HEADER LIGASE 14-JAN-25 9MUX TITLE STRUCTURE OF UBR1-RWA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UBR1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBR-BOX DOMAIN (UNP RESIDUES 97-168); COMPND 5 SYNONYM: N-RECOGNIN-1,UBIQUITIN-PROTEIN LIGASE E3-ALPHA-1,UBIQUITIN- COMPND 6 PROTEIN LIGASE E3-ALPHA-I; COMPND 7 EC: 2.3.2.27; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ARG-TRP-ALA-NH2 PEPTIDE; COMPND 11 CHAIN: D; 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: UBR1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1-HUBR1-UBRBOX; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS UBR, E3 LIGASE, NATURAL LIGANDS, PROTEIN BINDING, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR S.HUANG,J.WU,S.TAYLOR,Y.CHEN REVDAT 2 25-FEB-26 9MUX 1 JRNL REVDAT 1 13-AUG-25 9MUX 0 JRNL AUTH S.T.HUANG,D.H.CHEN,T.REN,N.THOMAS,J.WU,B.SANKARAN,R.JONES, JRNL AUTH 2 S.TAYLOR,Y.CHEN JRNL TITL AN ALTERNATIVE POCKET FOR BINDING THE N-DEGRONS BY THE UBR1 JRNL TITL 2 AND UBR2 UBIQUITIN E3 LIGASES. JRNL REF PROTEIN SCI. V. 34 70248 2025 JRNL REFN ESSN 1469-896X JRNL PMID 40880185 JRNL DOI 10.1002/PRO.70248 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.2_5419: ???) 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 14057 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.510 REMARK 3 FREE R VALUE TEST SET COUNT : 634 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 25.2500 - 2.2100 0.98 2862 132 0.1411 0.1439 REMARK 3 2 2.2000 - 1.7500 0.97 2772 126 0.1444 0.1484 REMARK 3 3 1.7500 - 1.5300 0.96 2718 121 0.1272 0.1531 REMARK 3 4 1.5300 - 1.3900 0.94 2659 131 0.1454 0.1435 REMARK 3 5 1.3900 - 1.2900 0.86 2412 124 0.1609 0.1930 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.060 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 : 0.007 646 REMARK 3 ANGLE : 0.928 876 REMARK 3 CHIRALITY : 0.076 89 REMARK 3 PLANARITY : 0.008 117 REMARK 3 DIHEDRAL : 13.421 229 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 9MUX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000291219. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-24 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14074 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : 0.04200 REMARK 200 FOR THE DATA SET : 19.4710 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.10400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 19.47 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 (%): 31.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES BUFFER 25%PEG3350, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283.15K 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 21.90450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 VAL A 122 N CA C O CB CG1 CG2 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 A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 99 SG REMARK 620 2 CYS A 124 SG 111.9 REMARK 620 3 CYS A 127 SG 105.7 96.1 REMARK 620 4 CYS A 149 SG 113.1 116.1 112.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 112 SG REMARK 620 2 CYS A 115 SG 113.3 REMARK 620 3 HIS A 133 ND1 110.3 103.3 REMARK 620 4 HIS A 136 ND1 111.6 105.9 112.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 127 SG REMARK 620 2 CYS A 151 SG 112.1 REMARK 620 3 CYS A 163 SG 112.3 113.8 REMARK 620 4 HIS A 166 ND1 106.0 111.9 99.7 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9DNO RELATED DB: PDB REMARK 900 RELATED ID: 9DNP RELATED DB: PDB REMARK 900 RELATED ID: 9DNQ RELATED DB: PDB REMARK 900 RELATED ID: 9DNR RELATED DB: PDB DBREF 9MUX A 97 168 UNP Q8IWV7 UBR1_HUMAN 97 168 DBREF 9MUX D 1 4 PDB 9MUX 9MUX 1 4 SEQADV 9MUX GLY A 92 UNP Q8IWV7 EXPRESSION TAG SEQADV 9MUX PRO A 93 UNP Q8IWV7 EXPRESSION TAG SEQADV 9MUX LEU A 94 UNP Q8IWV7 EXPRESSION TAG SEQADV 9MUX GLY A 95 UNP Q8IWV7 EXPRESSION TAG SEQADV 9MUX SER A 96 UNP Q8IWV7 EXPRESSION TAG SEQRES 1 A 77 GLY PRO LEU GLY SER GLN LEU CYS GLY ARG VAL PHE LYS SEQRES 2 A 77 SER GLY GLU THR THR TYR SER CYS ARG ASP CYS ALA ILE SEQRES 3 A 77 ASP PRO THR CYS VAL LEU CYS MET ASP CYS PHE GLN ASP SEQRES 4 A 77 SER VAL HIS LYS ASN HIS ARG TYR LYS MET HIS THR SER SEQRES 5 A 77 THR GLY GLY GLY PHE CYS ASP CYS GLY ASP THR GLU ALA SEQRES 6 A 77 TRP LYS THR GLY PRO PHE CYS VAL ASN HIS GLU PRO SEQRES 1 D 4 ARG TRP ALA NH2 HET NH2 D 4 1 HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION FORMUL 2 NH2 H2 N FORMUL 3 ZN 3(ZN 2+) FORMUL 6 HOH *81(H2 O) HELIX 1 AA1 CYS A 124 ASP A 130 1 7 HELIX 2 AA2 SER A 131 HIS A 136 5 6 SHEET 1 AA1 2 THR A 108 CYS A 112 0 SHEET 2 AA1 2 TYR A 138 THR A 142 -1 O LYS A 139 N SER A 111 LINK C ALA D 3 N NH2 D 4 1555 1555 1.33 LINK SG CYS A 99 ZN ZN A 201 1555 1555 2.29 LINK SG CYS A 112 ZN ZN A 203 1555 1555 2.30 LINK SG CYS A 115 ZN ZN A 203 1555 1555 2.30 LINK SG CYS A 124 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 127 ZN ZN A 201 1555 1555 2.38 LINK SG CYS A 127 ZN ZN A 202 1555 1555 2.36 LINK ND1 HIS A 133 ZN ZN A 203 1555 1555 2.07 LINK ND1 HIS A 136 ZN ZN A 203 1555 1555 2.02 LINK SG CYS A 149 ZN ZN A 201 1555 1555 2.32 LINK SG CYS A 151 ZN ZN A 202 1555 1555 2.30 LINK SG CYS A 163 ZN ZN A 202 1555 1555 2.30 LINK ND1 HIS A 166 ZN ZN A 202 1555 1555 2.06 CRYST1 27.091 43.809 27.085 90.00 111.27 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 0.036913 0.000000 0.014369 0.00000 SCALE2 0.000000 0.022826 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039619 0.00000 CONECT 52 631 CONECT 157 633 CONECT 182 633 CONECT 251 631 CONECT 273 631 632 CONECT 321 633 CONECT 348 633 CONECT 450 631 CONECT 464 632 CONECT 555 632 CONECT 577 632 CONECT 626 629 CONECT 629 626 CONECT 631 52 251 273 450 CONECT 632 273 464 555 577 CONECT 633 157 182 321 348 MASTER 233 0 4 2 2 0 0 6 699 2 16 7 END