HEADER PROTEIN BINDING 29-MAY-17 5VZM TITLE SOLUTION NMR STRUCTURE OF HUMAN REV1 (932-1039) IN COMPLEX WITH TITLE 2 UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-76; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA REPAIR PROTEIN REV1; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 933-1040; COMPND 10 SYNONYM: ALPHA INTEGRIN-BINDING PROTEIN 80,AIBP80,REV1-LIKE TERMINAL COMPND 11 DEOXYCYTIDYL TRANSFERASE; COMPND 12 EC: 2.7.7.-; COMPND 13 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: UBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSUB; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: REV1, REV1L; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PTEV KEYWDS TRANSLESION DNA SYNTHESIS, DNA REPAIR, DNA REPLICATION, REV1, KEYWDS 2 UBIQUITIN, PCNA, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.CUI,M.V.BOTUYAN,G.MER REVDAT 3 04-DEC-19 5VZM 1 REMARK REVDAT 2 04-JUL-18 5VZM 1 JRNL REVDAT 1 23-MAY-18 5VZM 0 JRNL AUTH G.CUI,M.V.BOTUYAN,G.MER JRNL TITL STRUCTURAL BASIS FOR THE INTERACTION OF MUTASOME ASSEMBLY JRNL TITL 2 FACTOR REV1 WITH UBIQUITIN. JRNL REF J. MOL. BIOL. V. 430 2042 2018 JRNL REFN ESSN 1089-8638 JRNL PMID 29778604 JRNL DOI 10.1016/J.JMB.2018.05.017 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5VZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000228147. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 303 REMARK 210 PH : 7.0; 6.8 REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOSPHATE; 50 MM REMARK 210 SODIUM PHOSPHATE REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 UBIQUITIN, 20 MM SODIUM REMARK 210 PHOSPHATE BUFFER, 90% H2O/10% REMARK 210 D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] REV1, 3 MM UBIQUITIN, 50 MM REMARK 210 SODIUM PHOSPHATE BUFFER, 90% H2O/ REMARK 210 10% D2O; 3 MM REV1, 1 MM [U-100% REMARK 210 13C; U-100% 15N] UBIQUITIN, 50 REMARK 210 MM SODIUM PHOSPHATE BUFFER, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HNCO; REMARK 210 3D HN(CA)CO; 3D HBHA(CO)NH; 3D REMARK 210 H(CCO)NH; 3D (H)CC(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D 1H-13C NOESY AROMATIC; 13C, REMARK 210 15N-FILETERED/EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, NMRDRAW, REMARK 210 NMRVIEW, SANE, TALOS, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING 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 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 3 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 9 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 10 ARG A 54 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 11 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 14 TYR B1035 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 15 ARG A 54 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 15 TYR B1035 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 18 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.2 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 46 38.41 39.61 REMARK 500 1 GLN A 62 -161.23 -120.69 REMARK 500 1 GLU A 64 51.91 39.69 REMARK 500 1 SER B 935 13.61 -141.78 REMARK 500 1 GLN B 936 -4.51 -159.75 REMARK 500 1 CYS B 957 -179.16 -177.34 REMARK 500 1 ASP B 967 -33.45 65.53 REMARK 500 1 ASN B 977 26.76 49.85 REMARK 500 1 THR B 987 -32.84 -130.04 REMARK 500 1 ASN B 999 51.33 -145.69 REMARK 500 1 PRO B1010 103.20 -51.68 REMARK 500 1 GLN