HEADER STRUCTURAL PROTEIN 15-AUG-19 6U19 TITLE SOLUTION STRUCTURE OF THE RAZUL DOMAIN FROM 26S PROTEASOME SUBUNIT TITLE 2 HRPN10/S5A COMPLEXED WITH THE AZUL DOMAIN FROM E3 LIGASE E6AP/UBE3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 305-377; COMPND 5 SYNONYM: 26S PROTEASOME REGULATORY SUBUNIT RPN10,26S PROTEASOME COMPND 6 REGULATORY SUBUNIT S5A,ANTISECRETORY FACTOR 1,ASF,MULTIUBIQUITIN COMPND 7 CHAIN-BINDING PROTEIN; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UBIQUITIN-PROTEIN LIGASE E3A; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 24-87; COMPND 13 SYNONYM: E6AP UBIQUITIN-PROTEIN LIGASE,HECT-TYPE UBIQUITIN COMPND 14 TRANSFERASE E3A,HUMAN PAPILLOMAVIRUS E6-ASSOCIATED PROTEIN,ONCOGENIC COMPND 15 PROTEIN-ASSOCIATED PROTEIN E6-AP,RENAL CARCINOMA ANTIGEN NY-REN-54; COMPND 16 EC: 2.3.2.26; COMPND 17 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: PSMD4, MCB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: UBE3A, E6AP, EPVE6AP, HPVE6A; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEASOME, SUBUNIT, COMPLEX, UBIQUITINATION, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR X.CHEN,K.J.WALTERS REVDAT 5 22-MAY-24 6U19 1 REMARK REVDAT 4 14-JUN-23 6U19 1 REMARK REVDAT 3 20-MAY-20 6U19 1 TITLE REVDAT 2 25-MAR-20 6U19 1 JRNL REVDAT 1 18-MAR-20 6U19 0 JRNL AUTH G.R.BUEL,X.CHEN,R.CHARI,M.J.O'NEILL,D.L.EBELLE,C.JENKINS, JRNL AUTH 2 V.SRIDHARAN,S.G.TARASOV,N.I.TARASOVA,T.ANDRESSON,K.J.WALTERS JRNL TITL STRUCTURE OF E3 LIGASE E6AP WITH A PROTEASOME-BINDING SITE JRNL TITL 2 PROVIDED BY SUBSTRATE RECEPTOR HRPN10. JRNL REF NAT COMMUN V. 11 1291 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32157086 JRNL DOI 10.1038/S41467-020-15073-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6U19 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243701. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N; REMARK 210 U-35% 2H] 26S PROTEASOME NON- REMARK 210 ATPASE REGULATORY SUBUNIT 4 (305- REMARK 210 377), 0.75 MM UBIQUITIN-PROTEIN REMARK 210 LIGASE E3A (24-87), 10 MM MOPS, REMARK 210 50 MM SODIUM CHLORIDE, 5 MM DTT, REMARK 210 10 UM ZINC SULPHATE, 0.1 % REMARK 210 SODIUM AZIDE, 1 MM PEFABLOC, 95% REMARK 210 H2O/5% D2O; 0.5 MM [U-100% 13C; REMARK 210 U-100% 15N; U-35% 2H] 26S REMARK 210 PROTEASOME NON-ATPASE REGULATORY REMARK 210 SUBUNIT 4 (305-377), 0.75 MM REMARK 210 UBIQUITIN-PROTEIN LIGASE E3A (24- REMARK 210 87), 10 MM MOPS, 50 MM SODIUM REMARK 210 CHLORIDE, 5 MM DTT, 10 UM ZINC REMARK 210 SULPHATE, 0.1 % SODIUM AZIDE, 1 REMARK 210 MM PEFABLOC, 100% D2O; 0.5 MM [U- REMARK 210 100% 13C; U-100% 15N] UBIQUITIN- REMARK 210 PROTEIN LIGASE E3A (24-87), 0.75 REMARK 210 MM 26S PROTEASOME NON-ATPASE REMARK 210 REGULATORY SUBUNIT 4 (305-377), REMARK 210 10 MM MOPS, 50 MM SODIUM REMARK 210 CHLORIDE, 5 MM DTT, 10 UM ZINC REMARK 210 SULPHATE, 0.1 % SODIUM AZIDE, 1 REMARK 210 MM PEFABLOC, 95% H2O/5% D2O; 0.5 REMARK 210 MM [U-100% 13C; U-100% 15N] REMARK 210 UBIQUITIN-PROTEIN LIGASE E3A (24- REMARK 210 87), 0.75 MM 26S PROTEASOME NON- REMARK 210 ATPASE REGULATORY SUBUNIT 4 (305- REMARK 210 377), 10 MM MOPS, 50 MM SODIUM REMARK 210 CHLORIDE, 5 MM DTT, 10 UM ZINC REMARK 210 SULPHATE, 0.1 % SODIUM AZIDE, 1 REMARK 210 MM PEFABLOC, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D HNCACB; 3D HN(CA)CO; 3D HNCO; REMARK 210 2D 1H-13C HSQC; 3D 13C-HALF REMARK 210 FILTER NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D HCCH-TOCSY; 2D REMARK 210 NOESYGPPHWGXF; 3D CBCA(CO)NH; 3D REMARK 210 HN(CO)CA; 3D CCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ; 800 MHZ; 700 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, XEASY, X-PLOR REMARK 210 NIH, TALOS, PROCHECK / PROCHECK- REMARK 210 NMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 1610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 1 LYS A 321 -109.23 -91.10 REMARK 500 1 GLU A 322 -95.42 57.37 REMARK 500 1 GLU B 42 -66.88 -124.31 REMARK 500 1 SER B 56 -20.56 75.81 REMARK 500 2 GLU B 42 -99.37 -116.68 REMARK 500 2 THR B 50 62.10 -110.70 REMARK 500 2 PHE B 53 61.66 -101.64 REMARK 500 3 ALA B 48 54.84 -93.81 REMARK 500 3 PHE B 53 59.08 -91.45 REMARK 500 4 ALA A 310 -101.55 52.14 REMARK 500 4 PRO A 319 -10.06 -45.87 REMARK 500 4 LYS A 321 -158.16 -55.73 REMARK 500 4 GLU A 322 -82.94 54.81 REMARK 500 4 TYR A 326 93.03 39.40 REMARK 500 4 GLU B 42 -70.63 -118.04 REMARK 500 4 PHE B 53 59.89 -94.37 REMARK 500 5 THR A 364 178.39 45.70 REMARK 500 5 GLU B 42 -77.36 -106.38 REMARK 500 5 THR B 50 56.42 -95.19 REMARK 500 5 CYS B 54 143.82 -171.53 REMARK 500 6 LYS A 376 -125.00 44.85 REMARK 500 7 THR A 316 134.94 75.81 REMARK 500 7 TYR A 326 136.39 -39.83 REMARK 500 7 SER A 361 -178.51 55.50 REMARK 500 7 ALA A 363 8.78 56.90 REMARK 500 7 ASP A 375 -124.27 47.14 REMARK 500 7 GLU B 42 -67.38 -121.68 REMARK 500 7 PHE B 53 59.45 -92.46 REMARK 500 7 SER B 56 -21.17 76.31 REMARK 500 8 SER A 312 16.13 54.16 REMARK 500 8 LEU A 342 107.64 -45.28 REMARK 500 8 GLU A 373 -131.93 51.67 REMARK 500 8 GLU B 42 -80.98 -127.50 REMARK 500 8 PHE B 53 59.39 -93.51 REMARK 500 8 CYS B 83 84.11 38.90 REMARK 500 9 LYS A 368 -119.75 44.89 REMARK 500 9 GLU B 42 -71.34 -123.50 REMARK 500 9 THR B 50 77.57 -103.06 REMARK 500 9 PHE B 53 64.82 -105.69 REMARK 500 10 SER A 312 145.49 66.72 REMARK 500 10 ALA A 320 -97.96 39.37 REMARK 500 10 LYS A 321 -174.99 55.76 REMARK 500 10 GLU A 322 -74.78 63.92 REMARK 500 10 TYR A 326 130.81 -38.06 REMARK 500 10 GLU A 374 -120.18 58.40 REMARK 500 10 GLU B 42 -64.34 -145.50 REMARK 500 10 PHE B 53 59.39 -93.29 REMARK 500 10 SER B 56 -4.76 67.17 REMARK 500 11 ALA A 306 -61.15 75.01 REMARK 500 11 GLU A 322 -36.67 73.28 REMARK 500 REMARK 500 THIS ENTRY HAS 71 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL 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 B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 44 SG REMARK 620 2 CYS B 49 SG 110.1 REMARK 620 3 CYS B 54 SG 109.2 109.6 REMARK 620 4 CYS B 83 SG 109.3 109.4 109.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KR1 RELATED DB: PDB REMARK 900 RELATED ID: 27875 RELATED DB: BMRB DBREF 6U19 A 305 377 UNP P55036 PSMD4_HUMAN 305 377 DBREF 6U19 B 24 87 UNP Q05086 UBE3A_HUMAN 24 87 SEQRES 1 A 73 SER ALA ASP ILE ASP ALA SER SER ALA MET ASP THR SER SEQRES 2 A 73 GLU PRO ALA LYS GLU GLU ASP ASP TYR ASP VAL MET GLN SEQRES 3 A 73 ASP PRO GLU PHE LEU GLN SER VAL LEU GLU ASN LEU PRO SEQRES 4 A 73 GLY VAL ASP PRO ASN ASN GLU ALA ILE ARG ASN ALA MET SEQRES 5 A 73 GLY SER LEU ALA SER GLN ALA THR LYS ASP GLY LYS LYS SEQRES 6 A 73 ASP LYS LYS GLU GLU ASP LYS LYS SEQRES 1 B 64 MET LYS ARG ALA ALA ALA LYS HIS LEU ILE GLU ARG TYR SEQRES 2 B 64 TYR HIS GLN LEU THR GLU GLY CYS GLY ASN GLU ALA CYS SEQRES 3 B 64 THR ASN GLU PHE CYS ALA SER CYS PRO THR PHE LEU ARG SEQRES 4 B 64 MET ASP ASN ASN ALA ALA ALA ILE LYS ALA LEU GLU LEU SEQRES 5 B 64 TYR LYS ILE ASN ALA LYS LEU CYS ASP PRO HIS PRO HET ZN B 201 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ HELIX 1 AA1 LYS A 321 TYR A 326 5 6 HELIX 2 AA2 ASP A 327 GLN A 330 5 4 HELIX 3 AA3 ASP A 331 LEU A 342 1 12 HELIX 4 AA4 ASN A 349 THR A 364 1 16 HELIX 5 AA5 LYS B 25 GLU B 42 1 18 HELIX 6 AA6 ASP B 64 ASN B 79 1 16 LINK SG CYS B 44 ZN ZN B 201 1555 1555 2.49 LINK SG CYS B 49 ZN ZN B 201 1555 1555 2.39 LINK SG CYS B 54 ZN ZN B 201 1555 1555 2.37 LINK SG CYS B 83 ZN ZN B 201 1555 1555 2.46 SITE 1 AC1 4 CYS B 44 CYS B 49 CYS B 54 CYS B 83 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1