HEADER LIGASE 31-JAN-24 8Y4Z TITLE MONOMERIC HERC5 HECT C-LOBE STRUCTURE IN SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 ISG15--PROTEIN LIGASE HERC5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYCLIN-E-BINDING PROTEIN 1,HECT DOMAIN AND RCC1-LIKE DOMAIN- COMPND 5 CONTAINING PROTEIN 5; COMPND 6 EC: 2.3.2.-; COMPND 7 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: HERC5, CEB1, CEBP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN, HECT LIGASE, E3, UBIQUITIN, ISG15, ISGYLATION, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.DAG,M.LAMBERT,K.KAHRAMAN,F.LOHN,W.LEE,O.GOCENLER,P.GUNTERT,V.DOTSCH REVDAT 2 15-MAY-24 8Y4Z 1 REMARK REVDAT 1 14-FEB-24 8Y4Z 0 JRNL AUTH C.DAG,M.LAMBERT,K.KAHRAMAN,F.LOHN,W.LEE,O.GOCENLER, JRNL AUTH 2 P.GUNTERT,V.DOTSCH JRNL TITL MONOMERIC HERC5 HECT C-LOBE STRUCTURE IN SOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.15, POKY REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 MANTHEY, TONELLI, CLOS II, RAHIMI, MARKLEY AND LEE REMARK 3 (POKY) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8Y4Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300044416. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 3 MM DTT, 2 MM REMARK 210 TCEP, 20 UM DSS, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HNCACB; 3D HN(COCA) REMARK 210 CB; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D 1H- REMARK 210 15N NOESY; 3D H(CCO)NH; 3D HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 900 MHZ; 1200 MHZ; 800 REMARK 210 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III; AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, POKY, POKY 3.98.15 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLY A 114 O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL 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 6 ARG A 15 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 ARG A 111 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 10 ARG A 54 N - CA - CB ANGL. DEV. = -11.5 DEGREES REMARK 500 12 VAL A 99 CA - CB - CG2 ANGL. DEV. = 9.4 DEGREES REMARK 500 17 PHE A 30 CB - CG - CD2 ANGL. DEV. = -4.5 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 ARG A 54 51.78 30.22 REMARK 500 1 PRO A 70 153.88 -39.53 REMARK 500 1 ASN A 109 92.80 65.86 REMARK 500 1 ASN A 110 10.87 -63.29 REMARK 500 1 ARG A 111 178.53 57.74 REMARK 500 2 ASN A 2 87.78 -5.97 REMARK 500 2 ARG A 54 57.69 30.59 REMARK 500 2 PRO A 70 161.31 -46.09 REMARK 500 2 CYS A 84 -61.88 -18.41 REMARK 500 2 PHE A 85 30.01 -143.50 REMARK 500 2 ASN A 109 107.04 92.88 REMARK 500 3 ASN A 2 95.73 12.05 REMARK 500 3 ASP A 4 -160.92 57.74 REMARK 500 3 TYR A 5 154.86 62.74 REMARK 500 3 ASP A 6 79.21 -109.01 REMARK 500 3 ARG A 54 38.26 38.92 REMARK 500 3 PRO A 70 155.02 -33.95 REMARK 500 3 SER A 72 43.09 -142.20 REMARK 500 3 PRO A 78 152.73 -47.57 REMARK 500 3 PHE A 85 32.17 -153.00 REMARK 500 3 ARG A 111 101.49 55.02 REMARK 500 4 ASN A 2 143.14 80.87 REMARK 500 4 ASP A 4 101.62 -55.90 REMARK 500 4 TYR A 5 148.28 -175.66 REMARK 500 4 ASP A 