HEADER RNA BINDING PROTEIN 08-OCT-24 9JUR TITLE CRYSTAL STRUCTURE OF NHL DOMAIN OF HUMAN E3 UBIQUITIN-PROTEIN LIGASE TITLE 2 TRIM71 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE TRIM71; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NHL DOMAIN; COMPND 5 SYNONYM: PROTEIN LIN-41 HOMOLOG,RING-TYPE E3 UBIQUITIN TRANSFERASE COMPND 6 TRIM71,TRIPARTITE MOTIF-CONTAINING PROTEIN 71; COMPND 7 EC: 2.3.2.27; 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: TRIM71, LIN41; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS NHL DOMAIN, E3 UBIQUITIN-PROTEIN LIGASE, RNA BINDING, RNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.Q.LV,E.H.KAZY REVDAT 1 30-APR-25 9JUR 0 JRNL AUTH L.LIN,M.K.E.HASAN,X.GU,S.U.KHAN,A.HOSSAIN,M.O.FARUQE, JRNL AUTH 2 S.SHAHRIAR,M.N.H.JOY,M.M.H.SOUROV,M.I.KHAN,L.ZHANG,M.LV, JRNL AUTH 3 Y.SHI JRNL TITL HUMAN TRIPARTITE MOTIF-CONTAINING PROTEIN 71 JRNL TITL 2 NCL-1/HT2A/LIN-41 DOMAIN CRYSTAL STRUCTURE AND ITS POTENTIAL JRNL TITL 3 NATURAL INHIBITORS. JRNL REF INT.J.BIOL.MACROMOL. V. 309 42764 2025 JRNL REFN ISSN 0141-8130 JRNL PMID 40180090 JRNL DOI 10.1016/J.IJBIOMAC.2025.142764 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19_4092: ???) 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 5652 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.420 REMARK 3 FREE R VALUE TEST SET COUNT : 250 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 32.6300 - 3.5900 0.94 2715 99 0.1962 0.2185 REMARK 3 2 3.5900 - 2.8500 0.96 2687 151 0.2256 0.2938 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.990 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 : 0.002 2197 REMARK 3 ANGLE : 0.500 2966 REMARK 3 CHIRALITY : 0.048 302 REMARK 3 PLANARITY : 0.003 404 REMARK 3 DIHEDRAL : 14.382 786 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 9JUR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 11-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052294. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-23 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5652 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 32.633 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.24500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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 (%): 38.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% V/V POLYETHYLENE GLYCOL MONOMETHYL REMARK 280 ETHER 550, 0.05 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1 M HEPES PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 32.27200 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: 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 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 LYS A 581 REMARK 465 SER A 582 REMARK 465 GLY A 583 REMARK 465 ARG A 584 REMARK 465 SER A 585 REMARK 465 TYR A 586 REMARK 465 VAL A 587 REMARK 465 GLY A 588 REMARK 465 ILE A 589 REMARK 465 GLY A 590 REMARK 465 LEU A 591 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 LYS A 616 CG CD CE NZ REMARK 470 GLU A 692 CG CD OE1 OE2 REMARK 470 LYS A 696 CG CD CE NZ REMARK 470 LYS A 745 CG CD CE NZ 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 TRP A 610 -79.77 -136.53 REMARK 500 ARG A 655 70.60 61.71 REMARK 500 ALA A 657 -66.10 -95.70 REMARK 500 LYS A 672 -71.01 -54.01 REMARK 500 TYR A 702 74.02 62.47 REMARK 500 TRP A 704 -71.09 -105.26 REMARK 500 ARG A 751 -86.14 -129.00 REMARK 500 GLN A 779 -26.99 68.74 REMARK 500 GLN A 798 -110.28 -110.51 REMARK 500 SER A 813 -70.81 -52.68 REMARK 500 ARG A 843 75.73 52.63 REMARK 500 SER A 845 -85.53 -113.