HEADER LIGASE 04-MAY-23 8J9R TITLE CRYSTAL STRUCTURE OF UBR BOX OF YIFS-UBR4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UBR4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 600 KDA RETINOBLASTOMA PROTEIN-ASSOCIATED FACTOR,N-RECOGNIN- COMPND 5 4,RING-TYPE E3 UBIQUITIN TRANSFERASE UBR4,RETINOBLASTOMA-ASSOCIATED COMPND 6 FACTOR OF 600 KDA,RBAF600,P600,ZINC FINGER UBR1-TYPE PROTEIN 1; 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: UBR4, KIAA0462, KIAA1307, RBAF600, ZUBR1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E3 LIGASE, UBR BOX, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR D.-E.JEONG,S.-J.KIM,H.-C.SHIN REVDAT 2 13-DEC-23 8J9R 1 JRNL REVDAT 1 06-DEC-23 8J9R 0 JRNL AUTH D.E.JEONG,H.S.LEE,B.KU,C.H.KIM,S.J.KIM,H.C.SHIN JRNL TITL INSIGHTS INTO THE RECOGNITION MECHANISM IN THE UBR BOX OF JRNL TITL 2 UBR4 FOR ITS SPECIFIC SUBSTRATES. JRNL REF COMMUN BIOL V. 6 1214 2023 JRNL REFN ESSN 2399-3642 JRNL PMID 38030679 JRNL DOI 10.1038/S42003-023-05602-7 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.-E.JEONG,H.-C.SHIN REMARK 1 TITL CRYSTAL STRUCTURE OF UBR BOX OF UBR4 WITH YIFS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 9760 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 489 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 27.7000 - 2.3800 1.00 3216 170 0.2263 0.2822 REMARK 3 2 2.3800 - 1.8900 0.99 3049 160 0.2535 0.3065 REMARK 3 3 1.8900 - 1.6500 0.99 3008 159 0.2291 0.2713 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) : 0.179 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.04 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 : 0.008 611 REMARK 3 ANGLE : 0.994 827 REMARK 3 CHIRALITY : 0.054 87 REMARK 3 PLANARITY : 0.005 104 REMARK 3 DIHEDRAL : 7.641 81 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 8J9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1300037486. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-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 : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.282 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9760 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 27.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: ALPHAFOLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS (PH5.6), 29% (W/V) REMARK 280 POLYETHYLENE GLYCOL 3350 (PEG3350), 0.2 M LITHIUM SULFATE REMARK 280 MONOHYDRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K 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 18.29000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.70000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.70000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.29000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.14000 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: 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 VAL A 1728 REMARK 465 LYS A 1729 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 1927 O HOH A 1968 1.87 REMARK 500 OD2 ASP A 1686 O HOH A 1901 1.88 REMARK 500 OG1 THR A 1692 O HOH A 1902 1.92 REMARK 500 OG SER A 1723 O HOH A 1903 1.99 REMARK 500 O HOH A 1931 O HOH A 1956 2.10 REMARK 500 O HOH A 1926 O HOH A 1936 2.11 REMARK 500 O HOH A 1984 O HOH A 2002 2.11 REMARK 500 O HOH A 1908 O HOH A 1979 2.14 REMARK 500 O HOH A 1962 O HOH A 1999 2.16 REMARK 500 O HOH A 1970 O HOH A 1978 2.18 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 GLN A1668 -143.71 48.85 REMARK 500 ASP A1686 -118.39 59.42 REMARK 500 ASP A1686 -116.91 58.77 REMARK 500 VAL A1697 -66.11 -100.73 REMARK 500 ALA A1707 -75.58 -93.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 ZN A 1801 REMARK 615 ZN A 1802 REMARK 615 ZN A 1803 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1662 SG REMARK 620 2 CYS A1691 SG 117.9 REMARK 620 3 CYS A1694 SG 103.2 104.0 REMARK 620 4 CYS A1714 SG 106.6 113.6 111.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1803 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1679 SG REMARK 620 2 CYS A1682 SG 115.9 REMARK 620 3 HIS A1699 ND1 113.3 110.5 REMARK 620 4 HIS A1702 ND1 108.0 108.0 99.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1694 SG REMARK 620 2 CYS A1698 SG 111.6 REMARK 620 3 CYS A1716 SG 110.7 108.7 REMARK 620 4 CYS A1724 SG 102.5 105.3 117.8 REMARK 620 N 1 2 3 DBREF 8J9R A 1660 1729 UNP Q5T4S7 UBR4_HUMAN 1660 1729 SEQADV 8J9R TYR A 1656 UNP Q5T4S7 LINKER SEQADV 8J9R ILE A 1657 UNP Q5T4S7 LINKER SEQADV 8J9R PHE A 1658 UNP Q5T4S7 LINKER SEQADV 8J9R SER A 1659 UNP Q5T4S7 LINKER SEQRES 1 A 74 TYR ILE PHE SER LYS LEU CYS THR PHE THR ILE THR GLN SEQRES 2 A 74 LYS GLU PHE MET ASN GLN HIS TRP TYR HIS CYS HIS THR SEQRES 3 A 74 CYS LYS MET VAL ASP GLY VAL GLY VAL CYS THR VAL CYS SEQRES 4 A 74 ALA LYS VAL CYS HIS LYS ASP HIS GLU ILE SER TYR ALA SEQRES 5 A 74 LYS TYR GLY SER PHE PHE CYS ASP CYS GLY ALA LYS GLU SEQRES 6 A 74 ASP GLY SER CYS LEU ALA LEU VAL LYS HET ZN A1801 1 HET ZN A1802 1 HET ZN A1803 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) FORMUL 5 HOH *102(H2 O) HELIX 1 AA1 THR A 1663 GLN A 1668 1 6 HELIX 2 AA2 THR A 1692 VAL A 1697 1 6 SHEET 1 AA1 3 VAL A1690 CYS A1691 0 SHEET 2 AA1 3 MET A1672 CYS A1679 -1 N TYR A1677 O VAL A1690 SHEET 3 AA1 3 ILE A1704 PHE A1712 -1 O SER A1705 N HIS A1678 LINK SG CYS A1662 ZN ZN A1802 1555 1555 2.31 LINK SG CYS A1679 ZN ZN A1803 1555 1555 2.28 LINK SG CYS A1682 ZN ZN A1803 1555 1555 2.19 LINK SG CYS A1691 ZN ZN A1802 1555 1555 2.29 LINK SG CYS A1694 ZN ZN A1801 1555 1555 2.34 LINK SG CYS A1694 ZN ZN A1802 1555 1555 2.31 LINK SG CYS A1698 ZN ZN A1801 1555 1555 2.29 LINK ND1 HIS A1699 ZN ZN A1803 1555 1555 2.05 LINK ND1 HIS A1702 ZN ZN A1803 1555 1555 2.06 LINK SG CYS A1714 ZN ZN A1802 1555 1555 2.33 LINK SG CYS A1716 ZN ZN A1801 1555 1555 2.32 LINK SG CYS A1724 ZN ZN A1801 1555 1555 2.36 CRYST1 36.580 38.280 55.400 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 0.027337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018051 0.00000 CONECT 117 1110 CONECT 409 1111 CONECT 457 1111 CONECT 592 1110 CONECT 646 1109 1110 CONECT 704 1109 CONECT 715 1111 CONECT 766 1111 CONECT 959 1110 CONECT 981 1109 CONECT 1064 1109 CONECT 1109 646 704 981 1064 CONECT 1110 117 592 646 959 CONECT 1111 409 457 715 766 MASTER 287 0 3 2 3 0 0 6 672 1 14 6 END