HEADER CELL ADHESION 17-OCT-11 2LKO TITLE STRUCTURAL BASIS OF PHOSPHOINOSITIDE BINDING TO KINDLIN-2 PLECKSTRIN TITLE 2 HOMOLOGY DOMAIN IN REGULATING INTEGRIN ACTIVATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERMITIN FAMILY HOMOLOG 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PH DOMAIN RESIDUES 367-500; COMPND 5 SYNONYM: KINDLIN-2, MITOGEN-INDUCIBLE GENE 2 PROTEIN, MIG-2, COMPND 6 PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY C MEMBER 1, PH DOMAIN- COMPND 7 CONTAINING FAMILY C MEMBER 1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FERMT2, KIND2, MIG2, PLEKHC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS CELL ADHESION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.LIU,K.FUKUDA,Z.XU REVDAT 3 14-JUN-23 2LKO 1 REMARK SEQADV REVDAT 2 28-DEC-11 2LKO 1 JRNL REVDAT 1 26-OCT-11 2LKO 0 JRNL AUTH J.LIU,K.FUKUDA,Z.XU,Y.Q.MA,J.HIRBAWI,X.MAO,C.WU,E.F.PLOW, JRNL AUTH 2 J.QIN JRNL TITL STRUCTURAL BASIS OF PHOSPHOINOSITIDE BINDING TO KINDLIN-2 JRNL TITL 2 PROTEIN PLECKSTRIN HOMOLOGY DOMAIN IN REGULATING INTEGRIN JRNL TITL 3 ACTIVATION. JRNL REF J.BIOL.CHEM. V. 286 43334 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 22030399 JRNL DOI 10.1074/JBC.M111.295352 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY, X-PLOR NIH, ARIA REMARK 3 AUTHORS : GODDARD (SPARKY), SCHWIETERS, KUSZEWSKI, TJANDRA REMARK 3 AND CLORE (X-PLOR NIH), LINGE, O'DONOGHUE AND REMARK 3 NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000102498. 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 : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 KINDLIN2-PH, 2 MM INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE, 90% H2O/ REMARK 210 10% D2O; 1 MM [U-100% 13C; U-100% 15N] KINDLIN2-PH, 2 MM REMARK 210 INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCO; 3D HN(CO)CA; 3D HBHA(CO)NH; REMARK 210 3D H(CCO)NH; 3D 1H-15N NOESY; REMARK 210 3D HCCH-COSY; 3D 1H-13C NOESY; REMARK 210 3D 15N/13C FILTERED (F1) [1H-13C] REMARK 210 -NOESY-HSQC; 1D 15N/13C FILTERED REMARK 210 (F1) NOESY; 2D 15N/13C FILTERED REMARK 210 (F1) TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, XWINNMR, ARIA, X-PLOR REMARK 210 NIH, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: NULL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HZ2 LYS A 400 HG SER A 405 1.29 REMARK 500 O LEU A 487 HD21 ASN A 491 1.45 REMARK 500 O TRP A 467 H CYS A 471 1.51 REMARK 500 O ASN A 460 H GLN A 463 1.51 REMARK 500 O ALA A 470 H ALA A 474 1.55 REMARK 500 O ARG A 457 HE22 GLN A 463 1.59 REMARK 500 O THR A 479 H ALA A 481 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 9 TYR A 464 CB - CG - CD2 ANGL. DEV. = -4.5 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 SER A 364 79.01 -158.33 REMARK 500 1 HIS A 365 -88.21 -140.92 REMARK 500 1 MET A 366 -80.08 -75.86 REMARK 500 1 LYS A 385 131.29 60.52 REMARK 500 1 LEU A 387 -71.55 -94.36 REMARK 500 1 THR A 388 -67.88 -161.14 REMARK 500 1 LEU A 389 -159.25 48.90 REMARK 500 1 TYR A 392 96.71 50.98 REMARK 500 1 ASP A 401 -65.50 -24.71 REMARK 500 1 SER A 409 110.60 -162.55 REMARK 500 1 LYS A 410 -9.85 -48.55 REMARK 500 1 GLU A 412 25.38 37.29 REMARK 500 1 SER A 413 -37.63 69.58 REMARK 500 1 ARG A 424 -171.17 43.31 REMARK 500 1 ASP A 431 85.26 -153.58 REMARK 