HEADER LIGASE 14-JUN-21 7OVC TITLE STRUCTURE OF THE HUMAN UFC1 PROTEIN IN COMPLEX WITH THE UBA5 C- TITLE 2 TERMINAL UFC1-BINDING MOTIF. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-FOLD MODIFIER-CONJUGATING ENZYME 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UFM1-CONJUGATING ENZYME 1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 5; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: UBIQUITIN-ACTIVATING ENZYME 5,THIFP1,UFM1-ACTIVATING ENZYME, COMPND 10 UBIQUITIN-ACTIVATING ENZYME E1 DOMAIN-CONTAINING PROTEIN 1; COMPND 11 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: UFC1, CGI-126, HSPC155; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: NEB T7 EXPRESS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET39_UB19; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: UBA5, UBE1DC1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: NEB T7 EXPRESS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET39_UB19 KEYWDS UFM1, UBA5, UFC1, UFMYLATION, COMPLEX STRUCTURE, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.WESCH,F.LOEHR,N.ROGOVA,V.DOETSCH,V.V.ROGOV REVDAT 2 14-JUN-23 7OVC 1 REMARK REVDAT 1 04-AUG-21 7OVC 0 JRNL AUTH N.WESCH,F.LOHR,N.ROGOVA,V.DOTSCH,V.V.ROGOV JRNL TITL A CONCERTED ACTION OF UBA5 C-TERMINAL UNSTRUCTURED REGIONS JRNL TITL 2 IS IMPORTANT FOR TRANSFER OF ACTIVATED UFM1 TO UFC1. JRNL REF INT J MOL SCI V. 22 2021 JRNL REFN ESSN 1422-0067 JRNL PMID 34299007 JRNL DOI 10.3390/IJMS22147390 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPALP 1.4 REMARK 3 AUTHORS : KORADI, R., BILLETER, M. AND GUENTERT, P REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7OVC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292116464. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-100% 13C; U-100% 15N] REMARK 210 UBIQUITIN-FOLD MODIFIER- REMARK 210 CONJUGATING ENZYME 1, 1.0 MM REMARK 210 UBIQUITIN-LIKE MODIFIER- REMARK 210 ACTIVATING ENZYME 5, 50 MM TRIS, REMARK 210 100 MM SODIUM CHLORIDE, 2 MM REMARK 210 TCEP, 5 MM AEBSF PROTEASE REMARK 210 INHIBITOR, 0.15 MM DSS, 95% H2O/ REMARK 210 5% D2O; 1.2 MM UBIQUITIN-FOLD REMARK 210 MODIFIER-CONJUGATING ENZYME 1, REMARK 210 0.3 MM [U-100% 13C; U-100% 15N] REMARK 210 UBIQUITIN-LIKE MODIFIER- REMARK 210 ACTIVATING ENZYME 5, 50 MM TRIS, REMARK 210 100 MM SODIUM CHLORIDE, 2 MM REMARK 210 TCEP, 5 MM AEBSF PROTEASE REMARK 210 INHIBITOR, 0.15 MM DSS, 95% H2O/ REMARK 210 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D [15N,1H]-TROSY-(H)C(CC)(CO)NH REMARK 210 -TOCSY; 3D [15N,1H]-TROSY-H(C)(CC)(CO)NH-TOCSY; 3D BEST-[15N,1H]- REMARK 210 TROSY-HNCACB; 3D F1-13C/15N-FILTERED NOESY-[13C,1H]-HSQC; 3D F1- REMARK 210 13C/15N-FILTERED NOESY-[15N,1H]-SOFAST-HMQC; 3D F1-13C/15N- REMARK 210 FILTERED NOESY-[13C,1H]-SOFAST-HMQC (ARO); 3D NOESY-[13C,1H]- REMARK 210 SOFAST-HMQC (ARO); 3D NOESY-[13C,1H]-HSQC (ALIPHATIC REGION); 3D REMARK 210 NOESY-BEST-[15N,1H]-TROSY; 3D NOESY [13C,1H]-HSQC; 3D [15N,1H]- REMARK 210 TROSY-H(CC)(CO)NH-TOCSY; 3D NOESY-[15N,1H]-SOFAST-HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ; 900 REMARK 210 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II; AVANCE III HD; AVANCE REMARK 210 NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.6.2, SPARKY 3.114, REMARK 210 CYANA 3.98 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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: 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 5 ARG A 31 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 13 ARG A 64 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 13 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 13 ARG A 64 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 16 ARG A 31 NE - CZ - NH1 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 LYS A 17 -54.12 -141.64 REMARK 500 1 ALA A 20 170.14 -58.58 REMARK 500 1 TRP A 53 -22.51 -140.40 REMARK 500 1 ALA A 94 157.75 -47.80 REMARK 500 1 ASP A 119 -68.81 -28.54 REMARK 500 1 ASN A 166 -100.26 -125.78 REMARK 500 1 VAL B 387 150.88 -44.95 REMARK 500 1 GLU B 388 34.65 -75.89 REMARK 500 2 LYS A 17 -31.38 -137.80 REMARK 500 2 LYS A 108 101.38 -57.76 REMARK 500 2 VAL A 129 52.35 -143.86 REMARK 500 2 ASP B 389 83.57 -68.54 REMARK 500 3 LYS A 17 -53.94 -135.82 REMARK 500 3 TRP A 53 -27.06 -146.58 REMARK 500 3 ARG A 111 94.00 -69.92 REMARK 500 3 VAL A 129 57.67 -142.98 REMARK 500 3 VAL B 382 -78.08 -132.96 REMARK 500 3 GLU B 388 36.72 -78.91 REMARK 500 3 ASP B 389 87.12 -62.93 REMARK 500 3 SER B 390 51.43 -116.98 REMARK 500 4 LYS A 17 -53.42 -133.24 REMARK 500 4 TRP A 53 -31.23 -145.69 REMARK 500 4 ASP A 103 95.75 -67.52 REMARK 500 4 CYS A 116 94.24 -68.35 REMARK 500 4 VAL A 129 55.68 -145.98 REMARK 500 4 LYS A 131 11.15 -140.15 REMARK 500 4 ASN A 166 -63.96 -120.26 REMARK 500 4 VAL B 382 -55.73 -123.85 REMARK 500 4 THR B 383 -62.27 -147.97 REMARK 500 5 LYS A 17 -60.90 -133.90 REMARK 500 5 TRP A 53 -26.78 -156.89 REMARK 500 5 ALA A 94 154.49 -48.20 REMARK 500 5 ASP A 119 -70.62 -27.69 REMARK 500 5 PHE A 132 136.45 -39.76 REMARK 500 5 ASN A 166 -87.95 -125.49 REMARK 500 5 GLU B 388 39.54 -78.77 REMARK 500 5 ASP B 389 84.81 -66.45 REMARK 500 6 LYS A 17 -66.00 -130.08 REMARK 500 6 ASP A 52 94.57 -60.95 REMARK 500 6 ALA A 94 153.91 -49.19 REMARK 500 6 LEU A 117 159.20 -45.84 REMARK 500 6 VAL A 129 53.83 -147.74 REMARK 500 6 LYS A 164 5.33 -68.09 REMARK 500 6 ASN A 166 -50.03 -125.39 REMARK 500 6 GLU B 388 34.43 -74.55 REMARK 500 6 ASP B 389 91.41 -66.09 REMARK 500 6 SER B 390 48.50 -109.06 REMARK 500 7 LYS A 17 -48.67 -141.58 REMARK 500 7 ARG A 25 -70.72 -55.10 REMARK 500 7 ALA A 94 155.80 -48.51 REMARK 500 REMARK 500 THIS ENTRY HAS 169 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 