HEADER GENE REGULATION 18-AUG-21 7RUP TITLE STRUCTURE OF THE HUMAN GIGYF2-TNRC6A COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: GRB10-INTERACTING GYF PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PERQ AMINO ACID-RICH WITH GYF DOMAIN-CONTAINING PROTEIN 2, COMPND 5 TRINUCLEOTIDE REPEAT-CONTAINING GENE 15 PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TRINUCLEOTIDE REPEAT-CONTAINING GENE 6A PROTEIN; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: CAG REPEAT PROTEIN 26,EMSY INTERACTOR PROTEIN,GW182 COMPND 11 AUTOANTIGEN,PROTEIN GW1,GLYCINE-TRYPTOPHAN PROTEIN OF 182 KDA; 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: GIGYF2, KIAA0642, PERQ2, TNRC15; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: TNRC6A, CAGH26, KIAA1460, TNRC6; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MIRNA, 4EHP, TRANSLATIONAL REPRESSION, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.SOBTI,B.J.MEAD,C.IGREJA,A.G.STEWART,M.CHRISTIE REVDAT 5 15-NOV-23 7RUP 1 REMARK REVDAT 4 25-OCT-23 7RUP 1 REMARK REVDAT 3 31-MAY-23 7RUP 1 JRNL REVDAT 2 15-MAR-23 7RUP 1 JRNL REVDAT 1 24-AUG-22 7RUP 0 JRNL AUTH M.SOBTI,B.J.MEAD,A.G.STEWART,C.IGREJA,M.CHRISTIE JRNL TITL MOLECULAR BASIS FOR GIGYF-TNRC6 COMPLEX ASSEMBLY. JRNL REF RNA V. 29 724 2023 JRNL REFN ESSN 1469-9001 JRNL PMID 36854607 JRNL DOI 10.1261/RNA.079596.123 REMARK 2 REMARK 2 RESOLUTION. 1.23 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 23369 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 1111 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 19.4250 - 2.4586 1.00 2958 139 0.1710 0.1797 REMARK 3 2 2.4586 - 1.9520 1.00 2791 155 0.1475 0.1731 REMARK 3 3 1.9520 - 1.7054 1.00 2787 141 0.1301 0.1677 REMARK 3 4 1.7054 - 1.5496 1.00 2762 133 0.1233 0.1665 REMARK 3 5 1.5496 - 1.4386 1.00 2738 144 0.1277 0.1667 REMARK 3 6 1.4386 - 1.3538 1.00 2728 156 0.1385 0.1989 REMARK 3 7 1.3538 - 1.2860 1.00 2763 114 0.1587 0.1754 REMARK 3 8 1.2860 - 1.2300 1.00 2731 129 0.1785 0.2149 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.120 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 : 0.015 625 REMARK 3 ANGLE : 1.389 854 REMARK 3 CHIRALITY : 0.100 78 REMARK 3 PLANARITY : 0.013 115 REMARK 3 DIHEDRAL : 3.707 464 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 7RUP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000259089. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4-7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL 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 : 23420 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 REMARK 200 RESOLUTION RANGE LOW (A) : 19.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 3FMA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0-1.4 M NA/K PHOSPHATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.38950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.03200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.15950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.03200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.38950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.15950 REMARK 290 SMTRY3 4 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 TOTAL BURIED SURFACE AREA: 860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL 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 525 REMARK 465 PRO A 526 REMARK 465 LEU A 527 REMARK 465 GLU A 528 REMARK 465 MET A 529 REMARK 465 HIS A 530 REMARK 465 GLU A 531 REMARK 465 ALA A 532 REMARK 465 MET A 533 REMARK 465 ALA A 597 REMARK 465 GLY B 1471 REMARK 465 PRO B 1472 REMARK 465 LEU B 1473 REMARK 465 GLY B 1474 REMARK 465 SER B 1475 REMARK 465 ALA B 1476 REMARK 465 PRO B 1477 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 GLN A 534 CG CD OE1 NE2 REMARK 470 LYS A 535 CG CD CE NZ REMARK 470 LYS A 585 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 727 O HOH A 737 2.10 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RUP A 529 597 UNP Q6Y7W6 GGYF2_HUMAN 529 597 DBREF 7RUP B 1476 1486 UNP Q8NDV7 TNR6A_HUMAN 1729 1739 SEQADV 7RUP GLY A 525 UNP Q6Y7W6 EXPRESSION TAG SEQADV 7RUP PRO A 526 UNP Q6Y7W6 EXPRESSION TAG SEQADV 7RUP LEU A 527 UNP Q6Y7W6 EXPRESSION TAG SEQADV 7RUP GLU A 528 UNP Q6Y7W6 EXPRESSION TAG SEQADV 7RUP GLY B 1471 UNP Q8NDV7 EXPRESSION TAG SEQADV 7RUP PRO B 1472 UNP Q8NDV7 EXPRESSION TAG SEQADV 7RUP LEU B 1473 UNP Q8NDV7 EXPRESSION TAG SEQADV 7RUP GLY B 1474 UNP Q8NDV7 EXPRESSION TAG SEQADV 7RUP SER B 1475 UNP Q8NDV7 EXPRESSION TAG SEQRES 1 A 73 GLY PRO LEU GLU MET HIS GLU ALA MET GLN LYS TRP TYR SEQRES 2 A 73 TYR LYS ASP PRO GLN GLY GLU ILE GLN GLY PRO PHE ASN SEQRES 3 A 73 ASN GLN GLU MET ALA GLU TRP PHE GLN ALA GLY TYR PHE SEQRES 4 A 73 THR MET SER LEU LEU VAL LYS ARG ALA CSO ASP GLU SER SEQRES 5 A 73 PHE GLN PRO LEU GLY ASP ILE MET LYS MET TRP GLY ARG SEQRES 6 A 73 VAL PRO PHE SER PRO GLY PRO ALA SEQRES 1 B 16 GLY PRO LEU GLY SER ALA PRO SER ARG PRO PRO PRO GLY SEQRES 2 B 16 LEU THR GLY MODRES 7RUP CSO A 573 CYS MODIFIED RESIDUE HET CSO A 573 12 HET SO4 A 601 5 HETNAM CSO S-HYDROXYCYSTEINE HETNAM SO4 SULFATE ION FORMUL 1 CSO C3 H7 N O3 S FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *96(H2 O) HELIX 1 AA1 ASN A 550 GLY A 561 1 12 HELIX 2 AA2 LEU A 580 GLY A 588 1 9 SHEET 1 AA1 4 ILE A 545 PHE A 549 0 SHEET 2 AA1 4 TRP A 536 LYS A 539 -1 N TYR A 538 O GLN A 546 SHEET 3 AA1 4 LEU A 568 ARG A 571 -1 O LYS A 570 N TYR A 537 SHEET 4 AA1 4 GLN A 578 PRO A 579 -1 O GLN A 578 N VAL A 569 LINK C ALA A 572 N CSO A 573 1555 1555 1.33 LINK C CSO A 573 N ASP A 574 1555 1555 1.33 CISPEP 1 GLY A 547 PRO A 548 0 6.10 CRYST1 32.779 38.319 62.064 90.00 90.00 90.00 P 21 21 21 4 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 0.030507 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026097 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016112 0.00000