PDB Short entry for 6MJL HEADER TRANSCRIPTION/PEPTIDE 21-SEP-18 6MJL TITLE CRYSTAL STRUCTURE OF CHREBP NLS PEPTIDE BOUND TO IMPORTIN ALPHA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMPORTIN SUBUNIT ALPHA-1; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: IMPORTIN ALPHA P1,KARYOPHERIN SUBUNIT ALPHA-2,PENDULIN,PORE COMPND 5 TARGETING COMPLEX 58 KDA SUBUNIT,PTAC58,RAG COHORT PROTEIN 1,SRP1- COMPND 6 ALPHA; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: IMPORTIN ALPHA DELTA IBB; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CHREBP PEPTIDE ASN-TYR-TRP-LYS-ARG-ARG-ILE-GLU-VAL; COMPND 11 CHAIN: A; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: KPNA2, RCH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS CHREBP, IMPORTIN ALPHA, TRANSCRIPTION, TRANSCRIPTION-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.JUNG,K.UYEDA REVDAT 3 13-MAR-24 6MJL 1 REMARK REVDAT 2 07-OCT-20 6MJL 1 JRNL REVDAT 1 25-SEP-19 6MJL 0 JRNL AUTH H.JUNG,T.TAKESHIMA,T.NAKAGAWA,K.S.MACMILLAN,R.M.WYNN,H.WANG, JRNL AUTH 2 H.SAKIYAMA,S.WEI,Y.LI,R.K.BRUICK,B.A.POSNER, JRNL AUTH 3 J.K.DE BRABANDER,K.UYEDA JRNL TITL THE STRUCTURE OF IMPORTIN ALPHA AND THE NUCLEAR LOCALIZATION JRNL TITL 2 PEPTIDE OF CHREBP, AND SMALL COMPOUND INHIBITORS OF JRNL TITL 3 CHREBP-IMPORTIN ALPHA INTERACTIONS. JRNL REF BIOCHEM.J. V. 477 3253 2020 JRNL REFN ESSN 1470-8728 JRNL PMID 32776146 JRNL DOI 10.1042/BCJ20200520 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.3 REMARK 3 NUMBER OF REFLECTIONS : 20071 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 981 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.4403 - 4.7807 0.98 3346 170 0.1925 0.2171 REMARK 3 2 4.7807 - 3.7953 0.98 3205 175 0.1709 0.2360 REMARK 3 3 3.7953 - 3.3158 0.99 3175 175 0.1956 0.2454 REMARK 3 4 3.3158 - 3.0127 0.94 3022 156 0.2224 0.2851 REMARK 3 5 3.0127 - 2.7968 0.84 2695 125 0.2281 0.2783 REMARK 3 6 2.7968 - 2.6319 0.68 2178 96 0.2216 0.2256 REMARK 3 7 2.6319 - 2.5001 0.46 1469 84 0.2198 0.3024 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3389 REMARK 3 ANGLE : 0.962 4614 REMARK 3 CHIRALITY : 0.050 554 REMARK 3 PLANARITY : 0.006 589 REMARK 3 DIHEDRAL : 2.878 2052 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6MJL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000237045. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23621 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.54200 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 500 MM NA CITRATE 10 MM DTT 20 MM REMARK 280 HEPES PH 6.5, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 38.71700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.16600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.84550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.16600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.71700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.84550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER B 342 CA CB OG 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 ASN B 75 80.36 21.75 REMARK 500 ASN B 88 44.16 -100.56 REMARK 500 GLN B 109 74.51 26.93 REMARK 500 ALA B 214 72.74 -69.39 REMARK 500 ASN B 239 139.76 75.18 REMARK 500 GLU B 456 11.81 -146.