ARG A 7 0.11 SIDE CHAIN REMARK 500 1 ARG A 31 0.09 SIDE CHAIN REMARK 500 1 ARG A 41 0.08 SIDE CHAIN REMARK 500 1 ARG A 55 0.11 SIDE CHAIN REMARK 500 1 ARG A 111 0.08 SIDE CHAIN REMARK 500 2 ARG A 7 0.11 SIDE CHAIN REMARK 500 3 ARG A 7 0.08 SIDE CHAIN REMARK 500 3 ARG A 8 0.08 SIDE CHAIN REMARK 500 6 ARG A 127 0.08 SIDE CHAIN REMARK 500 7 ARG A 55 0.11 SIDE CHAIN REMARK 500 8 ARG A 41 0.10 SIDE CHAIN REMARK 500 9 ARG A 41 0.10 SIDE CHAIN REMARK 500 11 ARG A 7 0.08 SIDE CHAIN REMARK 500 11 ARG A 55 0.08 SIDE CHAIN REMARK 500 14 TYR A 42 0.09 SIDE CHAIN REMARK 500 15 TYR A 42 0.07 SIDE CHAIN REMARK 500 15 PHE A 66 0.07 SIDE CHAIN REMARK 500 16 ARG A 111 0.10 SIDE CHAIN REMARK 500 17 ARG A 111 0.08 SIDE CHAIN REMARK 500 18 ARG A 7 0.09 SIDE CHAIN REMARK 500 18 ARG A 8 0.08 SIDE CHAIN REMARK 500 18 ARG A 64 0.08 SIDE CHAIN REMARK 500 20 ARG A 7 0.09 SIDE CHAIN REMARK 500 20 ARG A 23 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34638 RELATED DB: BMRB REMARK 900 STRUCTURE OF THE HUMAN UFC1 PROTEIN IN COMPLEX WITH THE UBA5 C- REMARK 900 TERMINAL UFC1-BINDING MOTIF. DBREF 7OVC A 1 167 UNP Q9Y3C8 UFC1_HUMAN 1 167 DBREF 7OVC B 381 404 UNP Q9GZZ9 UBA5_HUMAN 381 404 SEQADV 7OVC GLY B 379 UNP Q9GZZ9 EXPRESSION TAG SEQADV 7OVC MET B 380 UNP Q9GZZ9 EXPRESSION TAG SEQADV 7OVC TRP B 405 UNP Q9GZZ9 EXPRESSION TAG SEQRES 1 A 167 MET ALA ASP GLU ALA THR ARG ARG VAL VAL SER GLU ILE SEQRES 2 A 167 PRO VAL LEU LYS THR ASN ALA GLY PRO ARG ASP ARG GLU SEQRES 3 A 167 LEU TRP VAL GLN ARG LEU LYS GLU GLU TYR GLN SER LEU SEQRES 4 A 167 ILE ARG TYR VAL GLU ASN ASN LYS ASN ALA ASP ASN ASP SEQRES 5 A 167 TRP PHE ARG LEU GLU SER ASN LYS GLU GLY THR ARG TRP SEQRES 6 A 167 PHE GLY LYS CYS TRP TYR ILE HIS ASP LEU LEU LYS TYR SEQRES 7 A 167 GLU PHE ASP ILE GLU PHE ASP ILE PRO ILE THR TYR PRO SEQRES 8 A 167 THR THR ALA PRO GLU ILE ALA VAL PRO GLU LEU ASP GLY SEQRES 9 A 167 LYS THR ALA LYS MET TYR ARG GLY GLY LYS ILE CYS LEU SEQRES 10 A 167 THR ASP HIS PHE LYS PRO LEU TRP ALA ARG ASN VAL PRO SEQRES 11 A 167 LYS PHE GLY LEU ALA HIS LEU MET ALA LEU GLY LEU GLY SEQRES 12 A 167 PRO TRP LEU ALA VAL GLU ILE PRO ASP LEU ILE GLN LYS SEQRES 13 A 167 GLY VAL ILE GLN HIS LYS GLU LYS CYS ASN GLN SEQRES 1 B 27 GLY MET SER VAL THR GLU LEU THR VAL GLU ASP SER GLY SEQRES 2 B 27 GLU SER LEU GLU ASP LEU MET ALA LYS MET LYS ASN MET SEQRES 3 B 27 TRP HELIX 1 AA1 ALA A 2 ILE A 13 1 12 HELIX 2 AA2 ASP A 24 ALA A 49 1 26 HELIX 3 AA3 VAL A 99 ASP A 103 5 5 HELIX 4 AA4 HIS A 120 ASN A 128 1 9 HELIX 5 AA5 GLY A 133 GLY A 141 1 9 HELIX 6 AA6 GLY A 141 GLY A 157 1 17 HELIX 7 AA7 LYS A 162 ASN A 166 5 5 HELIX 8 AA8 SER B 393 TRP B 405 1 13 SHEET 1 AA1 3 PHE A 54 SER A 58 0 SHEET 2 AA1 3 ARG A 64 HIS A 73 -1 O PHE A 66 N GLU A 57 SHEET 3 AA1 3 LEU A 76 ASP A 85 -1 O PHE A 84 N TRP A 65 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