HEADER APOPTOSIS 24-JUN-10 2KZT TITLE STRUCTURE OF THE TANDEM MA-3 REGION OF PDCD4 CAVEAT 2KZT CHIRALITY ERROR AT CA CENTER OF VAL B 371, MODEL 35 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MA-3 REGION, RESIDUES 157-318; COMPND 5 SYNONYM: PDCD4, NUCLEAR ANTIGEN H731-LIKE, NEOPLASTIC TRANSFORMATION COMPND 6 INHIBITOR PROTEIN, PROTEIN 197/15A; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 4; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: MA-3 REGION, RESIDUES 319-449; COMPND 12 SYNONYM: PDCD4, TOPOISOMERASE-INHIBITOR SUPPRESSED PROTEIN, PROTEIN COMPND 13 MA-3; COMPND 14 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-2; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-2 KEYWDS PDCD4, MA-3, EIF4A, HEAT, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 73 AUTHOR L.C.WATERS,S.L.STRONG,O.OKA,F.W.MUSKETT,V.VEVERKA,S.BANERJEE, AUTHOR 2 T.SCHMEDT,A.J.HENRY,K.H.KLEMPNAUER,M.D.CARR REVDAT 2 23-NOV-11 2KZT 1 JRNL CAVEAT REVDAT 1 16-MAR-11 2KZT 0 JRNL AUTH L.C.WATERS,S.L.STRONG,E.FERLEMANN,O.OKA,F.W.MUSKETT, JRNL AUTH 2 V.VEVERKA,S.BANERJEE,T.SCHMEDT,A.J.HENRY,K.H.KLEMPNAUER, JRNL AUTH 3 M.D.CARR JRNL TITL STRUCTURE OF THE TANDEM MA-3 REGION OF PDCD4 PROTEIN AND JRNL TITL 2 CHARACTERIZATION OF ITS INTERACTIONS WITH EIF4A AND EIF4G: JRNL TITL 3 MOLECULAR MECHANISMS OF A TUMOR SUPPRESSOR JRNL REF J.BIOL.CHEM. V. 286 17270 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21454508 JRNL DOI 10.1074/JBC.M110.166157 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 2.0, X-PLOR_NIH REMARK 3 AUTHORS : CYRIL DOMINGUEZ, ROLF BOELENS AND ALEXANDRE M.J.J. REMARK 3 BONVIN (HADDOCK), SCHWIETERS, KUSZEWSKI, TJANDRA REMARK 3 AND CLORE (X-PLOR_NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINED AS PART OF THE HADDOCK DOCKING REMARK 3 PROTOCOL REMARK 4 REMARK 4 2KZT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUL-10. REMARK 100 THE RCSB ID CODE IS RCSB101778. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.15-0.5MM [U-99% 13C; U-99% REMARK 210 15N] PDCD4 MA-3 M-C; 25MM SODIUM REMARK 210 PHOSPHATE; 100MM SODIUM CHLORIDE; REMARK 210 2.5MM DTT; 2.5MM TCEP; 0.05MM REMARK 210 EDTA; 0.2MM AEBSF PROTEASE REMARK 210 INHIBITOR; 0.02% SODIUM AZIDE; REMARK 210 95% H2O/5% D2O; 0.5MM [U-99% 13C; REMARK 210 U-99% 15N] PDCD4 MA-3 M-C; 25MM REMARK 210 SODIUM PHOSPHATE; 100MM SODIUM REMARK 210 CHLORIDE; 2.5MM DTT; 2.5MM TCEP; REMARK 210 0.05MM EDTA; 0.2MM AEBSF PROTEASE REMARK 210 INHIBITOR; 0.02% SODIUM AZIDE; REMARK 210 95% H2O/5% D2O; 0.25MM [U-99% REMARK 