B1014 -13.57 -148.84 REMARK 500 2 ALA A 46 44.30 36.63 REMARK 500 2 GLN A 62 -162.60 -118.52 REMARK 500 2 GLU B 963 -31.20 -146.05 REMARK 500 2 ASP B 967 -42.45 61.40 REMARK 500 2 VAL B 985 47.45 -144.69 REMARK 500 2 THR B 987 -53.35 -127.72 REMARK 500 2 VAL B 988 34.74 -141.01 REMARK 500 2 GLU B 994 -38.48 -141.60 REMARK 500 2 ALA B1008 16.48 50.41 REMARK 500 2 PRO B1010 93.92 -48.21 REMARK 500 2 GLN B1014 -12.17 -146.77 REMARK 500 3 ALA A 46 40.55 38.14 REMARK 500 3 GLN A 62 -167.47 -122.19 REMARK 500 3 LEU A 73 32.52 72.48 REMARK 500 3 GLN B 936 -89.30 -122.28 REMARK 500 3 LEU B 937 14.97 -152.10 REMARK 500 3 VAL B 956 156.60 67.60 REMARK 500 3 ALA B 958 51.13 -152.03 REMARK 500 3 VAL B 973 -27.55 52.04 REMARK 500 3 ASN B 974 65.17 -151.66 REMARK 500 3 VAL B 988 7.88 -69.59 REMARK 500 3 ALA B1008 16.08 51.53 REMARK 500 3 PRO B1010 100.81 -52.06 REMARK 500 3 GLN B1014 -18.14 -144.48 REMARK 500 3 GLN B1037 0.56 -65.67 REMARK 500 4 ALA A 46 41.28 38.01 REMARK 500 4 GLN A 62 -161.96 -119.74 REMARK 500 4 ARG A 74 -47.35 66.51 REMARK 500 4 LEU B 937 -50.81 -170.71 REMARK 500 4 CYS B 957 57.16 39.95 REMARK 500 4 GLU B 963 11.86 -143.48 REMARK 500 4 PRO B 972 24.07 -76.95 REMARK 500 4 GLN B 996 -175.21 57.57 REMARK 500 4 ALA B1008 25.29 46.71 REMARK 500 4 PRO B1010 107.01 -55.23 REMARK 500 5 ALA A 46 40.18 38.98 REMARK 500 5 GLN A 62 -167.14 -120.24 REMARK 500 5 CYS B 957 -151.37 48.26 REMARK 500 REMARK 500 THIS ENTRY HAS 213 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 6 ARG A 42 0.09 SIDE CHAIN REMARK 500 16 ARG A 42 0.10 SIDE CHAIN REMARK 500 20 ARG A 42 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30300 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF HUMAN REV1 (932-1039) IN COMPLEX WITH REMARK 900 UBIQUITIN DBREF 5VZM A 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 5VZM B 932 1039 UNP Q9UBZ9 REV1_HUMAN 933 1040 SEQADV 5VZM GLY B -3 UNP Q9UBZ9 EXPRESSION TAG SEQADV 5VZM HIS B -2 UNP Q9UBZ9 EXPRESSION TAG SEQADV 5VZM MET B -1 UNP Q9UBZ9 EXPRESSION TAG SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 111 GLY HIS MET PRO SER PRO SER GLN LEU ASP GLN SER VAL SEQRES 2 B 111 LEU GLU ALA LEU PRO PRO ASP LEU ARG GLU GLN VAL GLU SEQRES 3 B 111 GLN VAL CYS ALA VAL GLN GLN ALA GLU SER HIS GLY ASP SEQRES 4 B 111 LYS LYS LYS GLU PRO VAL ASN GLY CYS ASN THR GLY ILE SEQRES 5 B 111 LEU PRO GLN PRO VAL GLY THR VAL LEU LEU GLN ILE PRO SEQRES 6 B 111 GLU PRO GLN GLU SER ASN SER ASP ALA GLY ILE ASN LEU SEQRES 7 B 111 ILE ALA LEU PRO ALA PHE SER GLN VAL ASP PRO GLU VAL SEQRES 8 B 111 PHE ALA ALA LEU PRO ALA GLU LEU GLN ARG GLU LEU LYS SEQRES 9 B 111 ALA ALA TYR ASP GLN ARG GLN HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 ASP A 39 5 3 HELIX 3 AA3 LEU A 56 ASN A 60 5 5 HELIX 4 AA4 ASP B 938 GLU B 943 1 6 HELIX 5 AA5 PRO B 946 GLN B 955 1 10 HELIX 6 AA6 ALA B 958 GLU B 963 5 6 HELIX 7 AA7 GLN B 983 THR B 987 5 5 HELIX 8 AA8 ASP B 1016 LEU B 1023 1 8 HELIX 9 AA9 PRO B 1024 GLN B 1037 1 14 SHEET 1 AA1 5 THR A 12 GLU A 16 0 SHEET 2 AA1 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13 SHEET 3 AA1 5 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6 SHEET 4 AA1 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 AA1 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SSBOND 1 CYS B 957 CYS B 976 1555 1555 2.04 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