HEADER METAL BINDING PROTEIN 30-SEP-11 2LJX TITLE STRUCTURE OF THE MONOMERIC N-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 7-89; 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 STRAIN: TYPE 16; SOURCE 5 GENE: E6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 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 2LJX 1 REMARK SEQADV LINK REVDAT 2 25-APR-12 2LJX 1 JRNL REVDAT 1 04-APR-12 2LJX 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 2LJX 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_1000102472. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 50 MM 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; 800 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 STUCTURE 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 TYR A 81 REMARK 465 SER A 82 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 TYR A 60 N TYR A 60 CA -0.141 REMARK 500 2 PRO A 59 C PRO A 59 O 0.129 REMARK 500 2 TYR A 60 N TYR A 60 CA -0.124 REMARK 500 3 PRO A 59 C PRO A 59 O 0.121 REMARK 500 3 TYR A 60 N TYR A 60 CA -0.143 REMARK 500 4 TYR A 60 N TYR A 60 CA -0.152 REMARK 500 5 TYR A 60 N TYR A 60 CA -0.130 REMARK 500 6 TYR A 60 N TYR A 60 CA -0.129 REMARK 500 7 PRO A 59 C PRO A 59 O 0.128 REMARK 500 7 TYR A 60 N TYR A 60 CA -0.132 REMARK 500 8 PRO A 59 C PRO A 59 O 0.121 REMARK 500 8 TYR A 60 N TYR A 60 CA -0.135 REMARK 500 9 PRO A 59 C PRO A 59 O 0.132 REMARK 500 9 TYR A 60 N TYR A 60 CA -0.140 REMARK 500 10 TYR A 60 N TYR A 60 CA -0.135 REMARK 500 11 TYR A 60 N TYR A 60 CA -0.132 REMARK 500 12 TYR A 60 N TYR A 60 CA -0.125 REMARK 500 13 TYR A 60 N TYR A 60 CA -0.134 REMARK 500 14 TYR A 60 N TYR A 60 CA -0.125 REMARK 500 15 PRO A 59 C PRO A 59 O 0.127 REMARK 500 15 TYR A 60 N TYR A 60 CA -0.131 REMARK 500 16 TYR A 60 N TYR A 60 CA -0.132 REMARK 500 17 TYR A 60 N TYR A 60 CA -0.136 REMARK 500 18 TYR A 60 N TYR A 60 CA -0.141 REMARK 500 19 TYR A 60 N TYR A 60 CA -0.142 REMARK 500 20 TYR A 60 N TYR A 60 CA -0.136 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 8 130.55 70.03 REMARK 500 1 PRO A 9 -154.21 -84.84 REMARK 500 1 ASP A 25 -39.45 -131.47 REMARK 500 1 ARG A 48 -150.42 -118.45 REMARK 500 1 ASP A 56 -53.82 71.16 REMARK 500 1 GLU A 75 104.01 74.06 REMARK 500 2 GLN A 6 73.80 -114.72 REMARK 500 2 PRO A 9 -154.66 -80.18 REMARK 500 2 ASP A 25 -34.86 -147.74 REMARK 500 2 ARG A 48 -156.13 -112.09 REMARK 500 2 ASP A 56 -74.05 69.50 REMARK 500 2 SER A 74 -47.74 -139.86 REMARK 500 3 ARG A 8 160.89 62.25 REMARK 500 3 PRO A 9 -158.99 -91.58 REMARK 500 3 ASP A 25 -28.25 -140.18 REMARK 500 3 ARG A 48 -149.69 -122.43 REMARK 500 3 ASP A 56 -84.50 72.79 REMARK 500 4 ARG A 8 119.84 76.43 REMARK 500 4 PRO A 9 -155.97 -82.88 REMARK 500 4 LEU A 19 1.10 -69.00 REMARK 500 4 ARG A 48 -152.33 -116.72 REMARK 500 4 ASP A 56 -64.92 70.70 REMARK 500 4 TYR A 70 -86.60 -113.56 REMARK 500 4 SER A 71 -75.94 60.79 REMARK 500 4 SER A 74 -50.74 -129.64 REMARK 500 4 HIS A 78 73.87 -104.51 REMARK 500 5 ALA A 0 -44.20 69.33 REMARK 500 5 GLN A 6 79.92 4.40 REMARK 500 5 ARG A 8 140.97 68.51 REMARK 500 5 PRO A 9 -159.85 -88.44 REMARK 500 5 ASP A 25 -34.33 -135.15 REMARK 500 5 ARG A 48 -145.25 -123.29 REMARK 500 5 ASP A 49 