HEADER LIGASE 14-DEC-17 6F98 TITLE SOLUTION STRUCTURE OF THE RING DOMAIN OF THE E3 UBIQUITIN LIGASE HRD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: HRD1, SCKG_1066; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RING DOMAIN, UBIQUITIN, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.KNISS,S.KAZEMI,F.LOHR,P.GUNTERT,V.DOTSCH REVDAT 3 14-JUN-23 6F98 1 REMARK REVDAT 2 08-MAY-19 6F98 1 REMARK REVDAT 1 30-JAN-19 6F98 0 JRNL AUTH A.KNISS JRNL TITL SOLUTION STRUCTURE OF THE RING DOMAIN OF THE E3 UBIQUITIN JRNL TITL 2 LIGASE HRD1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.9, OPAL REMARK 3 AUTHORS : PETER GUNTERT (CYANA), LUGINBUHL, GUNTERT, REMARK 3 BILLETER AND WUTHRICH (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ZINC INCLUDED REMARK 4 REMARK 4 6F98 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007961. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT BAR REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-98% 13C; U-98% 15N] E3 REMARK 210 UBIQUITIN LIGASE HRD1, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D HNCACB; 2D 1H-15N REMARK 210 HSQC; 2D 1H-13C HSQC ALIPHATIC; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D 1H REMARK 210 TOCSY; 3D HNCO; 3D HNCACO; 3D REMARK 210 HN(COCA)CB; 2D HCBCGCDH TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.13 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 4 ARG A 400 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES 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 1 ALA A 336 18.55 55.20 REMARK 500 1 GLN A 340 -11.41 66.93 REMARK 500 1 SER A 342 79.02 -165.58 REMARK 500 1 ILE A 398 -66.29 -92.23 REMARK 500 2 GLN A 340 123.49 -170.12 REMARK 500 2 PRO A 360 2.89 -68.34 REMARK 500 2 ASN A 361 -81.77 -133.04 REMARK 500 2 ILE A 398 -67.10 -99.22 REMARK 500 3 ASN A 361 24.32 47.51 REMARK 500 3 GLN A 363 78.12 -110.61 REMARK 500 3 ILE A 398 -66.34 -109.74 REMARK 500 3 ASP A 405 172.26 -57.85 REMARK 500 4 ASN A 341 -6.17 -57.12 REMARK 500 4 THR A 364 -119.21 -81.25 REMARK 500 4 ASN A 409 76.08 -154.84 REMARK 500 5 VAL A 403 -179.80 -67.21 REMARK 500 5 VAL A 411 115.25 -162.17 REMARK 500 6 MET A 353 18.37 58.27 REMARK 500 6 ASN A 361 -60.11 -131.88 REMARK 500 6 THR A 364 -70.24 -57.79 REMARK 500 6 PRO A 372 96.35 -69.36 REMARK 500 7 ASP A 346 16.39 -143.42 REMARK 500 7 ASN A 347 21.80 -148.44 REMARK 500 7 ILE A 357 149.12 -174.73 REMARK 500 7 LYS A 370 31.28 -93.76 REMARK 500 7 PRO A 372 93.39 -68.12 REMARK 500 7 VAL A 403 -167.60 -112.32 REMARK 500 8 ASN A 344 -75.34 -113.70 REMARK 500 8 THR A 364 -85.53 -139.24 REMARK 500 8 PRO A 397 4.78 -69.00 REMARK 500 8 ILE A 398 -66.56 -107.55 REMARK 500 9 ALA A 336 -89.75 -125.05 REMARK 500 9 ASN A 361 -81.25 -126.01 REMARK 500 9 GLN A 363 96.60 -67.42 REMARK 500 10 SER A 342 91.34 -60.41 REMARK 500 10 ASN A 344 66.19 75.92 REMARK 500 10 ILE A 357 102.77 -174.84 REMARK 500 10 THR A 364 -81.70 -128.33 REMARK 500 10 ILE A 398 -66.13 -108.46 REMARK 500 10 VAL A 411 49.06 -74.96 REMARK 500 11 ALA A 336 16.55 56.91 REMARK 500 11 GLN A 340 -67.02 -108.84 REMARK 500 11 ASN A 361 -30.18 -132.02 