PDB Short entry for 1H5P HEADER NUCLEAR PROTEIN 24-MAY-01 1H5P TITLE SOLUTION STRUCTURE OF THE HUMAN SP100B SAND DOMAIN BY HETERONUCLEAR TITLE 2 NMR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR AUTOANTIGEN SP100-B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 595-688; COMPND 5 SYNONYM: SAND DOMAIN, KDWK DOMAIN, SPECKLED 100 KDA, NUCLEAR DOT- COMPND 6 ASSOCIATED SP100 PROTEIN, LYSP100B; COMPND 7 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET-24D; SOURCE 8 EXPRESSION_SYSTEM_GENE: EXPRESSED AS FUSION PROTEIN WITH N-TERMINAL SOURCE 9 6-HISTIDINE TAG AND A TEV PROTEASE CLEAVAGE SITE KEYWDS TRANSCRIPTION, DNA BINDING, SP100B, SAND DOMAIN, KDWK, ANTIGEN, KEYWDS 2 NUCLEAR PROTEIN, ALTERNATIVE SPLICING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.J.BOTTOMLEY,Z.LIU,M.W.COLLARD,J.I.HUGGENVIK,T.J.GIBSON,M.SATTLER REVDAT 3 28-MAR-18 1H5P 1 SOURCE JRNL REVDAT 2 24-FEB-09 1H5P 1 VERSN REVDAT 1 06-JUL-01 1H5P 0 JRNL AUTH M.J.BOTTOMLEY,M.W.COLLARD,J.I.HUGGENVIK,Z.LIU,T.J.GIBSON, JRNL AUTH 2 M.SATTLER JRNL TITL THE SAND DOMAIN STRUCTURE DEFINES A NOVEL DNA-BINDING FOLD JRNL TITL 2 IN TRANSCRIPTIONAL REGULATION. JRNL REF NAT. STRUCT. BIOL. V. 8 626 2001 JRNL REFN ISSN 1072-8368 JRNL PMID 11427895 JRNL DOI 10.1038/89675 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.J.MICHELSON,M.W.COLLARD,A.J.ZIEMBA,J.PERSINGER, REMARK 1 AUTH 2 B.BARTHOLOMEW,J.I.HUGGENVIK REMARK 1 TITL NUCLEAR DEAF-1-RELATED (NUDR) PROTEIN CONTAINS A NOVEL DNA REMARK 1 TITL 2 BINDING DOMAIN AND REPRESSES TRANSCRIPTION OF THE REMARK 1 TITL 3 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A2/B1 PROMOTER REMARK 1 REF J.BIOL.CHEM. V. 274 30510 1999 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 10521432 REMARK 1 DOI 10.1074/JBC.274.43.30510 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.J.GIBSON,C.RAMU,C.GEMUEND,R.AASLAND REMARK 1 TITL THE APECED POLYGLANDULAR AUTOIMMUNE SYNDROME PROTEIN, REMARK 1 TITL 2 AIRE-1, CONTAINS THE SAND DOMAIN AND IS PROBABLY A REMARK 1 TITL 3 TRANSCRIPTION FACTOR REMARK 1 REF TRENDS BIOCHEM.SCI. V. 23 242 1998 REMARK 1 REFN ISSN 0968-0004 REMARK 1 PMID 9697411 REMARK 1 DOI 10.1016/S0968-0004(98)01231-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.3 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DURING THE STRUCTURE CALCULATIONS, THE REMARK 3 PROGRAM ARIA 1.0 (M.NILGES & S.I.O'DONOGHUE) WAS USED TO EMPLOY REMARK 3 DISTANCE RESTRAINTS DERIVED FROM AMBIGUOUSLY ASSIGNED NOES. FROM REMARK 3 A TOTAL OF 2120 NOES, ABOUT 80% WERE MANUALLY ASSIGNED, THE REMARK 3 REMAINDER WAS ASSIGNED BY ARIA. REMARK 4 REMARK 4 1H5P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1290006126. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295.0 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.2 MM PROTEIN, 20 MM SODIUM REMARK 210 PHOSPHATE PH 6.5, 50 MM NACL, 4 REMARK 210 MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 13C-SEPARATED NOESY; 3D 15N REMARK 210 -SEPARATED NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, XEASY, ARIA 1.0, CNS REMARK 210 0.9 REMARK 210 METHOD USED : ARIA AMBIGUOUS DISTANCE REMARK 210 RESTRAINTS SIMULATED ANNEALING REMARK 210 WITH TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ACCEPTABLE COVALENT GEOMETRY, REMARK 210 FAVOURABLE NON-BOND ENERGY, REMARK 210 FEWEST RESTRAINT VIOLATIONS, REMARK 210 LOWEST OVERALL ENERGIES 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: 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: 