210 13C; U-99% 15N] PDCD4 MA-3 M-C; REMARK 210 25MM SODIUM PHOSPHATE; 100MM REMARK 210 SODIUM CHLORIDE; 2.5MM DTT; 2.5MM REMARK 210 TCEP; 0.05MM EDTA; 0.2MM AEBSF REMARK 210 PROTEASE INHIBITOR; 0.02% SODIUM REMARK 210 AZIDE; 10MG/ML PF1 PHAGE; 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D CBCA(CO)NH; 3D HNCO; 2D 1H- REMARK 210 15N HSQC; 3D 1H-15N NOESY-HSQC; REMARK 210 3D TROSY HN(CO)CA; 3D HNCA; 3D REMARK 210 IPAP TROSY HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, SPARKY 3.110, REMARK 210 HADDOCK 2.0 REMARK 210 METHOD USED : HADDOCK REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 73 REMARK 210 CONFORMERS, SELECTION CRITERIA : ACCEPTABLE RMSD TO LOWEST REMARK 210 HADDOCK SCORE STRUCTURE 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: 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 ASN A 192 93.62 65.20 REMARK 500 1 LYS A 283 47.48 -67.82 REMARK 500 1 THR A 285 36.75 -87.58 REMARK 500 1 VAL A 314 10.73 -150.79 REMARK 500 1 SER A 317 20.42 -155.01 REMARK 500 1 LEU B 327 -60.33 75.39 REMARK 500 1 GLU B 330 -70.04 -129.44 REMARK 500 1 ASP B 418 130.42 78.98 REMARK 500 1 VAL B 419 79.80 62.59 REMARK 500 1 PRO B 448 84.32 -62.46 REMARK 500 2 ASN A 192 81.46 57.96 REMARK 500 2 THR A 254 96.15 -165.82 REMARK 500 2 LEU B 327 -55.79 69.59 REMARK 500 2 LYS B 329 -37.50 77.03 REMARK 500 2 SER B 341 -70.05 -71.72 REMARK 500 2 GLU B 355 20.46 -78.60 REMARK 500 2 SER B 374 -163.36 -74.89 REMARK 500 2 ASP B 418 146.06 71.17 REMARK 500 2 VAL B 419 78.35 58.24 REMARK 500 2 PRO B 448 90.26 -67.81 REMARK 500 3 ASN A 192 90.53 60.16 REMARK 500 3 LYS A 283 51.01 -63.79 REMARK 500 3 SER A 313 -34.76 -130.44 REMARK 500 3 GLN B 321 -67.72 -106.51 REMARK 500 3 LEU B 327 -45.55 74.30 REMARK 500 3 GLU B 330 -94.14 -110.96 REMARK 500 3 ASP B 418 167.70 75.06 REMARK 500 3 PRO B 448 80.17 -65.38 REMARK 500 4 GLU A 177 -71.38 -104.88 REMARK 500 4 ASP A 190 15.04 -59.17 REMARK 500 4 ALA A 208 -0.22 -47.24 REMARK 500 4 THR A 254 87.35 -155.98 REMARK 500 4 LYS A 283 46.45 -63.02 REMARK 500 4 LYS A 309 71.03 -112.62 REMARK 500 4 LYS B 329 -82.45 56.52 REMARK 500 4 LEU B 340 -63.42 -96.41 REMARK 500 4 LEU B 354 -164.35 -54.01 REMARK 500 4 GLU B 355 11.21 -140.33 REMARK 500 4 SER B 374 -168.49 -114.68 REMARK 500 4 PHE B 380 -75.54 -77.26 REMARK 500 4 SER B 394 -34.96 155.76 REMARK 500 4 THR B 395 -75.37 -57.52 REMARK 500 4 ASP B 418 147.73 76.86 REMARK 500 4 VAL B 419 80.78 59.99 REMARK 500 4 PRO B 420 41.21 -79.61 REMARK 500 4 ILE B 439 -154.47 -83.23 REMARK 500 5 ASP