6 76.43 -108.47 REMARK 500 4 ARG A 54 38.35 34.30 REMARK 500 4 PRO A 70 162.98 -44.66 REMARK 500 4 PRO A 78 163.03 -43.02 REMARK 500 4 SER A 86 64.52 61.34 REMARK 500 4 ASN A 109 119.94 93.15 REMARK 500 5 THR A 3 87.59 -156.72 REMARK 500 5 ARG A 54 55.03 35.01 REMARK 500 5 PRO A 70 163.71 -43.87 REMARK 500 5 SER A 86 64.34 71.58 REMARK 500 5 ASN A 109 116.69 71.70 REMARK 500 6 THR A 3 44.02 -142.38 REMARK 500 6 ASP A 4 75.27 59.55 REMARK 500 6 ARG A 54 55.22 24.09 REMARK 500 6 PRO A 70 156.04 -41.15 REMARK 500 6 SER A 86 65.67 75.04 REMARK 500 6 ARG A 111 109.50 -59.59 REMARK 500 7 ARG A 54 53.15 29.46 REMARK 500 7 PRO A 70 159.63 -42.33 REMARK 500 7 ASN A 109 95.32 75.85 REMARK 500 7 ARG A 111 -129.85 41.09 REMARK 500 8 ASN A 2 69.54 31.57 REMARK 500 8 ARG A 54 39.15 30.77 REMARK 500 8 PRO A 70 164.22 -48.51 REMARK 500 8 PHE A 85 35.20 -152.19 REMARK 500 8 ASN A 109 99.54 79.17 REMARK 500 REMARK 500 THIS ENTRY HAS 137 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 3 ARG A 80 0.08 SIDE CHAIN REMARK 500 4 ARG A 54 0.10 SIDE CHAIN REMARK 500 5 TYR A 20 0.08 SIDE CHAIN REMARK 500 5 ARG A 76 0.11 SIDE CHAIN REMARK 500 6 TYR A 93 0.08 SIDE CHAIN REMARK 500 7 TYR A 20 0.08 SIDE CHAIN REMARK 500 7 ARG A 54 0.09 SIDE CHAIN REMARK 500 7 ARG A 76 0.08 SIDE CHAIN REMARK 500 8 ARG A 80 0.12 SIDE CHAIN REMARK 500 9 TYR A 5 0.07 SIDE CHAIN REMARK 500 9 TYR A 20 0.07 SIDE CHAIN REMARK 500 11 ARG A 15 0.08 SIDE CHAIN REMARK 500 11 TYR A 20 0.07 SIDE CHAIN REMARK 500 12 ARG A 15 0.10 SIDE CHAIN REMARK 500 12 TYR A 16 0.07 SIDE CHAIN REMARK 500 13 TYR A 20 0.09 SIDE CHAIN REMARK 500 13 ARG A 54 0.09 SIDE CHAIN REMARK 500 15 TYR A 5 0.09 SIDE CHAIN REMARK 500 17 TYR A 20 0.08 SIDE CHAIN REMARK 500 17 ARG A 54 0.15 SIDE CHAIN REMARK 500 19 ARG A 15 0.08 SIDE CHAIN REMARK 500 20 ARG A 54 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36645 RELATED DB: BMRB REMARK 900 MONOMERIC HERC5 HECT C-LOBE STRUCTURE IN SOLUTION DBREF 8Y4Z A 1 114 UNP Q9UII4 HERC5_HUMAN 911 1024 SEQRES 1 A 114 GLY ASN THR ASP TYR ASP TRP LYS THR PHE GLU LYS ASN SEQRES 2 A 114 ALA ARG TYR GLU PRO GLY TYR ASN SER SER HIS PRO THR SEQRES 3 A 114 ILE VAL MET PHE TRP LYS ALA PHE HIS LYS LEU THR LEU SEQRES 4 A 114 GLU GLU LYS LYS LYS PHE LEU VAL PHE LEU THR GLY THR SEQRES 5 A 114 ASP ARG LEU GLN MET LYS ASP LEU ASN ASN MET LYS ILE SEQRES 6 A 114 THR PHE CYS CYS PRO GLU SER TRP ASN GLU ARG ASP PRO SEQRES 7 A 114 ILE ARG ALA LEU THR CYS PHE SER VAL LEU PHE LEU PRO SEQRES 8 A 114 LYS TYR SER THR MET GLU THR VAL GLU GLU ALA LEU GLN SEQRES 9 A 114 GLU ALA ILE ASN ASN ASN ARG GLY PHE GLY HELIX 1 AA1 ASP A 6 ALA A 14 1 9 HELIX 2 AA2 HIS A 24 LEU A 37 1 14 HELIX 3 AA3 THR A 38 THR A 50 1 13 HELIX 4 AA4 GLN A 56 ASN A 61 1 6 HELIX 5 AA5 THR A 95 ASN A 108 1 14 SHEET 1 AA1 4 ARG A 15 TYR A 16 0 SHEET 2 AA1 4 THR A 66 CYS A 68 1 O PHE A 67 N ARG A 15 SHEET 3 AA1 4 VAL A 87 PHE A 89 1 O LEU A 88 N THR A 66 SHEET 4 AA1 4 ARG A 80 LEU A 82 -1 N ARG A 80 O PHE A 89 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