HEADER SIGNALING PROTEIN 06-OCT-99 1D4W TITLE CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH SLAM TITLE 2 PHOSPHOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: T CELL SIGNAL TRANSDUCTION MOLECULE SAP; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SH2 DOMAIN; COMPND 5 SYNONYM: SAP; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE; COMPND 10 CHAIN: C, D; COMPND 11 FRAGMENT: CYTOPLASMIC TAIL SYNTHETIC PHOSPOPEPTIDE; COMPND 12 SYNONYM: SLAM; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BLOOD; SOURCE 6 CELL: T CELL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: T7-PRSET; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS SH2 DOMAIN, PHOSPHOTYROSINE RECOGNIITON, PEPTIDE RECOGNITION, SIGNAL KEYWDS 2 TRANSDUCTION, LYMPHOPROLIFERATIVE DISEASE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.POY,M.B.YAFFE,J.SAYOS,K.SAXENA,M.J.ECK REVDAT 5 31-JAN-18 1D4W 1 REMARK REVDAT 4 13-JUL-11 1D4W 1 VERSN REVDAT 3 24-FEB-09 1D4W 1 VERSN REVDAT 2 04-APR-00 1D4W 1 JRNL DBREF REMARK SEQADV REVDAT 1 14-OCT-99 1D4W 0 JRNL AUTH F.POY,M.B.YAFFE,J.SAYOS,K.SAXENA,M.MORRA,J.SUMEGI, JRNL AUTH 2 L.C.CANTLEY,C.TERHORST,M.J.ECK JRNL TITL CRYSTAL STRUCTURES OF THE XLP PROTEIN SAP REVEAL A CLASS OF JRNL TITL 2 SH2 DOMAINS WITH EXTENDED, PHOSPHOTYROSINE-INDEPENDENT JRNL TITL 3 SEQUENCE RECOGNITION. JRNL REF MOL.CELL V. 4 555 1999 JRNL REFN ISSN 1097-2765 JRNL PMID 10549287 JRNL DOI 10.1016/S1097-2765(00)80206-3 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.SAYOS,C.WU,M.MORRA,N.WANG,C.TERHORST REMARK 1 TITL THE X-LINKED LYMPHOPROLIFERATIVE DISEASE GENE PRODUCT SAP REMARK 1 TITL 2 REGULATES SIGNALS INDUCED THROUGH THE CO-RECEPTOR SLAM REMARK 1 REF NATURE V. 395 462 1998 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/26683 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS, 5% REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.172 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1790 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 413 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH& HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D4W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009796. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000, 20% GLYCEROL, 100 MM REMARK 280 SODIUM CITRATE, 10MM DTT, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 22K, TEMPERATURE 295.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 50.10000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.10000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 LYS C 276 REMARK 465 LYS D 276 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG B 78 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 79 CG CD CE NZ REMARK 470 LYS B 81 CG CD CE NZ 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 LYS B 10 44.75 -85.