HEADER PROTEIN BINDING 09-AUG-24 9D34 TITLE FIP200 C-TERMINAL CLAW DOMAIN (RESID. 1490-1594) IN COMPLEX WITH TITLE 2 PHOSPHORYLATED TNIP1 FIP200 INTERACTING PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RB1-INDUCIBLE COILED-COIL PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FAK FAMILY KINASE-INTERACTING PROTEIN OF 200 KDA,FIP200; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TNFAIP3-INTERACTING PROTEIN 1; COMPND 8 CHAIN: C; COMPND 9 SYNONYM: A20-BINDING INHIBITOR OF NF-KAPPA-B ACTIVATION 1,ABIN-1,HIV- COMPND 10 1 NEF-INTERACTING PROTEIN,NEF-ASSOCIATED FACTOR 1,NAF1,NIP40-1, COMPND 11 VIRION-ASSOCIATED NUCLEAR SHUTTLING PROTEIN,VAN,HVAN; COMPND 12 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: RB1CC1, KIAA0203, RBICC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: TNIP1, KIAA0113, NAF1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AUTOPHAGY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.M.RADFORD,W.ROSENCRANS,T.F.CHOU REVDAT 1 06-NOV-24 9D34 0 JRNL AUTH K.M.RADFORD,W.ROSENCRANS,T.F.CHOU JRNL TITL FIP200 C-TERMINAL CLAW DOMAIN (RESID. 1490-1594) IN COMPLEX JRNL TITL 2 WITH PHOSPHORYLATED TNIP1 FIP200 INTERACTING PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 22153 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1085 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 10.0000 - 2.8400 1.00 2941 139 0.2081 0.2367 REMARK 3 2 2.8400 - 2.2500 1.00 2791 122 0.2102 0.2250 REMARK 3 3 2.2500 - 1.9700 1.00 2707 158 0.1811 0.2122 REMARK 3 4 1.9700 - 1.7900 0.99 2693 135 0.1716 0.2375 REMARK 3 5 1.7900 - 1.6600 0.98 2637 147 0.2157 0.2841 REMARK 3 6 1.6600 - 1.5600 0.96 2586 138 0.1711 0.2133 REMARK 3 7 1.5600 - 1.4800 0.92 2441 132 0.1754 0.2278 REMARK 3 8 1.4800 - 1.4200 0.85 2272 114 0.2531 0.3454 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 775 REMARK 3 ANGLE : 1.254 1061 REMARK 3 CHIRALITY : 0.102 122 REMARK 3 PLANARITY : 0.011 132 REMARK 3 DIHEDRAL : 7.381 106 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9D34 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000286912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979460 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 -CRYSTAL SI(111) MONOCHROMATOR REMARK 200 WITH A 0.01% ENERGY BANDPASS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22984 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 33.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.49600 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS E4 (12.5% W/V PEG 1000, 12.5% REMARK 280 W/V PEG 3350, 12.5% V/V MPD, 0.03 M OF EACH ETHYLENE GLYCOL, 0.1 REMARK 280 M MES/IMIDAZOLE PH 6.5), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 44.14000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.66950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.66950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 66.21000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.66950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.66950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.07000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.66950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.66950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 66.21000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.66950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.66950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.07000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.14000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 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 SER A 1490 REMARK 465 ARG A 1491 REMARK 465 HIS A 1492 REMARK 465 SER A 1493 REMARK 465 GLY A 1543 REMARK 465 GLU A 1544 REMARK 465 GLY A 1545 REMARK 465 ALA A 1546 REMARK 465 SER A 1547 REMARK 465 GLY A 1548 REMARK 465 ALA A 1549 REMARK 465 SER A 1550 REMARK 465 ASN A 1591 REMARK 465 LYS A 1592 REMARK 465 LYS A 1593 REMARK 465 VAL A 1594 REMARK 465 GLY C 120 REMARK 465 THR C 121 REMARK 465 SER C 122 REMARK 465 THR C 129 REMARK 465 PRO C 130 REMARK 465 GLU C 131 REMARK 465 GLU C 132 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 GLU A1513 CG CD OE1 OE2 REMARK 470 ARG A1514 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1533 CG CD OE1 OE2 REMARK 470 LYS A1541 CG CD CE NZ REMARK 470 PRO A1542 CG CD REMARK 470 ARG A1551 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1552 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1562 CG CD CE NZ REMARK 470 LYS A1568 CG CD CE NZ REMARK 470 LYS A1569 CG CD CE NZ REMARK 470 GLN A1571 CG CD OE1 NE2 REMARK 470 ARG A1573 CG CD NE CZ NH1 NH2 REMARK 470 VAL C 127 CG1 CG2 REMARK 470 VAL C 128 CG1 CG2 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 PRO A1542 C - N - CA ANGL. DEV. = 10.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9D34 A 1490 1594 UNP Q8TDY2 RBCC1_HUMAN 1490 1594 DBREF 9D34 C 120 132 UNP Q15025 TNIP1_HUMAN 120 132 SEQRES 1 A 105 SER ARG HIS SER GLU LYS ILE ALA ILE ARG ASP PHE GLN SEQRES 2 A 105 VAL GLY ASP LEU VAL LEU ILE ILE LEU ASP GLU ARG HIS SEQRES 3 A 105 ASP ASN TYR VAL LEU PHE THR VAL SER PRO THR LEU TYR SEQRES 4 A 105 PHE LEU HIS SER GLU SER LEU PRO ALA LEU ASP LEU LYS SEQRES 5 A 105 PRO GLY GLU GLY ALA SER GLY ALA SER ARG ARG PRO TRP SEQRES 6 A 105 VAL LEU GLY LYS VAL MET GLU LYS GLU TYR CYS GLN ALA SEQRES 7 A 105 LYS LYS ALA GLN ASN ARG PHE LYS VAL PRO LEU GLY THR SEQRES 8 A 105 LYS PHE TYR ARG VAL LYS ALA VAL SER TRP ASN LYS LYS SEQRES 9 A 105 VAL SEQRES 1 C 13 GLY THR SER SEP GLU PHE GLU VAL VAL THR PRO GLU GLU MODRES 9D34 SEP C 123 SER MODIFIED RESIDUE HET SEP C 123 14 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 HOH *47(H2 O) HELIX 1 AA1 SER A 1532 LEU A 1535 5 4 SHEET 1 AA1 7 PHE C 125 VAL C 127 0 SHEET 2 AA1 7 TRP A1554 ALA A1567 -1 N GLN A1566 O GLU C 126 SHEET 3 AA1 7 LYS A1581 SER A1589 -1 O PHE A1582 N CYS A1565 SHEET 4 AA1 7 TYR A1528 LEU A1530 1 N PHE A1529 O VAL A1585 SHEET 5 AA1 7 ASN A1517 LEU A1520 -1 N TYR A1518 O LEU A1530 SHEET 6 AA1 7 LEU A1506 ASP A1512 -1 N ILE A1510 O VAL A1519 SHEET 7 AA1 7 TRP A1554 ALA A1567 -1 O VAL A1555 N ILE A1509 LINK C SEP C 123 N GLU C 124 1555 1555 1.32 CRYST1 51.339 51.339 88.280 90.00 90.00 90.00 P 43 21 2 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 0.019478 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019478 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011328 0.00000