REMARK 500 11 THR A 364 -96.18 -147.60 REMARK 500 11 ILE A 398 -66.87 -96.11 REMARK 500 12 GLU A 337 -52.33 -152.66 REMARK 500 12 ASN A 361 11.94 -143.15 REMARK 500 12 LYS A 370 33.50 -96.67 REMARK 500 13 SER A 342 76.38 -117.99 REMARK 500 13 ASN A 344 112.66 -166.19 REMARK 500 REMARK 500 THIS ENTRY HAS 84 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 GLU A 391 0.07 SIDE CHAIN REMARK 500 4 ARG A 400 0.09 SIDE CHAIN REMARK 500 5 GLU A 391 0.08 SIDE CHAIN REMARK 500 5 GLU A 406 0.08 SIDE CHAIN REMARK 500 9 ASP A 346 0.09 SIDE CHAIN REMARK 500 10 ASP A 346 0.07 SIDE CHAIN REMARK 500 11 ARG A 374 0.08 SIDE CHAIN REMARK 500 12 ASP A 354 0.08 SIDE CHAIN REMARK 500 12 ARG A 392 0.10 SIDE CHAIN REMARK 500 14 ASP A 405 0.08 SIDE CHAIN REMARK 500 15 ASP A 346 0.07 SIDE CHAIN REMARK 500 16 ASP A 354 0.07 SIDE CHAIN REMARK 500 16 ARG A 400 0.15 SIDE CHAIN REMARK 500 16 ASP A 405 0.08 SIDE CHAIN REMARK 500 19 ASP A 354 0.08 SIDE CHAIN REMARK 500 20 ASP A 346 0.07 SIDE CHAIN REMARK 500 20 ARG A 392 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 20 VAL A 411 10.47 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 A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 349 SG REMARK 620 2 CYS A 352 SG 123.2 REMARK 620 3 HIS A 382 ND1 95.0 102.3 REMARK 620 4 CYS A 385 SG 125.4 98.7 109.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 377 SG REMARK 620 2 HIS A 379 ND1 100.9 REMARK 620 3 CYS A 396 SG 86.3 109.1 REMARK 620 4 CYS A 399 SG 143.8 104.2 109.2 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 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34217 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE RING DOMAIN OF THE E3 UBIQUITIN LIGASE REMARK 900 HRD1 DBREF1 6F98 A 337 412 UNP A0A250WAY8_YEASX DBREF2 6F98 A A0A250WAY8 337 412 SEQADV 6F98 GLY A 335 UNP A0A250WAY EXPRESSION TAG SEQADV 6F98 ALA A 336 UNP A0A250WAY EXPRESSION TAG SEQRES 1 A 78 GLY ALA GLU GLN LEU GLN ASN SER ALA ASN ASP ASP ASN SEQRES 2 A 78 ILE CYS ILE ILE CYS MET ASP GLU LEU ILE HIS SER PRO SEQRES 3 A 78 ASN GLN GLN THR TRP LYS ASN LYS ASN LYS LYS PRO LYS SEQRES 4 A 78 ARG LEU PRO CYS GLY HIS ILE LEU HIS LEU SER CYS LEU SEQRES 5 A 78 LYS ASN TRP MET GLU ARG SER GLN THR CYS PRO ILE CYS SEQRES 6 A 78 ARG LEU PRO VAL PHE ASP GLU LYS GLY ASN VAL VAL GLN HET ZN A 501 1 HET ZN A 502 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 ASN A 367 LYS A 370 5 4 HELIX 2 AA2 LEU A 383 GLU A 391 1 9 SHEET 1 AA1 2 PRO A 372 ARG A 374 0 SHEET 2 AA1 2 ILE A 380 HIS A 382 -1 O LEU A 381 N LYS A 373 LINK SG CYS A 349 ZN ZN A 501 1555 1555 2.47 LINK SG CYS A 352 ZN ZN A 501 1555 1555 2.47 LINK SG CYS A 377 ZN ZN A 502 1555 1555 2.46 LINK ND1 HIS A 379 ZN ZN A 502 1555 1555 2.26 LINK ND1 HIS A 382 ZN ZN A 501 1555 1555 2.27 LINK SG CYS A 385 ZN ZN A 501 1555 1555 2.47 LINK SG CYS A 396 ZN ZN A 502 1555 1555 2.46 LINK SG CYS A 399 ZN ZN A 502 1555 1555 2.46 SITE 1 AC1 4 CYS A 349 CYS A 352 HIS A 382 CYS A 385 SITE 1 AC2 4 CYS A 377 HIS A 379 CYS A 396 CYS A 399 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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