HEADER GENE REGULATION 22-JAN-09 2KE1 TITLE MOLECULAR BASIS OF NON-MODIFIED HISTONE H3 TAIL RECOGNITION BY THE TITLE 2 FIRST PHD FINGER OF AUTOIMMUNE REGULATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOIMMUNE REGULATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FIRST PHD DOMAIN, UNP RESIDUES 293-354; COMPND 5 SYNONYM: AUTOIMMUNE POLYENDOCRINOPATHY CANDIDIASIS ECTODERMAL COMPND 6 DYSTROPHY PROTEIN, APECED PROTEIN; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: H3K4ME0; COMPND 10 CHAIN: B; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: MODIFIED PET24D; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHESIZED PEPTIDE KEYWDS AIRE, PHD FINGER, HISTONE H3, DISEASE MUTATION, METAL-BINDING, KEYWDS 2 NUCLEUS, TRANSCRIPTION, TRANSCRIPTION REGULATION, ZINC, ZINC-FINGER, KEYWDS 3 GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.CHIGNOLA,M.GAETANI,A.REBANE,T.ORG,L.MOLLICA,C.ZUCCHELLI, AUTHOR 2 A.SPITALERI,V.MANNELLA,P.PETERSON,G.MUSCO REVDAT 3 16-MAR-22 2KE1 1 REMARK SEQADV REVDAT 2 16-JUN-09 2KE1 1 JRNL REVDAT 1 26-MAY-09 2KE1 0 JRNL AUTH F.CHIGNOLA,M.GAETANI,A.REBANE,T.ORG,L.MOLLICA,C.ZUCCHELLI, JRNL AUTH 2 A.SPITALERI,V.MANNELLA,P.PETERSON,G.MUSCO JRNL TITL THE SOLUTION STRUCTURE OF THE FIRST PHD FINGER OF AUTOIMMUNE JRNL TITL 2 REGULATOR IN COMPLEX WITH NON-MODIFIED HISTONE H3 TAIL JRNL TITL 3 REVEALS THE ANTAGONISTIC ROLE OF H3R2 METHYLATION JRNL REF NUCLEIC ACIDS RES. V. 37 2951 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19293276 JRNL DOI 10.1093/NAR/GKP166 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.2, ARIA 2.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KE1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000101004. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.1-0.5 MM [U-99% 13C; U-99% REMARK 210 15N] AIRE-PHD1-1, 90% H2O/10% REMARK 210 D2O; 0.5 MM [U-99% 13C; U-99% REMARK 210 15N] AIRE-PHD1+H3K4ME0-2, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HNCA; 3D HNCACB; 3D REMARK 210 HCCH-TOCSY; 3D HNHA; 3D H(CCO)NH; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL 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: 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 THR A 344 67.97 -68.21 REMARK 500 1 GLN A 349 84.90 58.85 REMARK 500 1 ARG A 351 35.24 -99.81 REMARK 500 2 SER A 332 53.86 -94.07 REMARK 500 2 GLU A 353 92.10 67.34 REMARK 500 3 MET A 291 13.32 -143.37 REMARK 500 3 SER A 332 52.07 -96.32 REMARK 500 3 THR A 344 45.56 -143.09 REMARK 500 3 GLN A 346 80.34 60.67 REMARK 500 3 VAL A 348 65.51 -107.28 REMARK 500 3 THR B 6 -160.63 52.09 REMARK 500 4 ALA A 343 42.08 -83.79 REMARK 500 4 THR A 344 72.87 -65.09 REMARK 500 4 LYS B 9 -77.68 -96.81 REMARK 500 5 ALA A 290 -63.19 71.82 REMARK 500 5 GLN A 293 105.21 -161.10 REMARK 500 5 SER A 332 57.52 -94.03 REMARK 500 5 GLN A 346 -80.65 -82.93 REMARK 500 5 GLU A 353 177.66 70.19 REMARK 500 5 GLN B 5 78.06 -107.95 REMARK 500 6 MET A 291 72.92 51.57 REMARK 500 6 SER A 332 38.43 -89.43 REMARK 500 6 VAL A 345 -68.28 -91.12 REMARK 500 6 GLN A 346 130.09 69.23 REMARK 500 6 GLN A 349 153.46 71.13 REMARK 500 6 ARG A 351 -78.68 -135.54 REMARK 500 6 ALA A 352 80.67 49.47 REMARK 500 6 GLU A 353 26.22 -79.02 REMARK 500 7 SER A 332 40.73 -91.96 REMARK 500 7 VAL A 348 75.78 54.97 REMARK 500 7 GLN A 349 91.42 63.80 REMARK 500 7 ALA A 352 58.53 -103.31 REMARK 500 7 GLU A 353 -66.41 -93.93 REMARK 500 8 SER A 332 52.44 -93.20 REMARK 500 8 VAL A 348 30.81 -163.02 REMARK 500 8 GLN B 5 74.10 -104.95 REMARK 500 9 MET A 291 58.31 -92.74 