HEADER METAL BINDING PROTEIN 30-SEP-11 2LJZ TITLE STRUCTURE OF THE C-TERMINAL DOMAIN OF HPV16 E6 ONCOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN E6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGER CONTAINING RESIDUES 87-158; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN PAPILLOMAVIRUS; SOURCE 3 ORGANISM_TAXID: 333760; SOURCE 4 GENE: E6; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PETM41 KEYWDS METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.ZANIER,A.MUHAMED SIDI,C.BOULADE-LADAME,V.RYBIN,A.CHAPPELLE, AUTHOR 2 A.ATKINSON,B.KIEFFER,G.TRAVE REVDAT 3 14-JUN-23 2LJZ 1 REMARK SEQADV LINK REVDAT 2 25-APR-12 2LJZ 1 JRNL REVDAT 1 04-APR-12 2LJZ 0 JRNL AUTH K.ZANIER,A.OULD M'HAMED OULD SIDI,C.BOULADE-LADAME,V.RYBIN, JRNL AUTH 2 A.CHAPPELLE,A.ATKINSON,B.KIEFFER,G.TRAVE JRNL TITL SOLUTION STRUCTURE ANALYSIS OF THE HPV16 E6 ONCOPROTEIN JRNL TITL 2 REVEALS A SELF-ASSOCIATION MECHANISM REQUIRED FOR JRNL TITL 3 E6-MEDIATED DEGRADATION OF P53. JRNL REF STRUCTURE V. 20 604 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22483108 JRNL DOI 10.1016/J.STR.2012.02.001 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, X-PLOR NIH REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LJZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000102474. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 286 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 50 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM E6, 90% H2O/10% D2O; 1 MM REMARK 210 [U-100% 13C; U-100% 15N] E6, 90% REMARK 210 H2O/10% D2O; 1 MM [U-100% 15N] REMARK 210 E6, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HBHA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, CARA 1.8.3, REMARK 210 ATNOS/CANDID, X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: THE STRUCTURE WAS DETERMINED USING NOE AND DIHEDRAL ANGLE REMARK 210 RESTRAINTS 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 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: 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 TRP A 132 CE2 TRP A 132 CD2 -0.077 REMARK 500 1 CYS A 139 CA CYS A 139 CB -0.088 REMARK 500 2 TRP A 132 CE2 TRP A 132 CD2 -0.078 REMARK 500 3 TRP A 132 CE2 TRP A 132 CD2 -0.076 REMARK 500 5 TRP A 132 CE2 TRP A 132 CD2 -0.076 REMARK 500 5 CYS A 139 CA CYS A 139 CB -0.079 REMARK 500 7 TRP A 132 CE2 TRP A 132 CD2 -0.076 REMARK 500 9 TRP A 132 CE2 TRP A 132 CD2 -0.076 REMARK 500 9 CYS A 139 CA CYS A 139 CB -0.083 REMARK 500 11 TRP A 132 CE2 TRP A 132 CD2 -0.079 REMARK 500 12 CYS A 139 CA CYS A 139 CB -0.079 REMARK 500 15 TRP A 132 CE2 TRP A 132 CD2 -0.075 REMARK 500 16 TRP A 132 CE2 TRP A 132 CD2 -0.075 REMARK 500 17 TRP A 132 CE2 TRP A 132 CD2 -0.075 REMARK 500 18 TRP A 132 CE2 TRP A 132 CD2 -0.080 REMARK 500 18 CYS A 139 CA CYS A 139 CB -0.081 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 CYS A 136 CA - CB - SG ANGL. DEV. = 9.2 DEGREES REMARK 500 4 CYS A 136 CA - CB - SG ANGL. DEV. = 10.2 DEGREES REMARK 500 10 CYS A 136 CA - CB - SG ANGL. DEV. = 7.0 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 78 146.58 -175.31 REMARK 500 1 MET A 79 164.38 177.77 REMARK 500 1 ASN A 93 -1.37 75.16 REMARK 500 1 ARG A 141 -62.98 -95.43 REMARK 500 1 SER A 142 43.39 -87.54 REMARK 500 1 GLN A 150 11.31 57.87 REMARK 500 2 MET A 79 86.14 65.33 REMARK 500 2 ARG A 124 166.01 74.74 REMARK 500 2 PHE A 125 -165.28 -166.23 REMARK 500 2 ARG A 146 94.71 -68.80 REMARK 500 3 ALA A 78 34.93 -90.09 REMARK 500 3 SER A 80 103.05 53.02 REMARK 500 3 LEU A 119 -61.37 -90.81 REMARK 