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 9JUR A 581 868 UNP Q2Q1W2 LIN41_HUMAN 581 868 SEQRES 1 A 288 LYS SER GLY ARG SER TYR VAL GLY ILE GLY LEU PRO GLY SEQRES 2 A 288 LEU SER PHE GLY SER GLU GLY ASP SER ASP GLY LYS LEU SEQRES 3 A 288 CYS ARG PRO TRP GLY VAL SER VAL ASP LYS GLU GLY TYR SEQRES 4 A 288 ILE ILE VAL ALA ASP ARG SER ASN ASN ARG ILE GLN VAL SEQRES 5 A 288 PHE LYS PRO CYS GLY ALA PHE HIS HIS LYS PHE GLY THR SEQRES 6 A 288 LEU GLY SER ARG PRO GLY GLN PHE ASP ARG PRO ALA GLY SEQRES 7 A 288 VAL ALA CYS ASP ALA SER ARG ARG ILE VAL VAL ALA ASP SEQRES 8 A 288 LYS ASP ASN HIS ARG ILE GLN ILE PHE THR PHE GLU GLY SEQRES 9 A 288 GLN PHE LEU LEU LYS PHE GLY GLU LYS GLY THR LYS ASN SEQRES 10 A 288 GLY GLN PHE ASN TYR PRO TRP ASP VAL ALA VAL ASN SER SEQRES 11 A 288 GLU GLY LYS ILE LEU VAL SER ASP THR ARG ASN HIS ARG SEQRES 12 A 288 ILE GLN LEU PHE GLY PRO ASP GLY VAL PHE LEU ASN LYS SEQRES 13 A 288 TYR GLY PHE GLU GLY ALA LEU TRP LYS HIS PHE ASP SER SEQRES 14 A 288 PRO ARG GLY VAL ALA PHE ASN HIS GLU GLY HIS LEU VAL SEQRES 15 A 288 VAL THR ASP PHE ASN ASN HIS ARG LEU LEU VAL ILE HIS SEQRES 16 A 288 PRO ASP CYS GLN SER ALA ARG PHE LEU GLY SER GLU GLY SEQRES 17 A 288 THR GLY ASN GLY GLN PHE LEU ARG PRO GLN GLY VAL ALA SEQRES 18 A 288 VAL ASP GLN GLU GLY ARG ILE ILE VAL ALA ASP SER ARG SEQRES 19 A 288 ASN HIS ARG VAL GLN MET PHE GLU SER ASN GLY SER PHE SEQRES 20 A 288 LEU CYS LYS PHE GLY ALA GLN GLY SER GLY PHE GLY GLN SEQRES 21 A 288 MET ASP ARG PRO SER GLY ILE ALA ILE THR PRO ASP GLY SEQRES 22 A 288 MET ILE VAL VAL VAL ASP PHE GLY ASN ASN ARG ILE LEU SEQRES 23 A 288 VAL PHE HET MG A 901 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *7(H2 O) HELIX 1 AA1 ASP A 673 HIS A 675 5 3 HELIX 2 AA2 GLU A 740 ASP A 748 5 9 SHEET 1 AA1 4 LEU A 594 PHE A 596 0 SHEET 2 AA1 4 ARG A 864 PHE A 868 -1 O ILE A 865 N PHE A 596 SHEET 3 AA1 4 ILE A 855 ASP A 859 -1 N VAL A 857 O LEU A 866 SHEET 4 AA1 4 PRO A 844 ILE A 849 -1 N ALA A 848 O VAL A 856 SHEET 1 AA2 2 SER A 598 GLU A 599 0 SHEET 2 AA2 2 LYS A 605 LEU A 606 1 O LEU A 606 N SER A 598 SHEET 1 AA3 4 VAL A 612 VAL A 614 0 SHEET 2 AA3 4 ILE A 620 ASP A 624 -1 O ILE A 621 N SER A 613 SHEET 3 AA3 4 ARG A 629 PHE A 633 -1 O PHE A 633 N ILE A 620 SHEET 4 AA3 4 PHE A 639 PHE A 643 -1 O PHE A 643 N ILE A 630 SHEET 1 AA4 4 PRO A 656 CYS A 661 0 SHEET 2 AA4 4 ARG A 666 ASP A 671 -1 O VAL A 668 N ALA A 660 SHEET 3 AA4 4 ARG A 676 THR A 681 -1 O PHE A 680 N ILE A 667 SHEET 4 AA4 4 PHE A 686 PHE A 690 -1 O PHE A 690 N ILE A 677 SHEET 1 AA5 4 PRO A 703 VAL A 708 0 SHEET 2 AA5 4 ILE A 714 ASP A 718 -1 O LEU A 715 N ALA A 707 SHEET 3 AA5 4 ARG A 723 PHE A 727 -1 O PHE A 727 N ILE A 714 SHEET 4 AA5 4 PHE A 733 GLY A 738 -1 O ASN A 735 N LEU A 726 SHEET 1 AA6 4 PRO A 750 PHE A 755 0 SHEET 2 AA6 4 LEU A 761 ASP A 765 -1 O VAL A 762 N ALA A 754 SHEET 3 AA6 4 ARG A 770 ILE A 774 -1 O ILE A 774 N LEU A 761 SHEET 4 AA6 4 ALA A 781 LEU A 784 -1 O LEU A 784 N LEU A 771 SHEET 1 AA7 2 SER A 786 GLU A 787 0 SHEET 2 AA7 2 GLN A 793 PHE A 794 1 O PHE A 794 N SER A 786 SHEET 1 AA8 4 PRO A 797 VAL A 802 0 SHEET 2 AA8 4 ILE A 808 ASP A 812 -1 O ILE A 809 N ALA A 801 SHEET 3 AA8 4 ARG A 817 PHE A 821 -1 O PHE A 821 N ILE A 808 SHEET 4 AA8 4 PHE A 827 PHE A 831 -1 O CYS A 829 N MET A 820 CRYST1 45.674 64.544 46.139 90.00 110.97 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 0.021894 0.000000 0.008391 0.00000 SCALE2 0.000000 0.015493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023211 0.00000 TER 2144 PHE A 868 HETATM 2145 MG MG A 901 -20.652 8.848 14.915 1.00 34.06 MG HETATM 2146 O HOH A1001 -6.402 21.352 -4.886 1.00 26.92 O HETATM 2147 O HOH A1002 -22.658 12.094 -13.911 1.00 21.85 O HETATM 2148 O HOH A1003 -17.430 7.202 -18.279 1.00 34.61 O HETATM 2149 O HOH A1004 -2.791 18.827 -3.508 1.00 28.47 O HETATM 2150 O HOH A1005 -9.228 30.881 6.809 1.00 28.44 O HETATM 2151 O HOH A1006 -16.222 1.509 5.586 1.00 22.38 O HETATM 2152 O HOH A1007 17.389 20.920 6.728 1.00 28.66 O MASTER 238 0 1 2 28 0 0 6 2151 1 0 23 END