HEADER LIGASE 26-APR-21 7EP3 TITLE CRYSTAL STRUCTURE OF ZER1 BOUND TO GAGN DEGRON COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ZER-1 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 520-766; COMPND 5 SYNONYM: HZYG,ZYG-11 HOMOLOG B-LIKE PROTEIN,ZYG11B-LIKE PROTEIN; COMPND 6 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: ZER1, C9ORF60, ZYG, ZYG11BL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E3 LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR X.YAN,Y.LI REVDAT 3 29-NOV-23 7EP3 1 REMARK REVDAT 2 01-SEP-21 7EP3 1 JRNL REVDAT 1 14-JUL-21 7EP3 0 JRNL AUTH X.YAN,Y.LI,G.WANG,Z.ZHOU,G.SONG,Q.FENG,Y.ZHAO,W.MI,Z.MA, JRNL AUTH 2 C.DONG JRNL TITL MOLECULAR BASIS FOR RECOGNITION OF GLY/N-DEGRONS BY CRL2 JRNL TITL 2 ZYG11B AND CRL2 ZER1 . JRNL REF MOL.CELL V. 81 3262 2021 JRNL REFN ISSN 1097-2765 JRNL PMID 34214466 JRNL DOI 10.1016/J.MOLCEL.2021.06.010 REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 43322 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1983 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 1.5670 - 1.5130 0.91 0 192 0.2845 0.2880 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.50 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 : 0.006 2008 REMARK 3 ANGLE : 0.752 2712 REMARK 3 CHIRALITY : 0.047 294 REMARK 3 PLANARITY : 0.005 347 REMARK 3 DIHEDRAL : 23.208 757 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 7EP3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300020718. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 80 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 : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979191 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 0.7.4 REMARK 200 DATA SCALING SOFTWARE : XDS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43366 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 59.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.2_4158 REMARK 200 STARTING MODEL: 7EP0 REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FORMATE, 23% (WT/VOL) REMARK 280 POLYETHYLENE GLYCOL 3,350, 0.033% (WT/VOL) ANTHRONE, 0.033% (WT/ REMARK 280 VOL) CONGO RED, 0.033% (WT/VOL) N-(2-ACETAMIDO)-2- REMARK 280 AMINOETHANESULFONIC ACID, 0.002 M HEPES SODIUM PH 6.8, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.98500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.21000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.98500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.21000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.98500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 60.21000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 34.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.98500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 60.21000 REMARK 290 SMTRY3 8 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: 1900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLU A 760 REMARK 465 ASN A 761 REMARK 465 MET A 762 REMARK 465 ASP A 763 REMARK 465 THR A 764 REMARK 465 SER A 765 REMARK 465 ARG A 766 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 A 759 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 ASP A 541 -168.39 -106.42 REMARK 500 ASN A 677 63.84 -111.96 REMARK 500 REMARK 500 REMARK: NULL DBREF 7EP3 A 520 766 UNP Q7Z7L7 ZER1_HUMAN 520 766 SEQADV 7EP3 GLY A 516 UNP Q7Z7L7 EXPRESSION TAG SEQADV 7EP3 ALA A 517 UNP Q7Z7L7 EXPRESSION TAG SEQADV 7EP3 GLY A 518 UNP Q7Z7L7 EXPRESSION TAG SEQADV 7EP3 ASN A 519 UNP Q7Z7L7 EXPRESSION TAG SEQRES 1 A 251 GLY ALA GLY ASN LYS MET GLY PHE VAL VAL THR MET LEU SEQRES 2 A 251 LYS LEU ILE GLN LYS LYS LEU LEU ASP LYS THR CYS ASP SEQRES 3 A 251 GLN VAL MET GLU PHE SER TRP SER ALA LEU TRP ASN ILE SEQRES 4 A 251 THR ASP GLU THR PRO ASP ASN CYS GLU MET PHE LEU ASN SEQRES 5 A 251 PHE ASN GLY MET LYS LEU PHE LEU ASP CYS LEU LYS GLU SEQRES 6 A 251 PHE PRO GLU LYS GLN GLU LEU HIS ARG ASN MET LEU GLY SEQRES 7 A 251 LEU LEU GLY ASN VAL ALA GLU VAL LYS GLU LEU ARG PRO SEQRES 8 A 251 GLN LEU MET THR SER GLN PHE ILE SER VAL PHE SER ASN SEQRES 9 A 251 LEU LEU GLU SER LYS ALA ASP GLY ILE GLU VAL SER TYR SEQRES 10 A 251 ASN ALA CYS GLY VAL LEU SER HIS ILE MET PHE ASP GLY SEQRES 11 A 251 PRO GLU ALA TRP GLY VAL CYS GLU PRO GLN ARG GLU GLU SEQRES 12 A 251 VAL GLU GLU ARG MET TRP ALA ALA ILE GLN SER TRP ASP SEQRES 13 A 251 ILE ASN SER ARG ARG ASN ILE ASN TYR ARG SER PHE GLU SEQRES 14 A 251 PRO ILE LEU ARG LEU LEU PRO GLN GLY ILE SER PRO VAL SEQRES 15 A 251 SER GLN HIS TRP ALA THR TRP ALA LEU TYR ASN LEU VAL SEQRES 16 A 251 SER VAL TYR PRO ASP LYS TYR CYS PRO LEU LEU ILE LYS SEQRES 17 A 251 GLU GLY GLY MET PRO LEU LEU ARG ASP ILE ILE LYS MET SEQRES 18 A 251 ALA THR ALA ARG GLN GLU THR LYS GLU MET ALA ARG LYS SEQRES 19 A 251 VAL ILE GLU HIS CYS SER ASN PHE LYS GLU GLU ASN MET SEQRES 20 A 251 ASP THR SER ARG FORMUL 2 HOH *95(H2 O) HELIX 1 AA1 ASN A 519 ASP A 537 1 19 HELIX 2 AA2 ASP A 541 THR A 555 1 15 HELIX 3 AA3 THR A 558 PHE A 568 1 11 HELIX 4 AA4 ASN A 569 PHE A 581 1 13 HELIX 5 AA5 LYS A 584 GLU A 600 1 17 HELIX 6 AA6 VAL A 601 MET A 609 5 9 HELIX 7 AA7 THR A 610 LEU A 621 1 12 HELIX 8 AA8 ILE A 628 ASP A 644 1 17 HELIX 9 AA9 GLY A 645 TRP A 649 5 5 HELIX 10 AB1 GLN A 655 TRP A 670 1 16 HELIX 11 AB2 PHE A 683 ARG A 688 1 6 HELIX 12 AB3 SER A 695 TYR A 713 1 19 HELIX 13 AB4 TYR A 713 GLU A 724 1 12 HELIX 14 AB5 GLY A 725 LYS A 735 1 11 HELIX 15 AB6 ARG A 740 GLU A 759 1 20 CISPEP 1 GLU A 653 PRO A 654 0 -0.47 CRYST1 67.970 120.420 68.000 90.00 90.00 90.00 C 2 2 21 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 0.014712 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008304 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014706 0.00000