500 3 ARG A 135 114.97 -165.68 REMARK 500 3 GLU A 148 -66.89 -97.12 REMARK 500 4 ALA A 78 -169.05 61.56 REMARK 500 4 SER A 80 97.51 67.70 REMARK 500 4 THR A 86 -30.82 -38.55 REMARK 500 4 ASN A 93 -8.71 79.66 REMARK 500 4 LEU A 119 -60.47 -96.18 REMARK 500 4 ARG A 124 160.41 69.83 REMARK 500 4 PHE A 125 -166.54 -163.19 REMARK 500 4 THR A 149 38.04 -158.81 REMARK 500 5 SER A 80 100.51 50.81 REMARK 500 5 THR A 86 -18.50 -47.63 REMARK 500 5 ARG A 129 96.61 -59.58 REMARK 500 5 ARG A 135 110.98 -164.36 REMARK 500 5 CYS A 136 171.35 -57.35 REMARK 500 5 SER A 142 96.01 -59.09 REMARK 500 5 ARG A 146 82.48 35.47 REMARK 500 5 THR A 149 23.88 -156.00 REMARK 500 5 GLN A 150 86.69 62.52 REMARK 500 6 MET A 79 174.52 71.71 REMARK 500 6 ASN A 93 -6.54 75.73 REMARK 500 6 THR A 149 24.04 -151.81 REMARK 500 7 ALA A 78 176.71 70.86 REMARK 500 7 MET A 79 169.65 73.64 REMARK 500 7 GLN A 91 -68.74 -93.54 REMARK 500 7 LYS A 94 79.88 -154.28 REMARK 500 7 LEU A 119 -62.46 -93.13 REMARK 500 7 THR A 149 36.88 -166.55 REMARK 500 8 MET A 79 165.30 75.62 REMARK 500 8 LEU A 119 -60.87 -93.89 REMARK 500 8 PHE A 125 -158.57 -149.95 REMARK 500 8 THR A 145 -67.06 69.26 REMARK 500 8 ARG A 146 -51.67 -175.87 REMARK 500 9 MET A 79 164.69 72.45 REMARK 500 9 THR A 86 -16.85 -48.48 REMARK 500 9 LEU A 88 -19.88 -49.88 REMARK 500 9 PHE A 125 -168.73 -105.07 REMARK 500 REMARK 500 THIS ENTRY HAS 100 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 117 0.10 SIDE CHAIN REMARK 500 1 ARG A 147 0.07 SIDE CHAIN REMARK 500 6 ARG A 117 0.10 SIDE CHAIN REMARK 500 8 ARG A 117 0.11 SIDE CHAIN REMARK 500 12 ARG A 117 0.09 SIDE CHAIN REMARK 500 19 ARG A 147 0.13 SIDE CHAIN 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 103 SG REMARK 620 2 CYS A 106 SG 110.8 REMARK 620 3 CYS A 136 SG 110.5 112.8 REMARK 620 4 CYS A 139 SG 107.2 106.5 108.8 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 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6407 RELATED DB: BMRB REMARK 900 RELATED ID: 2LJX RELATED DB: PDB REMARK 900 RELATED ID: 2LJZ RELATED DB: PDB DBREF 2LJZ A 80 151 UNP P03126 VE6_HPV16 87 158 SEQADV 2LJZ GLY A 77 UNP P03126 EXPRESSION TAG SEQADV 2LJZ ALA A 78 UNP P03126 EXPRESSION TAG SEQADV 2LJZ MET A 79 UNP P03126 EXPRESSION TAG SEQADV 2LJZ SER A 80 UNP P03126 CYS 87 ENGINEERED MUTATION SEQADV 2LJZ SER A 97 UNP P03126 CYS 104 ENGINEERED MUTATION SEQADV 2LJZ SER A 111 UNP P03126 CYS 118 ENGINEERED MUTATION SEQADV 2LJZ SER A 140 UNP P03126 CYS 147 ENGINEERED MUTATION SEQRES 1 A 75 GLY ALA MET SER TYR SER LEU TYR GLY THR THR LEU GLU SEQRES 2 A 75 GLN GLN TYR ASN LYS PRO LEU SER ASP LEU LEU ILE ARG SEQRES 3 A 75 CYS ILE ASN CYS GLN LYS PRO LEU SER PRO GLU GLU LYS SEQRES 4 A 75 GLN ARG HIS LEU ASP LYS LYS GLN ARG PHE HIS ASN ILE SEQRES 5 A 75 ARG GLY ARG TRP THR GLY ARG CYS MET SER CYS SER ARG SEQRES 6 A 75 SER SER ARG THR ARG ARG GLU THR GLN LEU HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 THR A 87 TYR A 92 1 6 HELIX 2 2 SER A 111 ASP A 120 1 10 HELIX 3 3 CYS A 136 SER A 142 1 7 SHEET 1 A 4 TYR A 81 TYR A 84 0 SHEET 2 A 4 ARG A 124 ASN A 127 -1 O ASN A 127 N TYR A 81 SHEET 3 A 4 ARG A 131 GLY A 134 -1 O THR A 133 N HIS A 126 SHEET 4 A 4 LEU A 100 CYS A 103 1 N ARG A 102 O GLY A 134 LINK SG CYS A 103 ZN ZN A 201 1555 1555 2.30 LINK SG CYS A 106 ZN ZN A 201 1555 1555 2.25 LINK SG CYS A 136 ZN ZN A 201 1555 1555 2.29 LINK SG CYS A 139 ZN ZN A 201 1555 1555 2.21 SITE 1 AC1 5 CYS A 103 ASN A 105 CYS A 106 CYS A 136 SITE 2 AC1 5 CYS A 139 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