81.19 -157.59 REMARK 500 5 CYS A 51 134.66 59.11 REMARK 500 5 ASP A 56 -68.65 73.44 REMARK 500 5 TYR A 70 73.87 -116.82 REMARK 500 5 HIS A 78 -66.19 -125.88 REMARK 500 5 TYR A 79 109.57 69.44 REMARK 500 6 PRO A 5 -76.77 -87.05 REMARK 500 6 PRO A 9 -163.71 -80.00 REMARK 500 6 ASP A 25 -36.73 -132.91 REMARK 500 6 LYS A 34 -3.82 70.06 REMARK 500 6 ARG A 48 -155.65 -113.54 REMARK 500 6 ASP A 56 -78.29 72.61 REMARK 500 6 CYS A 63 -179.27 -64.49 REMARK 500 6 TYR A 76 80.12 47.32 REMARK 500 6 HIS A 78 75.87 -111.38 REMARK 500 7 PRO A 5 -79.41 -88.60 REMARK 500 7 GLN A 6 3.39 56.48 REMARK 500 7 GLU A 7 -45.44 58.99 REMARK 500 REMARK 500 THIS ENTRY HAS 158 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 4 ARG A 39 0.08 SIDE CHAIN REMARK 500 6 ARG A 48 0.08 SIDE CHAIN REMARK 500 10 ARG A 10 0.07 SIDE CHAIN REMARK 500 11 ARG A 48 0.08 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 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 30 SG REMARK 620 2 CYS A 33 SG 109.7 REMARK 620 3 CYS A 63 SG 113.6 108.8 REMARK 620 4 CYS A 66 SG 109.2 107.2 108.1 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 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17967 RELATED DB: BMRB REMARK 900 RELATED ID: 2LJY RELATED DB: PDB REMARK 900 RELATED ID: 2LJZ RELATED DB: PDB DBREF 2LJX A 0 82 UNP P03126 VE6_HPV16 7 89 SEQADV 2LJX GLY A -1 UNP P03126 EXPRESSION TAG SEQADV 2LJX ARG A 47 UNP P03126 PHE 54 ENGINEERED MUTATION SEQADV 2LJX SER A 80 UNP P03126 CYS 87 ENGINEERED MUTATION SEQRES 1 A 84 GLY ALA MET PHE GLN ASP PRO GLN GLU ARG PRO ARG LYS SEQRES 2 A 84 LEU PRO GLN LEU CYS THR GLU LEU GLN THR THR ILE HIS SEQRES 3 A 84 ASP ILE ILE LEU GLU CYS VAL TYR CYS LYS GLN GLN LEU SEQRES 4 A 84 LEU ARG ARG GLU VAL TYR ASP PHE ALA ARG ARG ASP LEU SEQRES 5 A 84 CYS ILE VAL TYR ARG ASP GLY ASN PRO TYR ALA VAL CYS SEQRES 6 A 84 ASP LYS CYS LEU LYS PHE TYR SER LYS ILE SER GLU TYR SEQRES 7 A 84 ARG HIS TYR SER TYR SER HET ZN A 200 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 LYS A 11 LEU A 19 1 9 HELIX 2 2 LEU A 38 ARG A 48 1 11 HELIX 3 3 CYS A 63 SER A 71 1 9 SHEET 1 A 3 GLU A 29 CYS A 30 0 SHEET 2 A 3 ASN A 58 ALA A 61 1 O ALA A 61 N GLU A 29 SHEET 3 A 3 VAL A 53 ARG A 55 -1 N VAL A 53 O TYR A 60 LINK SG CYS A 30 ZN ZN A 200 1555 1555 2.30 LINK SG CYS A 33 ZN ZN A 200 1555 1555 2.28 LINK SG CYS A 63 ZN ZN A 200 1555 1555 2.28 LINK SG CYS A 66 ZN ZN A 200 1555 1555 2.27 CISPEP 1 ASP A 4 PRO A 5 1 6.26 CISPEP 2 ASP A 4 PRO A 5 2 -5.27 CISPEP 3 ASP A 4 PRO A 5 3 3.72 CISPEP 4 ASP A 4 PRO A 5 4 6.99 CISPEP 5 ASP A 4 PRO A 5 5 8.50 CISPEP 6 ASP A 4 PRO A 5 6 1.34 CISPEP 7 ASP A 4 PRO A 5 7 1.99 CISPEP 8 ASP A 4 PRO A 5 8 8.88 CISPEP 9 ASP A 4 PRO A 5 9 12.63 CISPEP 10 ASP A 4 PRO A 5 10 4.84 CISPEP 11 ASP A 4 PRO A 5 11 -1.51 CISPEP 12 ASP A 4 PRO A 5 12 -0.57 CISPEP 13 ASP A 4 PRO A 5 13 -0.78 CISPEP 14 ASP A 4 PRO A 5 14 -2.25 CISPEP 15 ASP A 4 PRO A 5 15 -4.69 CISPEP 16 ASP A 4 PRO A 5 16 6.50 CISPEP 17 ASP A 4 PRO A 5 17 2.98 CISPEP 18 ASP A 4 PRO A 5 18 4.80 CISPEP 19 ASP A 4 PRO A 5 19 7.90 CISPEP 20 ASP A 4 PRO A 5 20 3.11 SITE 1 AC1 4 CYS A 30 CYS A 33 CYS A 63 CYS A 66 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