500 1 ASP A 459 -38.27 -149.32 REMARK 500 1 THR A 479 -164.21 -112.55 REMARK 500 1 MET A 480 27.80 -60.09 REMARK 500 1 GLN A 499 129.48 -173.57 REMARK 500 2 HIS A 365 -25.21 -162.81 REMARK 500 2 ASP A 368 -159.05 -70.36 REMARK 500 2 PRO A 373 74.89 -101.25 REMARK 500 2 LYS A 385 103.65 52.69 REMARK 500 2 LEU A 387 -60.07 -92.05 REMARK 500 2 LEU A 389 -108.09 -31.00 REMARK 500 2 LYS A 390 -76.15 76.29 REMARK 500 2 ASP A 401 -97.68 51.43 REMARK 500 2 GLU A 412 26.66 39.90 REMARK 500 2 SER A 413 -65.09 65.75 REMARK 500 2 ARG A 424 169.84 49.75 REMARK 500 2 ASP A 482 -48.83 67.02 REMARK 500 2 MET A 498 -73.31 -76.36 REMARK 500 2 GLN A 499 30.44 172.40 REMARK 500 3 SER A 364 40.21 -86.19 REMARK 500 3 MET A 366 100.90 -164.40 REMARK 500 3 ASP A 368 -174.49 62.29 REMARK 500 3 THR A 370 19.10 56.38 REMARK 500 3 SER A 371 105.94 -46.05 REMARK 500 3 PRO A 373 53.12 -103.84 REMARK 500 3 PRO A 384 35.61 -99.47 REMARK 500 3 LYS A 385 -83.01 -37.34 REMARK 500 3 LYS A 386 -81.90 -103.91 REMARK 500 3 THR A 388 88.21 63.05 REMARK 500 3 LEU A 389 -90.96 -104.87 REMARK 500 3 ASP A 401 -45.67 -28.41 REMARK 500 3 THR A 402 -13.61 -163.97 REMARK 500 3 PRO A 417 141.34 -39.92 REMARK 500 3 GLN A 420 114.13 -160.60 REMARK 500 3 ARG A 424 154.70 54.07 REMARK 500 3 ASP A 431 89.42 -162.07 REMARK 500 REMARK 500 THIS ENTRY HAS 380 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4IP A 1228 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18002 RELATED DB: BMRB DBREF 2LKO A 367 500 UNP Q96AC1 FERM2_HUMAN 367 500 SEQADV 2LKO GLY A 363 UNP Q96AC1 EXPRESSION TAG SEQADV 2LKO SER A 364 UNP Q96AC1 EXPRESSION TAG SEQADV 2LKO HIS A 365 UNP Q96AC1 EXPRESSION TAG SEQADV 2LKO MET A 366 UNP Q96AC1 EXPRESSION TAG SEQRES 1 A 138 GLY SER HIS MET GLY ASP ILE THR SER ILE PRO GLU LEU SEQRES 2 A 138 ALA ASP TYR ILE LYS VAL PHE LYS PRO LYS LYS LEU THR SEQRES 3 A 138 LEU LYS GLY TYR LYS GLN TYR TRP CYS THR PHE LYS ASP SEQRES 4 A 138 THR SER ILE SER CYS TYR LYS SER LYS GLU GLU SER SER SEQRES 5 A 138 GLY THR PRO ALA HIS GLN MET ASN LEU ARG GLY CYS GLU SEQRES 6 A 138 VAL THR PRO ASP VAL ASN ILE SER GLY GLN LYS PHE ASN SEQRES 7 A 138 ILE LYS LEU LEU ILE PRO VAL ALA GLU GLY MET ASN GLU SEQRES 8 A 138 ILE TRP LEU ARG CYS ASP ASN GLU LYS GLN TYR ALA HIS SEQRES 9 A 138 TRP MET ALA ALA CYS ARG LEU ALA SER LYS GLY LYS THR SEQRES 10 A 138 MET ALA ASP SER SER TYR ASN LEU GLU VAL GLN ASN ILE SEQRES 11 A 138 LEU SER PHE LEU LYS MET GLN HIS HET 4IP A1228 36 HETNAM 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE FORMUL 2 4IP C6 H16 O18 P4 HELIX 1 1 ASN A 460 GLY A 477 1 18 HELIX 2 2 ASP A 482 GLN A 499 1 18 SHEET 1 A 7 HIS A 419 MET A 421 0 SHEET 2 A 7 ILE A 404 CYS A 406 -1 N ILE A 404 O MET A 421 SHEET 3 A 7 LYS A 393 PHE A 399 -1 N THR A 398 O SER A 405 SHEET 4 A 7 ALA A 376 PHE A 382 -1 N VAL A 381 O LYS A 393 SHEET 5 A 7 MET A 451 LEU A 456 -1 O TRP A 455 N PHE A 382 SHEET 6 A 7 LYS A 442 PRO A 446 -1 N ILE A 445 O ASN A 452 SHEET 7 A 7 GLU A 427 THR A 429 -1 N GLU A 427 O LEU A 444 SHEET 1 B 2 VAL A 432 ASN A 433 0 SHEET 2 B 2 LYS A 438 PHE A 439 -1 O LYS A 438 N ASN A 433 SITE 1 AC1 8 VAL A 381 LYS A 383 LYS A 385 LEU A 389 SITE 2 AC1 8 LYS A 390 LYS A 393 LYS A 408 HIS A 419 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