HEADER SIGNALING PROTEIN 12-JUL-23 8TGF TITLE CRYSTAL STRUCTURE OF CEPG5 LIR/LGG-1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN LGG-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ECTOPIC P GRANULES PROTEIN 5; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: LGG-1, ATG-8.1, C32D5.9; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 10 ORGANISM_TAXID: 6239 KEYWDS SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.W.S.CHEUNG,C.K.YIP REVDAT 1 17-JUL-24 8TGF 0 JRNL AUTH Y.W.S.CHEUNG,G.FAIRLIE,K.SCHEU,C.K.YIP JRNL TITL MOLECULAR BASIS OF THE MODE OF INTERACTION BETWEEN THE JRNL TITL 2 TANDEM LC3-INTERACTING REGION MOTIF OF THE AUTOPHAGY JRNL TITL 3 TETHERING FACTOR EPG5 AND ATG8 PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 14647 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 724 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 44.4800 - 2.7400 0.97 2874 151 0.1734 0.2047 REMARK 3 2 2.7400 - 2.1700 0.97 2783 132 0.1795 0.2191 REMARK 3 3 2.1700 - 1.9000 0.96 2720 156 0.1661 0.2110 REMARK 3 4 1.9000 - 1.7200 0.98 2790 149 0.1742 0.2302 REMARK 3 5 1.7200 - 1.6000 0.97 2756 136 0.1813 0.2295 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.149 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.093 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.52 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 : 0.010 1036 REMARK 3 ANGLE : 1.090 1393 REMARK 3 CHIRALITY : 0.070 146 REMARK 3 PLANARITY : 0.008 178 REMARK 3 DIHEDRAL : 2.640 872 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 78 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6094 2.7131 8.9549 REMARK 3 T TENSOR REMARK 3 T11: 0.0991 T22: 0.0527 REMARK 3 T33: 0.0873 T12: -0.0071 REMARK 3 T13: -0.0019 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 2.1773 L22: 2.4477 REMARK 3 L33: 2.5983 L12: -0.0241 REMARK 3 L13: -0.0364 L23: -0.0262 REMARK 3 S TENSOR REMARK 3 S11: 0.0182 S12: -0.0022 S13: -0.2019 REMARK 3 S21: -0.0053 S22: 0.0153 S23: 0.1292 REMARK 3 S31: 0.2192 S32: -0.1063 S33: -0.0390 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 505 THROUGH 513 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9334 15.4539 20.6892 REMARK 3 T TENSOR REMARK 3 T11: 0.2841 T22: 0.1395 REMARK 3 T33: 0.1538 T12: -0.0315 REMARK 3 T13: 0.0447 T23: -0.0500 REMARK 3 L TENSOR REMARK 3 L11: 5.3352 L22: 5.4126 REMARK 3 L33: 1.6107 L12: -0.9675 REMARK 3 L13: -1.8655 L23: 0.5542 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: -0.3945 S13: -0.0268 REMARK 3 S21: 0.2985 S22: -0.0300 S23: -0.1341 REMARK 3 S31: -0.0150 S32: -0.0769 S33: 0.0274 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1136 17.6999 5.1823 REMARK 3 T TENSOR REMARK 3 T11: 0.1229 T22: 0.0764 REMARK 3 T33: 0.0815 T12: -0.0090 REMARK 3 T13: 0.0071 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 1.3839 L22: 4.7903 REMARK 3 L33: 4.2075 L12: -1.0644 REMARK 3 L13: -1.4807 L23: -0.9231 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: 0.0405 S13: 0.0475 REMARK 3 S21: -0.0042 S22: 0.1203 S23: 0.1909 REMARK 3 S31: -0.2619 S32: -0.1922 S33: -0.0340 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 25 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.2538 9.7994 14.7183 REMARK 3 T TENSOR REMARK 3 T11: 0.1301 T22: 0.1123 REMARK 3 T33: 0.0720 T12: 0.0213 REMARK 3 T13: 0.0306 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 3.1634 L22: 3.9494 REMARK 3 L33: 2.1993 L12: 1.4248 REMARK 3 L13: -0.0868 L23: 0.0891 REMARK 3 S TENSOR REMARK 3 S11: -0.0676 S12: -0.0946 S13: 0.4111 REMARK 3 S21: 0.1674 S22: 0.0450 S23: 0.2157 REMARK 3 S31: -0.2464 S32: -0.2037 S33: 0.0587 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 57 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.1901 2.9126 21.3715 REMARK 