HEADER RNA BINDING PROTEIN 10-JUL-19 6S8R TITLE D. MELANOGASTER RNA HELICASE ME31B IN COMPLEX WITH GIGYF COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE ME31B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MATERNAL EXPRESSION AT 31B; COMPND 5 EC: 3.6.4.13; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GIGYF FAMILY PROTEIN CG11148; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: ME31B, CG4916; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 10 ORGANISM_COMMON: FRUIT FLY; SOURCE 11 ORGANISM_TAXID: 7227; SOURCE 12 GENE: CG11148; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSLATION, TRANSLATIONAL CONTROL, MRNA DECAY, MIRNA, RNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.PETER,E.VALKOV REVDAT 3 24-JAN-24 6S8R 1 REMARK REVDAT 2 09-OCT-19 6S8R 1 JRNL REVDAT 1 04-SEP-19 6S8R 0 JRNL AUTH D.PETER,V.RUSCICA,P.BAWANKAR,R.WEBER,S.HELMS,E.VALKOV, JRNL AUTH 2 C.IGREJA,E.IZAURRALDE JRNL TITL MOLECULAR BASIS FOR GIGYF-ME31B COMPLEX ASSEMBLY IN JRNL TITL 2 4EHP-MEDIATED TRANSLATIONAL REPRESSION. JRNL REF GENES DEV. V. 33 1355 2019 JRNL REFN ISSN 0890-9369 JRNL PMID 31439631 JRNL DOI 10.1101/GAD.329219.119 REMARK 2 REMARK 2 RESOLUTION. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.5 REMARK 3 NUMBER OF REFLECTIONS : 6800 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 326 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 39.7000 - 3.0400 0.99 3841 190 0.1934 0.2389 REMARK 3 2 3.0400 - 2.4100 0.71 2633 136 0.2302 0.3197 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.276 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.19 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 : 0.003 1616 REMARK 3 ANGLE : 0.459 2178 REMARK 3 CHIRALITY : 0.041 237 REMARK 3 PLANARITY : 0.002 285 REMARK 3 DIHEDRAL : 6.686 954 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 6S8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1292103176. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9996 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7712 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 42.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.18800 REMARK 200 FOR THE DATA SET : 8.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.5 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.06000 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: 5ANR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE (PH 5.0), 0.15 M REMARK 280 AMMONIUM CHLORIDE, 16% (W/V) PEG 6000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K 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 18.72000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.33500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.33500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.72000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.98000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10190 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 260 REMARK 465 PRO A 261 REMARK 465 HIS A 262 REMARK 465 MET A 263 REMARK 465 GLU A 264 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 601 O HOH A 609 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN A 281 OD2 ASP B 343 3445 2.16 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 SER A 352 -156.47 -90.48 REMARK 500 THR A 356 63.77 -118.91 REMARK 500 TYR A 430 15.00 -153.74 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 ACT A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 504 DBREF 6S8R A 264 431 UNP P23128 DDX6_DROME 264 431 DBREF 6S8R B 343 369 UNP Q7KQM6 GGYF1_DROME 343 369 SEQADV 6S8R GLY A 260 UNP P23128 EXPRESSION TAG SEQADV 6S8R PRO A 261 UNP P23128 EXPRESSION TAG SEQADV 6S8R HIS A 262 UNP P23128 EXPRESSION TAG SEQADV 6S8R MET A 263 UNP P23128 EXPRESSION TAG SEQRES 1 A 172 GLY PRO HIS MET GLU LEU THR LEU LYS GLY VAL THR GLN SEQRES 2 A 172 TYR TYR ALA PHE VAL GLN GLU ARG GLN LYS VAL HIS CYS SEQRES 3 A 172 LEU ASN THR LEU PHE SER LYS LEU GLN ILE ASN GLN SER SEQRES 4 A 172 ILE ILE PHE CYS ASN SER THR GLN ARG VAL GLU LEU LEU SEQRES 5 A 172 ALA LYS LYS ILE THR GLU LEU GLY TYR CYS CYS TYR TYR SEQRES 6 A 172 ILE HIS ALA LYS MET ALA GLN ALA HIS ARG ASN ARG VAL SEQRES 7 A 172 PHE HIS ASP PHE ARG GLN GLY LEU CYS ARG ASN LEU VAL SEQRES 8 A 172 CYS SER ASP LEU PHE THR ARG GLY ILE ASP VAL GLN ALA SEQRES 9 A 172 VAL ASN VAL VAL ILE ASN PHE ASP PHE PRO ARG MET ALA SEQRES 10 A 172 GLU THR TYR LEU HIS ARG ILE GLY ARG SER GLY ARG PHE SEQRES 11 A 172 GLY HIS LEU GLY ILE ALA ILE ASN LEU ILE THR TYR GLU SEQRES 12 A 172 ASP ARG PHE ASP LEU HIS ARG ILE GLU LYS GLU LEU GLY SEQRES 13 A 172 THR GLU ILE LYS PRO ILE PRO LYS VAL ILE ASP PRO ALA SEQRES 14 A 172 LEU TYR VAL SEQRES 1 B 27 ASP GLU ASN LEU PRO GLU TRP ALA ILE GLU ASN PRO SER SEQRES 2 B 27 LYS LEU GLY GLY SER PHE ASP ALA SER GLY ALA PHE HIS SEQRES 3 B 27 GLY HET ACT A 501 7 HET ACT A 502 7 HET ACT A 503 7 HET ACT A 504 7 HETNAM ACT ACETATE ION FORMUL 3 ACT 4(C2 H3 O2 1-) FORMUL 7 HOH *35(H2 O) HELIX 1 AA1 GLN A 278 ARG A 280 5 3 HELIX 2 AA2 GLN A 281 LEU A 293 1 13 HELIX 3 AA3 SER A 304 GLY A 319 1 16 HELIX 4 AA4 ALA A 330 GLY A 344 1 15 HELIX 5 AA5 MET A 375 GLY A 384 1 10 HELIX 6 AA6 THR A 400 GLU A 402 5 3 HELIX 7 AA7 ASP A 403 GLY A 415 1 13 HELIX 8 AA8 ASP A 426 TYR A 430 5 5 SHEET 1 AA1 7 TYR A 323 ILE A 325 0 SHEET 2 AA1 7 ASN A 348 CYS A 351 1 O ASN A 348 N TYR A 323 SHEET 3 AA1 7 GLN A 297 PHE A 301 1 N ILE A 300 O LEU A 349 SHEET 4 AA1 7 VAL A 364 ASN A 369 1 O ILE A 368 N PHE A 301 SHEET 5 AA1 7 GLY A 393 ILE A 399 1 O ILE A 396 N ASN A 369 SHEET 6 AA1 7 VAL A 270 PHE A 276 1 N TYR A 273 O ALA A 395 SHEET 7 AA1 7 LYS A 419 PRO A 420 1 O LYS A 419 N GLN A 272 SHEET 1 AA2 2 SER B 360 PHE B 361 0 SHEET 2 AA2 2 PHE B 367 HIS B 368 -1 O HIS B 368 N SER B 360 SSBOND 1 CYS A 321 CYS A 346 1555 1555 2.05 SITE 1 AC1 5 SER A 291 THR A 316 CYS A 322 HOH A 626 SITE 2 AC1 5 GLY B 358 SITE 1 AC2 3 GLU A 309 PRO A 422 VAL A 424 SITE 1 AC3 3 GLU A 279 LYS A 282 ASN A 303 SITE 1 AC4 4 GLN A 278 TYR A 401 HOH A 608 LEU B 346 CRYST1 37.440 41.960 122.670 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 0.026709 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008152 0.00000