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D1Z RELATED DB: PDB REMARK 900 STRUCTURE OF THE UNLIGANDED DOMAIN REMARK 900 RELATED ID: 1D4T RELATED DB: PDB REMARK 900 STRUCTURE OF THE SAP SH2 DOMAIN IN COMPLEX WITH NON-PHOSPHORYLATED REMARK 900 PEPTIDE DBREF 1D4W A 1 104 UNP O60880 SH21A_HUMAN 1 104 DBREF 1D4W B 1 104 UNP O60880 SH21A_HUMAN 1 104 DBREF 1D4W C 276 286 UNP Q13291 SLAF1_HUMAN 276 286 DBREF 1D4W D 276 286 UNP Q13291 SLAF1_HUMAN 276 286 SEQADV 1D4W PTR C 281 UNP Q13291 TYR 281 MODIFIED RESIDUE SEQADV 1D4W PTR D 281 UNP Q13291 TYR 281 MODIFIED RESIDUE SEQRES 1 A 104 MET ASP ALA VAL ALA VAL TYR HIS GLY LYS ILE SER ARG SEQRES 2 A 104 GLU THR GLY GLU LYS LEU LEU LEU ALA THR GLY LEU ASP SEQRES 3 A 104 GLY SER TYR LEU LEU ARG ASP SER GLU SER VAL PRO GLY SEQRES 4 A 104 VAL TYR CYS LEU CYS VAL LEU TYR HIS GLY TYR ILE TYR SEQRES 5 A 104 THR TYR ARG VAL SER GLN THR GLU THR GLY SER TRP SER SEQRES 6 A 104 ALA GLU THR ALA PRO GLY VAL HIS LYS ARG TYR PHE ARG SEQRES 7 A 104 LYS ILE LYS ASN LEU ILE SER ALA PHE GLN LYS PRO ASP SEQRES 8 A 104 GLN GLY ILE VAL ILE PRO LEU GLN TYR PRO VAL GLU LYS SEQRES 1 B 104 MET ASP ALA VAL ALA VAL TYR HIS GLY LYS ILE SER ARG SEQRES 2 B 104 GLU THR GLY GLU LYS LEU LEU LEU ALA THR GLY LEU ASP SEQRES 3 B 104 GLY SER TYR LEU LEU ARG ASP SER GLU SER VAL PRO GLY SEQRES 4 B 104 VAL TYR CYS LEU CYS VAL LEU TYR HIS GLY TYR ILE TYR SEQRES 5 B 104 THR TYR ARG VAL SER GLN THR GLU THR GLY SER TRP SER SEQRES 6 B 104 ALA GLU THR ALA PRO GLY VAL HIS LYS ARG TYR PHE ARG SEQRES 7 B 104 LYS ILE LYS ASN LEU ILE SER ALA PHE GLN LYS PRO ASP SEQRES 8 B 104 GLN GLY ILE VAL ILE PRO LEU GLN TYR PRO VAL GLU LYS SEQRES 1 C 11 LYS SER LEU THR ILE PTR ALA GLN VAL GLN LYS SEQRES 1 D 11 LYS SER LEU THR ILE PTR ALA GLN VAL GLN LYS MODRES 1D4W PTR C 281 TYR O-PHOSPHOTYROSINE MODRES 1D4W PTR D 281 TYR O-PHOSPHOTYROSINE HET PTR C 281 16 HET PTR D 281 16 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 3 PTR 2(C9 H12 N O6 P) FORMUL 5 HOH *413(H2 O) HELIX 1 1 SER A 12 GLY A 24 1 13 HELIX 2 2 LYS A 79 GLN A 88 1 10 HELIX 3 1 SER B 12 GLY B 24 1 13 HELIX 4 2 LYS B 79 GLN B 88 1 10 SHEET 1 A 5 TYR B 100 PRO B 101 0 SHEET 2 A 5 SER B 28 ASP B 33 1 N TYR B 29 O TYR B 100 SHEET 3 A 5 TYR B 41 TYR B 47 -1 N CYS B 42 O ARG B 32 SHEET 4 A 5 TYR B 50 GLN B 58 -1 O TYR B 50 N TYR B 47 SHEET 5 A 5 TRP B 64 ALA B 66 -1 O SER B 65 N SER B 57 SHEET 1 A1 5 TYR B 100 PRO B 101 0 SHEET 2 A1 5 SER B 28 ASP B 33 1 N TYR B 29 O TYR B 100 SHEET 3 A1 5 TYR B 41 TYR B 47 -1 N CYS B 42 O ARG B 32 SHEET 4 A1 5 TYR B 50 GLN B 58 -1 O TYR B 50 N TYR B 47 SHEET 5 A1 5 THR D 279 PTR D 281 1 O ILE D 280 N THR B 53 LINK C ILE C 280 N PTR C 281 1555 1555 1.32 LINK C PTR C 281 N ALA C 282 1555 1555 1.36 LINK C ILE D 280 N PTR D 281 1555 1555 1.29 LINK C PTR D 281 N ALA D 282 1555 1555 1.31 CRYST1 100.200 49.000 55.600 90.00 94.20 90.00 C 1 2 1 8 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 0.009980 0.000000 0.000733 0.00000 SCALE2 0.000000 0.020408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018034 0.00000