3 T TENSOR REMARK 3 T11: 0.3475 T22: 0.1192 REMARK 3 T33: 0.0670 T12: 0.0360 REMARK 3 T13: 0.0502 T23: 0.0963 REMARK 3 L TENSOR REMARK 3 L11: 0.8520 L22: 2.9930 REMARK 3 L33: 4.8991 L12: 0.2474 REMARK 3 L13: 0.5676 L23: -0.8579 REMARK 3 S TENSOR REMARK 3 S11: 0.0501 S12: -0.0032 S13: 0.0982 REMARK 3 S21: 0.4693 S22: 0.0239 S23: 0.3949 REMARK 3 S31: -0.2163 S32: -0.3364 S33: -0.2991 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 77 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5172 2.2322 18.9217 REMARK 3 T TENSOR REMARK 3 T11: 0.2425 T22: 0.4883 REMARK 3 T33: 0.3882 T12: 0.0498 REMARK 3 T13: 0.0776 T23: 0.1081 REMARK 3 L TENSOR REMARK 3 L11: 1.3233 L22: 0.3528 REMARK 3 L33: 1.0190 L12: 0.3084 REMARK 3 L13: -0.0959 L23: -0.4923 REMARK 3 S TENSOR REMARK 3 S11: -0.0460 S12: -0.6614 S13: -0.0063 REMARK 3 S21: 0.5391 S22: 0.0493 S23: 0.7339 REMARK 3 S31: -0.1233 S32: -0.7564 S33: 0.0131 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 8TGF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000275876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14650 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 44.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.03640 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11560 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 2.8.2 REMARK 200 STARTING MODEL: 5AZF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 4.6, 21% (W/V) REMARK 280 PEG 6000, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 18.97600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 LEU A 70 REMARK 465 ARG A 71 REMARK 465 PRO A 72 REMARK 465 VAL A 114 REMARK 465 TYR A 115 REMARK 465 GLY A 116 REMARK 465 GLY A 117 REMARK 465 GLU A 118 REMARK 465 VAL A 119 REMARK 465 GLU A 120 REMARK 465 LYS A 121 REMARK 465 LYS A 122 REMARK 465 GLU A 123 REMARK 465 ASP B 514 REMARK 465 ASP B 515 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 HIS A 42 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 73 CG CD OE1 OE2 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 ALA B 511 145.62 75.28 REMARK 500 REMARK 500 REMARK: NULL DBREF 8TGF A 1 123 UNP Q09490 LGG1_CAEEL 1 123 DBREF 8TGF B 505 515 UNP Q18892 EPG5_CAEEL 505 515 SEQADV 8TGF GLY A -1 UNP Q09490 EXPRESSION TAG SEQADV 8TGF SER A 0 UNP Q09490 EXPRESSION TAG SEQRES 1 A 125 GLY SER MET LYS TRP ALA TYR LYS GLU GLU ASN ASN PHE SEQRES 2 A 125 GLU LYS ARG ARG ALA GLU GLY ASP LYS ILE ARG ARG LYS SEQRES 3 A 125 TYR PRO ASP ARG ILE PRO VAL ILE VAL GLU LYS ALA PRO SEQRES 4 A 125 LYS SER LYS LEU HIS ASP LEU ASP LYS LYS LYS TYR LEU SEQRES 5 A 125 VAL PRO SER ASP LEU THR VAL GLY GLN PHE TYR PHE LEU SEQRES 6 A 125 ILE ARG LYS ARG ILE GLN LEU ARG PRO GLU ASP ALA LEU SEQRES 7 A 125 PHE PHE PHE VAL ASN ASN VAL ILE PRO GLN THR MET THR SEQRES 8 A 125 THR MET GLY GLN LEU TYR GLN ASP HIS HIS GLU GLU ASP SEQRES 9 A 125 LEU PHE LEU TYR ILE ALA TYR SER ASP GLU SER VAL TYR SEQRES 10 A 125 GLY GLY GLU VAL GLU LYS LYS GLU SEQRES 1 B 11 SER THR TRP GLU ILE LEU ALA ASP ASP ASP ASP HET ACT A 201 7 HETNAM ACT ACETATE ION FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *65(H2 O) HELIX 1 AA1 TRP A 3 ASN A 9 1 7 HELIX 2 AA2 ASN A 10 TYR A 25 1 16 HELIX 3 AA3 THR A 56 GLN A 69 1 14 HELIX 4 AA4 THR A 90 HIS A 99 1 10 SHEET 1 AA1 5 PHE A 77 PHE A 79 0 SHEET 2 AA1 5 LEU A 105 SER A 110 -1 O ALA A 108 N PHE A 79 SHEET 3 AA1 5 ARG A 28 LYS A 35 1 N ILE A 32 O LEU A 105 SHEET 4 AA1 5 LYS A 48 PRO A 52 -1 O VAL A 51 N ILE A 29 SHEET 5 AA1 5 GLU B 508 ILE B 509 1 O GLU B 508 N LEU A 50 CRYST1 33.991 37.952 45.177 90.00 100.10 90.00 P 1 21 1 2 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 0.029420 0.000000 0.005241 0.00000 SCALE2 0.000000 0.026349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022484 0.00000