A 160 78.66 66.88 REMARK 500 5 VAL A 230 -35.07 -130.77 REMARK 500 5 THR A 233 -35.52 -37.57 REMARK 500 5 LYS A 245 -74.45 -65.21 REMARK 500 REMARK 500 THIS ENTRY HAS 1189 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 2 LYS A 283 20.9 L L OUTSIDE RANGE REMARK 500 4 LYS A 283 24.1 L L OUTSIDE RANGE REMARK 500 4 LYS B 388 23.6 L L OUTSIDE RANGE REMARK 500 5 ILE B 344 23.5 L L OUTSIDE RANGE REMARK 500 5 SER B 345 24.8 L L OUTSIDE RANGE REMARK 500 6 ILE B 383 19.0 L L OUTSIDE RANGE REMARK 500 7 LYS A 283 24.8 L L OUTSIDE RANGE REMARK 500 8 LYS A 283 17.7 L L OUTSIDE RANGE REMARK 500 8 LYS B 352 24.8 L L OUTSIDE RANGE REMARK 500 8 HIS B 360 20.2 L L OUTSIDE RANGE REMARK 500 8 GLU B 362 17.7 L L OUTSIDE RANGE REMARK 500 9 HIS A 178 24.1 L L OUTSIDE RANGE REMARK 500 9 LYS A 283 21.0 L L OUTSIDE RANGE REMARK 500 10 LYS A 283 20.6 L L OUTSIDE RANGE REMARK 500 11 HIS A 178 24.4 L L OUTSIDE RANGE REMARK 500 11 LYS A 283 23.9 L L OUTSIDE RANGE REMARK 500 12 LYS A 283 22.2 L L OUTSIDE RANGE REMARK 500 13 VAL A 261 23.4 L L OUTSIDE RANGE REMARK 500 14 ARG A 267 24.3 L L OUTSIDE RANGE REMARK 500 18 LYS A 283 24.5 L L OUTSIDE RANGE REMARK 500 18 TYR B 338 25.0 L L OUTSIDE RANGE REMARK 500 19 LYS A 283 21.9 L L OUTSIDE RANGE REMARK 500 20 LYS A 283 22.8 L L OUTSIDE RANGE REMARK 500 21 LYS A 283 23.4 L L OUTSIDE RANGE REMARK 500 21 GLN B 435 24.6 L L OUTSIDE RANGE REMARK 500 22 HIS A 178 24.1 L L OUTSIDE RANGE REMARK 500 22 ILE B 368 19.9 L L OUTSIDE RANGE REMARK 500 24 LYS A 283 20.0 L L OUTSIDE RANGE REMARK 500 24 SER B 345 20.9 L L OUTSIDE RANGE REMARK 500 25 THR A 169 19.5 L L OUTSIDE RANGE REMARK 500 28 THR A 169 24.5 L L OUTSIDE RANGE REMARK 500 28 LYS A 283 24.4 L L OUTSIDE RANGE REMARK 500 30 LYS B 388 23.3 L L OUTSIDE RANGE REMARK 500 30 GLN B 435 24.2 L L OUTSIDE RANGE REMARK 500 31 GLN B 435 23.5 L L OUTSIDE RANGE REMARK 500 32 HIS A 178 24.8 L L OUTSIDE RANGE REMARK 500 32 LYS A 283 22.1 L L OUTSIDE RANGE REMARK 500 33 LYS A 283 21.2 L L OUTSIDE RANGE REMARK 500 33 LEU B 335 23.1 L L OUTSIDE RANGE REMARK 500 35 VAL B 369 23.1 L L OUTSIDE RANGE REMARK 500 35 VAL B 371 2.8 L L EXPECTING SP3 REMARK 500 35 LEU B 386 19.6 L L OUTSIDE RANGE REMARK 500 35 LYS B 388 20.3 L L OUTSIDE RANGE REMARK 500 36 LYS A 283 22.3 L L OUTSIDE RANGE REMARK 500 36 HIS B 349 24.8 L L OUTSIDE RANGE REMARK 500 37 THR A 181 24.8 L L OUTSIDE RANGE REMARK 500 37 LYS A 283 19.9 L L OUTSIDE RANGE REMARK 500 38 LYS A 283 20.6 L L OUTSIDE RANGE REMARK 500 38 GLU B 353 16.4 L L OUTSIDE RANGE REMARK 500 