 REVERSE HALF-FILTERED 2D- AND 3D-NOESY SPECTRA (300 MS MIXING REMARK 210 TIME) ON SAMPLE IN 99% D2O. METHYL PROCHIRAL ASSIGNMENTS WERE REMARK 210 MADE ON A 10% 13C-LABELED SAMPLE ACCORDING TO NERI ET AL REMARK 210 (BIOCHEMISTRY 28:7510; 1989). HACAN AND CBCA(CO)N(CA)HA REMARK 210 EXPERIMENTS WERE USED TO ASSIGN THE PROLINE RESIDUES IN THE CRK REMARK 210 SH2 DOMAIN ACCORDING TO KANELIS ET AL (JBNMR 16:253; 2000) 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 RES C SSSEQI REMARK 465 LYS C 122 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 ARG A 31 164.49 -49.28 REMARK 500 GLU A 53 -160.31 -75.02 REMARK 500 SER A 55 14.86 80.47 REMARK 500 PRO A 75 164.09 -49.77 REMARK 500 SER A 83 89.59 -151.10 REMARK 500 TYR A 108 45.86 -108.61 REMARK 500 THR A 112 -176.15 47.45 REMARK 500 GLN B 223 95.24 69.82 REMARK 500 SER B 225 -46.51 -133.71 REMARK 500 VAL B 226 71.30 53.63 REMARK 500 ASN B 227 -74.76 -138.22 REMARK 500 THR B 228 -170.68 53.34 REMARK 500 ASN C 64 40.61 -176.91 REMARK 500 ASP C 77 -161.80 -57.31 REMARK 500 PRO C 112 163.62 -49.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AWO RELATED DB: PDB REMARK 900 1AWO CONTAINS NMR STRUCTURE OF ABL SH3 DOMAIN IN AN SH(32) FRAGMENT REMARK 900 RELATED ID: 1BBZ RELATED DB: PDB REMARK 900 1BBZ CONTAINS CRYSTAL STRUCTURE OF ABL SH3 DOMAIN WITH HIGH- REMARK 900 AFFINITY LIGAND REMARK 900 RELATED ID: 2ABL RELATED DB: PDB REMARK 900 2ABL CONTAINS SH3-SH2 DOMAIN FRAGMENT OF HUMAN BCR-ABL TYROSINE REMARK 900 KINASE REMARK 900 RELATED ID: 1AYA RELATED DB: PDB REMARK 900 1AYA CONTAINS CRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO- REMARK 900 TERMINAL SH2 DOMAIN OF THE SYP TYROSINE PHOSPHATASE. REMARK 900 RELATED ID: 2PLD RELATED DB: PDB REMARK 900 2PLD CONTAINS NUCLEAR MAGNETIC RESONANCE STRUCTURE OF AN SH2 DOMAIN REMARK 900 OF PHOSPHOLIPASE C-1 COMPLEXED WITH A HIGH AFFINITY BINDING PEPTIDE. REMARK 900 RELATED ID: 1SPS RELATED DB: PDB REMARK 900 1SPS CONTAINS CRYSTAL STRUCTURE OF THE SRC SH2 IN COMPLEX WITH YEEI DBREF 1JU5 A 12 120 UNP P46108 CRK_HUMAN 12 120 DBREF 1JU5 B 217 228 UNP Q64010 CRK_MOUSE 217 228 DBREF 1JU5 C 62 122 UNP P00519 ABL1_HUMAN 62 122 SEQADV 1JU5 LYS C 122 UNP P00519 LEU 122 ENGINEERED MUTATION SEQRES 1 A 109 SER TRP TYR TRP GLY ARG LEU SER ARG GLN GLU ALA VAL SEQRES 2 A 109 ALA LEU LEU GLN GLY GLN ARG HIS GLY VAL PHE LEU VAL SEQRES 3 A 109 ARG ASP SER SER THR SER PRO GLY ASP TYR VAL LEU SER SEQRES 4 A 109 VAL SER GLU ASN SER ARG VAL SER HIS TYR ILE ILE ASN SEQRES 5 A 109 SER SER GLY PRO ARG PRO PRO VAL PRO PRO SER PRO ALA SEQRES 6 A 109 GLN PRO PRO PRO GLY VAL SER PRO SER ARG LEU ARG ILE SEQRES 7 A 109 GLY ASP GLN GLU PHE ASP SER LEU PRO ALA LEU LEU GLU SEQRES 8 A 109 PHE TYR LYS ILE HIS TYR LEU ASP THR THR THR LEU ILE SEQRES 9 A 109 GLU PRO VAL SER ARG SEQRES 1 B 13 GLU PRO GLY PRO PTR ALA GLN PRO SER VAL ASN THR LYS SEQRES 1 C 61 ASP PRO ASN LEU PHE VAL ALA LEU TYR ASP PHE VAL ALA SEQRES 2 C 61 SER GLY ASP ASN THR LEU SER ILE THR LYS GLY GLU LYS SEQRES 3 C 61 LEU ARG VAL LEU GLY TYR ASN HIS ASN GLY GLU TRP CYS SEQRES 4 C 61 GLU ALA GLN THR LYS ASN GLY GLN GLY TRP VAL PRO SER SEQRES 5 C 61 ASN TYR ILE THR PRO VAL ASN SER LYS MODRES 1JU5 PTR B 221 TYR O-PHOSPHOTYROSINE HET PTR B 221 24 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 PTR C9 H12 N O6 P HELIX 1 1 SER A 19 GLN A 28 1 10 HELIX 2 2 SER A 96 HIS A 107 1 12 SHEET 1 A 4 VAL A 57 ASN A 63 0 SHEET 2 A 4 ASP A 46 SER A 52 -1 N TYR A 47 O ILE A 62 SHEET 3 A 4 VAL A 34 ASP A 39 -1 N LEU A 36 O SER A 50 SHEET 4 A 4 TYR A 14 TRP A 15 1 N TRP A 15 O VAL A 37 SHEET 1 B 4 VAL A 57 ASN A 63 0 SHEET 2 B 4 ASP A 46 SER A 52 -1 N TYR A 47 O ILE A 62 SHEET 3 B 4 VAL A 34 ASP A 39 -1 N LEU A 36 O SER A 50 SHEET 4 B 4 GLU A 116 PRO A 117 1 O GLU A 116 N PHE A 35 SHEET 1 C 2 LEU A 87 ILE A 89 0 SHEET 2 C 2 GLN A 92 PHE A 94 -1 O GLN A 92 N ILE A 89 SHEET 1 D 5 GLY C 107 PRO C 112 0 SHEET 2 D 5 TRP C 99 THR C 104 -1 N CYS C 100 O VAL C 111 SHEET 3 D 5 LYS C 87 TYR C 93 -1 N ARG C 89 O GLN C 103 SHEET 4 D 5 PHE C 66 ALA C 68 -1 N PHE C 66 O LEU C 88 SHEET 5 D 5 ILE C 116 PRO C 118 -1 O THR C 117 N VAL C 67 LINK C PRO B 220 N PTR B 221 1555 1555 1.33 LINK C PTR B 221 N ALA B 222 1555 1555 1.33 CRYST1 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