REMARK 500 9 SER A 332 59.99 -90.48 REMARK 500 9 THR A 344 41.86 -79.75 REMARK 500 9 GLN A 346 145.79 71.45 REMARK 500 9 VAL A 348 67.40 39.52 REMARK 500 9 LYS B 9 113.16 77.82 REMARK 500 10 ASP A 297 35.19 -91.16 REMARK 500 10 SER A 332 48.40 -98.13 REMARK 500 10 VAL A 348 22.96 -144.74 REMARK 500 10 GLN A 349 107.87 70.51 REMARK 500 11 SER A 332 47.27 -98.27 REMARK 500 11 GLN A 346 -88.54 64.28 REMARK 500 11 GLN A 349 90.06 52.94 REMARK 500 11 GLN B 5 77.34 -100.37 REMARK 500 REMARK 500 THIS ENTRY HAS 87 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 10 ARG B 2 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 355 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 299 SG REMARK 620 2 CYS A 302 SG 118.7 REMARK 620 3 HIS A 319 ND1 84.3 88.5 REMARK 620 4 CYS A 322 SG 134.6 106.7 98.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 356 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 311 SG REMARK 620 2 CYS A 314 SG 123.8 REMARK 620 3 CYS A 337 SG 120.8 115.3 REMARK 620 4 CYS A 340 SG 100.6 84.3 87.8 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 355 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 356 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XWH RELATED DB: PDB REMARK 900 FREE AIRE-PHD1 REMARK 900 RELATED ID: 6374 RELATED DB: BMRB REMARK 900 FREE AIRE-PHD1 DBREF 2KE1 A 293 354 UNP O43918 AIRE_HUMAN 293 354 DBREF 2KE1 B 1 10 PDB 2KE1 2KE1 1 10 SEQADV 2KE1 GLY A 289 UNP O43918 EXPRESSION TAG SEQADV 2KE1 ALA A 290 UNP O43918 EXPRESSION TAG SEQADV 2KE1 MET A 291 UNP O43918 EXPRESSION TAG SEQADV 2KE1 ALA A 292 UNP O43918 EXPRESSION TAG SEQRES 1 A 66 GLY ALA MET ALA GLN LYS ASN GLU ASP GLU CYS ALA VAL SEQRES 2 A 66 CYS ARG ASP GLY GLY GLU LEU ILE CYS CYS ASP GLY CYS SEQRES 3 A 66 PRO ARG ALA PHE HIS LEU ALA CYS LEU SER PRO PRO LEU SEQRES 4 A 66 ARG GLU ILE PRO SER GLY THR TRP ARG CYS SER SER CYS SEQRES 5 A 66 LEU GLN ALA THR VAL GLN GLU VAL GLN PRO ARG ALA GLU SEQRES 6 A 66 GLU SEQRES 1 B 10 ALA ARG THR LYS GLN THR ALA ARG LYS SER HET ZN A 355 1 HET ZN A 356 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 1 CYS A 337 ALA A 343 1 7 SHEET 1 A 3 ALA A 317 HIS A 319 0 SHEET 2 A 3 GLU A 307 CYS A 310 -1 N ILE A 309 O PHE A 318 SHEET 3 A 3 ARG B 2 GLN B 5 -1 O LYS B 4 N LEU A 308 LINK SG CYS A 299 ZN ZN A 355 1555 1555 2.55 LINK SG CYS A 302 ZN ZN A 355 1555 1555 2.53 LINK SG CYS A 311 ZN ZN A 356 1555 1555 2.50 LINK SG CYS A 314 ZN ZN A 356 1555 1555 2.52 LINK ND1 HIS A 319 ZN ZN A 355 1555 1555 2.51 LINK SG CYS A 322 ZN ZN A 355 1555 1555 2.56 LINK SG CYS A 337 ZN ZN A 356 1555 1555 2.48 LINK SG CYS A 340 ZN ZN A 356 1555 1555 2.41 CISPEP 1 SER A 324 PRO A 325 1 0.46 CISPEP 2 SER A 324 PRO A 325 2 0.30 CISPEP 3 SER A 324 PRO A 325 3 2.03 CISPEP 4 SER A 324 PRO A 325 4 -2.70 CISPEP 5 SER A 324 PRO A 325 5 0.64 CISPEP 6 SER A 324 PRO A 325 6 5.03 CISPEP 7 SER A 324 PRO A 325 7 0.43 CISPEP 8 SER A 324 PRO A 325 8 -1.17 CISPEP 9 SER A 324 PRO A 325 9 -1.10 CISPEP 10 SER A 324 PRO A 325 10 0.88 CISPEP 11 SER A 324 PRO A 325 11 -1.94 CISPEP 12 SER A 324 PRO A 325 12 -2.91 CISPEP 13 SER A 324 PRO A 325 13 -0.96 CISPEP 14 SER A 324 PRO A 325 14 -1.29 CISPEP 15 SER A 324 PRO A 325 15 -0.38 CISPEP 16 SER A 324 PRO A 325 16 -0.59 CISPEP 17 SER A 324 PRO A 325 17 -0.06 CISPEP 18 SER A 324 PRO A 325 18 -2.24 CISPEP 19 SER A 324 PRO A 325 19 2.02 CISPEP 20 SER A 324 PRO A 325 20 -2.04 SITE 1 AC1 2 CYS A 299 CYS A 302 SITE 1 AC2 3 CYS A 311 CYS A 314 CYS A 337 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