39 LYS A 283 16.8 L L OUTSIDE RANGE REMARK 500 REMARK 500 THIS ENTRY HAS 100 CHIRALITY DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16542 RELATED DB: BMRB DBREF 2KZT A 157 318 UNP Q53EL6 PDCD4_HUMAN 157 318 DBREF 2KZT B 319 449 UNP Q61823 PDCD4_MOUSE 319 449 SEQADV 2KZT GLY A 156 UNP Q53EL6 EXPRESSION TAG SEQRES 1 A 163 GLY LEU PRO LEU ASP GLU ARG ALA PHE GLU LYS THR LEU SEQRES 2 A 163 THR PRO ILE ILE GLN GLU TYR PHE GLU HIS GLY ASP THR SEQRES 3 A 163 ASN GLU VAL ALA GLU MET LEU ARG ASP LEU ASN LEU GLY SEQRES 4 A 163 GLU MET LYS SER GLY VAL PRO VAL LEU ALA VAL SER LEU SEQRES 5 A 163 ALA LEU GLU GLY LYS ALA SER HIS ARG GLU MET THR SER SEQRES 6 A 163 LYS LEU LEU SER ASP LEU CYS GLY THR VAL MET SER THR SEQRES 7 A 163 THR ASP VAL GLU LYS SER PHE ASP LYS LEU LEU LYS ASP SEQRES 8 A 163 LEU PRO GLU LEU ALA LEU ASP THR PRO ARG ALA PRO GLN SEQRES 9 A 163 LEU VAL GLY GLN PHE ILE ALA ARG ALA VAL GLY ASP GLY SEQRES 10 A 163 ILE LEU CYS ASN THR TYR ILE ASP SER TYR LYS GLY THR SEQRES 11 A 163 VAL ASP CYS VAL GLN ALA ARG ALA ALA LEU ASP LYS ALA SEQRES 12 A 163 THR VAL LEU LEU SER MET SER LYS GLY GLY LYS ARG LYS SEQRES 13 A 163 ASP SER VAL TRP GLY SER GLY SEQRES 1 B 131 GLY GLY GLN GLN PRO VAL ASN HIS LEU VAL LYS GLU ILE SEQRES 2 B 131 ASP MET LEU LEU LYS GLU TYR LEU LEU SER GLY ASP ILE SEQRES 3 B 131 SER GLU ALA GLU HIS CYS LEU LYS GLU LEU GLU VAL PRO SEQRES 4 B 131 HIS PHE HIS HIS GLU LEU VAL TYR GLU ALA ILE VAL MET SEQRES 5 B 131 VAL LEU GLU SER THR GLY GLU SER ALA PHE LYS MET ILE SEQRES 6 B 131 LEU ASP LEU LEU LYS SER LEU TRP LYS SER SER THR ILE SEQRES 7 B 131 THR ILE ASP GLN MET LYS ARG GLY TYR GLU ARG ILE TYR SEQRES 8 B 131 ASN GLU ILE PRO ASP ILE ASN LEU ASP VAL PRO HIS SER SEQRES 9 B 131 TYR SER VAL LEU GLU ARG PHE VAL GLU GLU CYS PHE GLN SEQRES 10 B 131 ALA GLY ILE ILE SER LYS GLN LEU ARG ASP LEU CYS PRO SEQRES 11 B 131 SER HELIX 1 1 ASP A 160 GLY A 179 1 20 HELIX 2 2 ASP A 180 ASN A 192 1 13 HELIX 3 3 GLY A 194 LYS A 197 5 4 HELIX 4 4 SER A 198 GLY A 211 1 14 HELIX 5 5 LYS A 212 CYS A 227 1 16 HELIX 6 6 SER A 232 THR A 254 1 23 HELIX 7 7 ARG A 256 GLY A 272 1 17 HELIX 8 8 THR A 277 TYR A 282 1 6 HELIX 9 9 CYS A 288 LYS A 306 1 19 HELIX 10 10 GLU B 330 LEU B 340 1 11 HELIX 11 11 ASP B 343 LYS B 352 1 10 HELIX 12 12 PRO B 357 PHE B 359 5 3 HELIX 13 13 HIS B 360 SER B 374 1 15 HELIX 14 14 GLY B 376 SER B 393 1 18 HELIX 15 15 THR B 397 LEU B 417 1 21 HELIX 16 16 SER B 422 GLY B 437 1 16 HELIX 17 17 SER B 440 ASP B 445 1 6 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