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 ASP A 595 179.31 59.70 REMARK 500 1 GLU A 596 -96.70 -129.36 REMARK 500 1 SER A 603 -16.52 69.62 REMARK 500 1 GLU A 611 -5.38 71.69 REMARK 500 1 THR A 625 7.48 -67.75 REMARK 500 1 ASP A 648 -75.95 -94.15 REMARK 500 1 ARG A 649 -39.99 178.96 REMARK 500 1 LYS A 653 -71.67 68.16 REMARK 500 1 ASN A 672 -75.19 -88.94 REMARK 500 1 LYS A 673 -18.26 -176.58 REMARK 500 1 PRO A 676 -92.73 -64.78 REMARK 500 1 GLU A 677 161.07 61.32 REMARK 500 1 PRO A 679 102.78 -39.35 REMARK 500 1 THR A 681 -87.38 -156.89 REMARK 500 1 ARG A 682 -147.05 -174.58 REMARK 500 1 ILE A 687 134.30 65.82 REMARK 500 2 GLU A 596 -102.88 -104.77 REMARK 500 2 SER A 603 -28.54 73.20 REMARK 500 2 GLU A 611 -2.36 69.56 REMARK 500 2 GLU A 633 -55.71 74.76 REMARK 500 2 ASP A 634 -24.94 177.77 REMARK 500 2 LYS A 635 19.68 -176.25 REMARK 500 2 PRO A 640 -17.82 -46.92 REMARK 500 2 ASP A 648 -77.73 -123.62 REMARK 500 2 ARG A 649 -31.04 178.32 REMARK 500 2 LYS A 653 -79.30 65.39 REMARK 500 2 LYS A 673 -25.59 -178.45 REMARK 500 2 LEU A 675 93.66 38.11 REMARK 500 2 SER A 680 87.23 58.60 REMARK 500 2 VAL A 685 -120.86 -78.36 REMARK 500 2 THR A 686 90.36 57.83 REMARK 500 3 ASN A 597 -36.89 -161.61 REMARK 500 3 ASN A 599 -162.29 -71.56 REMARK 500 3 PHE A 600 -1.30 -156.29 REMARK 500 3 GLN A 602 8.46 -66.85 REMARK 500 3 SER A 603 -31.71 73.82 REMARK 500 3 GLU A 611 -4.19 73.91 REMARK 500 3 LYS A 622 -16.26 -49.73 REMARK 500 3 GLU A 633 -55.78 73.78 REMARK 500 3 ASP A 634 -25.38 176.16 REMARK 500 3 LYS A 635 15.62 -175.89 REMARK 500 3 PRO A 640 -19.95 -48.30 REMARK 500 3 ASP A 648 -75.24 -99.71 REMARK 500 3 ARG A 649 -30.66 -175.35 REMARK 500 3 SER A 652 -147.20 -73.70 REMARK 500 3 LYS A 653 -50.67 -178.33 REMARK 500 3 ASN A 672 -76.09 -87.34 REMARK 500 3 LYS A 673 -16.76 171.43 REMARK 500 3 GLU A 677 74.68 -117.36 REMARK 500 3 SER A 680 -107.73 -68.11 REMARK 500 REMARK 500 THIS ENTRY HAS 171 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5558 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE STRUCTURE IS FOR THE SPLICE VARIANT SP100B SAND DOMAIN. REMARK 999 THE RESIDUES 685 -688 (RILE IN ISOFORM SP100-A) ARE REMARK 999 (VTIK IN ISOFORM SP100-B) DIFFERENT IN THE TWO SPLICE VARIANTS REMARK 999 MET A 594 IS A CLONING ARTIFACT. DBREF 1H5P A 594 594 PDB 1H5P 1H5P 594 594 DBREF 1H5P A 595 688 UNP P23497 SP10_HUMAN 595 688 SEQADV 1H5P VAL A 685 UNP P23497 ARG 685 VARIANT SEQADV 1H5P THR A 686 UNP P23497 ILE 686 VARIANT SEQADV 1H5P ILE A 687 UNP P23497 LEU 687 VARIANT SEQADV 1H5P LYS A 688 UNP P23497 GLU 688 VARIANT SEQRES 1 A 95 MET ASP GLU ASN ILE ASN PHE LYS GLN SER GLU LEU PRO SEQRES 2 A 95 VAL THR CYS GLY GLU VAL LYS GLY THR LEU TYR LYS GLU SEQRES 3 A 95 ARG PHE LYS GLN GLY THR SER LYS LYS CYS ILE GLN SER SEQRES 4 A 95 GLU ASP LYS LYS TRP PHE THR PRO ARG GLU PHE GLU ILE SEQRES 5 A 95 GLU GLY ASP ARG GLY ALA SER LYS ASN TRP LYS LEU SER SEQRES 6 A 95 ILE ARG CYS GLY GLY TYR THR LEU LYS VAL LEU MET GLU SEQRES 7 A 95 ASN LYS PHE LEU PRO GLU PRO PRO SER THR ARG LYS LYS SEQRES 8 A 95 VAL THR ILE LYS HELIX 1 1 GLU A 619 LYS A 622 1 4 HELIX 2 2 ARG A 641 GLY A 647 1 7 HELIX 3 3 TRP A 655 SER A 658 1 4 HELIX 4 4 THR A 665 ASN A 672 1 8 SHEET 1 AA 5 LYS A 636 PHE A 638 0 SHEET 2 AA 5 ILE A 630 SER A 632 -1 O ILE A 630 N PHE A 638 SHEET 3 AA 5 LYS A 613 TYR A 617 -1 O THR A 615 N GLN A 631 SHEET 4 AA 5 GLU A 604 THR A 608 -1 O LEU A 605 N LEU A 616 SHEET 5 AA 5 ILE A 659 CYS A 661 -1 O ARG A 660 N THR A 608 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