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 6MJL B 72 497 UNP P52293 IMA1_MOUSE 72 497 DBREF 6MJL A 168 176 PDB 6MJL 6MJL 168 176 SEQRES 1 B 426 GLY THR VAL ASN TRP SER VAL GLU ASP ILE VAL LYS GLY SEQRES 2 B 426 ILE ASN SER ASN ASN LEU GLU SER GLN LEU GLN ALA THR SEQRES 3 B 426 GLN ALA ALA ARG LYS LEU LEU SER ARG GLU LYS GLN PRO SEQRES 4 B 426 PRO ILE ASP ASN ILE ILE ARG ALA GLY LEU ILE PRO LYS SEQRES 5 B 426 PHE VAL SER PHE LEU GLY LYS THR ASP CYS SER PRO ILE SEQRES 6 B 426 GLN PHE GLU SER ALA TRP ALA LEU THR ASN ILE ALA SER SEQRES 7 B 426 GLY THR SER GLU GLN THR LYS ALA VAL VAL ASP GLY GLY SEQRES 8 B 426 ALA ILE PRO ALA PHE ILE SER LEU LEU ALA SER PRO HIS SEQRES 9 B 426 ALA HIS ILE SER GLU GLN ALA VAL TRP ALA LEU GLY ASN SEQRES 10 B 426 ILE ALA GLY ASP GLY SER ALA PHE ARG ASP LEU VAL ILE SEQRES 11 B 426 LYS HIS GLY ALA ILE ASP PRO LEU LEU ALA LEU LEU ALA SEQRES 12 B 426 VAL PRO ASP LEU SER THR LEU ALA CYS GLY TYR LEU ARG SEQRES 13 B 426 ASN LEU THR TRP THR LEU SER ASN LEU CYS ARG ASN LYS SEQRES 14 B 426 ASN PRO ALA PRO PRO LEU ASP ALA VAL GLU GLN ILE LEU SEQRES 15 B 426 PRO THR LEU VAL ARG LEU LEU HIS HIS ASN ASP PRO GLU SEQRES 16 B 426 VAL LEU ALA ASP SER CYS TRP ALA ILE SER TYR LEU THR SEQRES 17 B 426 ASP GLY PRO ASN GLU ARG ILE GLU MET VAL VAL LYS LYS SEQRES 18 B 426 GLY VAL VAL PRO GLN LEU VAL LYS LEU LEU GLY ALA THR SEQRES 19 B 426 GLU LEU PRO ILE VAL THR PRO ALA LEU ARG ALA ILE GLY SEQRES 20 B 426 ASN ILE VAL THR GLY THR ASP GLU GLN THR GLN LYS VAL SEQRES 21 B 426 ILE ASP ALA GLY ALA LEU ALA VAL PHE PRO SER LEU LEU SEQRES 22 B 426 THR ASN PRO LYS THR ASN ILE GLN LYS GLU ALA THR TRP SEQRES 23 B 426 THR MET SER ASN ILE THR ALA GLY ARG GLN ASP GLN ILE SEQRES 24 B 426 GLN GLN VAL VAL ASN HIS GLY LEU VAL PRO PHE LEU VAL SEQRES 25 B 426 GLY VAL LEU SER LYS ALA ASP PHE LYS THR GLN LYS GLU SEQRES 26 B 426 ALA ALA TRP ALA ILE THR ASN TYR THR SER GLY GLY THR SEQRES 27 B 426 VAL GLU GLN ILE VAL TYR LEU VAL HIS CYS GLY ILE ILE SEQRES 28 B 426 GLU PRO LEU MET ASN LEU LEU SER ALA LYS ASP THR LYS SEQRES 29 B 426 ILE ILE GLN VAL ILE LEU ASP ALA ILE SER ASN ILE PHE SEQRES 30 B 426 GLN ALA ALA GLU LYS LEU GLY GLU THR GLU LYS LEU SER SEQRES 31 B 426 ILE MET ILE GLU GLU CYS GLY GLY LEU ASP LYS ILE GLU SEQRES 32 B 426 ALA LEU GLN ARG HIS GLU ASN GLU SER VAL TYR LYS ALA SEQRES 33 B 426 SER LEU ASN LEU ILE GLU LYS TYR PHE SER SEQRES 1 A 9 ASN TYR TRP LYS ARG ARG ILE GLU VAL FORMUL 3 HOH *71(H2 O) HELIX 1 AA1 SER B 77 SER B 87 1 11 HELIX 2 AA2 ASN B 89 SER B 105 1 17 HELIX 3 AA3 PRO B 111 ALA B 118 1 8 HELIX 4 AA4 LEU B 120 GLY B 129 1 10 HELIX 5 AA5 CYS B 133 SER B 149 1 17 HELIX 6 AA6 THR B 151 GLY B 161 1 11 HELIX 7 AA7 GLY B 162 LEU B 171 1 10 HELIX 8 AA8 HIS B 175 GLY B 191 1 17 HELIX 9 AA9 GLY B 193 HIS B 203 1 11 HELIX 10 AB1 ALA B 205 LEU B 212 1 8 HELIX 11 AB2 ASP B 217 LEU B 221 5 5 HELIX 12 AB3 ALA B 222 ARG B 238 1 17 HELIX 13 AB4 PRO B 245 LEU B 260 1 16 HELIX 14 AB5 ASP B 264 THR B 279 1 16 HELIX 15 AB6 PRO B 282 LYS B 292 1 11 HELIX 16 AB7 VAL B 294 LEU B 302 1 9 HELIX 17 AB8 GLU B 306 VAL B 321 1 16 HELIX 18 AB9 THR B 324 ALA B 334 1 11 HELIX 19 AC1 GLY B 335 ALA B 338 5 4 HELIX 20 AC2 VAL B 339 LEU B 344 1 6 HELIX 21 AC3 LYS B 348 ALA B 364 1 17 HELIX 22 AC4 ARG B 366 HIS B 376 1 11 HELIX 23 AC5 GLY B 377 LYS B 388 1 12 HELIX 24 AC6 ASP B 390 GLY B 408 1 19 HELIX 25 AC7 THR B 409 CYS B 419 1 11 HELIX 26 AC8 ILE B 421 LEU B 429 1 9 HELIX 27 AC9 ASP B 433 LEU B 454 1 22 HELIX 28 AD1 GLU B 456 CYS B 467 1 12 HELIX 29 AD2 GLY B 468 LEU B 476 1 9 HELIX 30 AD3 ASN B 481 PHE B 496 1 16 CISPEP 1 ASN B 241 PRO B 242 0 -4.10 CRYST1 77.434 89.691 96.332 90.00 90.00 90.00 P 21 21 21 4 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 0.012914 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010381 0.00000