PDB Short entry for 1LB6 HEADER SIGNALING PROTEIN 02-APR-02 1LB6 TITLE TRAF6-CD40 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TNF RECEPTOR-ASSOCIATED FACTOR 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 347-504; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CD40 ANTIGEN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: RESIDUES 230-238; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TRAF6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: CD40; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRAF6-CD40 COMPLEX, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.YE,J.R.ARRON,B.LAMOTHE,M.CIRILLI,T.KOBAYASHI,N.K.SHEVDE,D.SEGAL, AUTHOR 2 O.DZIVENU,M.VOLOGODSKAIA,M.YIM,K.DU,S.SINGH,J.W.PIKE,B.G.DARNAY, AUTHOR 3 Y.CHOI,H.WU REVDAT 6 03-APR-24 1LB6 1 REMARK REVDAT 5 14-FEB-24 1LB6 1 SEQADV REVDAT 4 11-OCT-17 1LB6 1 REMARK REVDAT 3 24-FEB-09 1LB6 1 VERSN REVDAT 2 01-APR-03 1LB6 1 JRNL REVDAT 1 31-JUL-02 1LB6 0 JRNL AUTH H.YE,J.R.ARRON,B.LAMOTHE,M.CIRILLI,T.KOBAYASHI,N.K.SHEVDE, JRNL AUTH 2 D.SEGAL,O.K.DZIVENU,M.VOLOGODSKAIA,M.YIM,K.DU,S.SINGH, JRNL AUTH 3 J.W.PIKE,B.G.DARNAY,Y.CHOI,H.WU JRNL TITL DISTINCT MOLECULAR MECHANISM FOR INITIATING TRAF6 JRNL TITL 2 SIGNALLING. JRNL REF NATURE V. 418 443 2002 JRNL REFN ISSN 0028-0836 JRNL PMID 12140561 JRNL DOI 10.1038/NATURE00888 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 6.0 REMARK 3 NUMBER OF REFLECTIONS : 15569 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 928 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1340 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.30 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LB6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-02. REMARK 100 THE DEPOSITION ID IS D_1000015806. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15569 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 33.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REPLACE REMARK 200 STARTING MODEL: TRAF6 APO FORM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, TRIS, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, 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 19.93950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.71750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.90750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.71750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.93950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.90750 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: 1150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 502 REMARK 465 PHE A 503 REMARK 465 ASP A 504 REMARK 465 LEU A 505 REMARK 465 GLU A 506 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 GLN A 347 CG CD OE1 NE2 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 SER A 438 -160.83 -79.20 REMARK 500 THR A 475 60.36 -108.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LB4 RELATED DB: PDB REMARK 900 TRAF6 APO STRUCTURE REMARK 900 RELATED ID: 1LB5 RELATED DB: PDB REMARK 900 TRAF6-RANK COMPLEX DBREF 1LB6 A 347 504 UNP Q9Y4K3 TRAF6_HUMAN 347 504 DBREF 1LB6 B 601 609 UNP P25942 TNR5_HUMAN 230 238 SEQADV 1LB6 LEU A 505 UNP Q9Y4K3 CLONING ARTIFACT SEQADV 1LB6 GLU A 506 UNP Q9Y4K3 CLONING ARTIFACT SEQADV 1LB6 ASP B 608 UNP P25942 ASN 237 CONFLICT SEQRES 1 A 160 GLN GLN CYS ASN GLY ILE TYR ILE TRP LYS ILE GLY ASN SEQRES 2 A 160 PHE GLY MET HIS LEU LYS CYS GLN GLU GLU GLU LYS PRO SEQRES 3 A 160 VAL VAL ILE HIS SER PRO GLY PHE TYR THR GLY LYS PRO SEQRES 4 A 160 GLY TYR LYS LEU CYS MET ARG LEU HIS LEU GLN LEU PRO SEQRES 5 A 160 THR ALA GLN ARG CYS ALA ASN TYR ILE SER LEU PHE VAL SEQRES 6 A 160 HIS THR MET GLN GLY GLU TYR ASP SER HIS LEU PRO TRP SEQRES 7 A 160 PRO PHE GLN GLY THR ILE ARG LEU THR ILE LEU ASP GLN SEQRES 8 A 160 SER GLU ALA PRO VAL ARG GLN ASN HIS GLU GLU ILE MET SEQRES 9 A 160 ASP ALA LYS PRO GLU LEU LEU ALA PHE GLN ARG PRO THR SEQRES 10 A 160 ILE PRO ARG ASN PRO LYS GLY PHE GLY TYR VAL THR PHE SEQRES 11 A 160 MET HIS LEU GLU ALA LEU ARG GLN ARG THR PHE ILE LYS SEQRES 12 A 160 ASP ASP THR LEU LEU VAL ARG CYS GLU VAL SER THR ARG SEQRES 13 A 160 PHE ASP LEU GLU SEQRES 1 B 9 LYS GLN GLU PRO GLN GLU ILE ASP PHE FORMUL 3 HOH *122(H2 O) HELIX 1 1 ASN A 359 GLU A 369 1 11 HELIX 2 2 TYR A 418 LEU A 422 5 5 HELIX 3 3 LEU A 456 GLN A 460 5 5 HELIX 4 4 GLU A 480 GLN A 484 5 5 SHEET 1 A 4 GLY A 351 ILE A 357 0 SHEET 2 A 4 LEU A 493 SER A 500 -1 O VAL A 495 N TRP A 355 SHEET 3 A 4 THR A 429 ILE A 434 -1 N THR A 433 O ARG A 496 SHEET 4 A 4 HIS A 446 ASP A 451 -1 O HIS A 446 N ILE A 434 SHEET 1 B 5 GLN B 605 ASP B 608 0 SHEET 2 B 5 LYS A 469 HIS A 478 -1 N GLY A 470 O ILE B 607 SHEET 3 B 5 TYR A 406 MET A 414 -1 N ILE A 407 O MET A 477 SHEET 4 B 5 LYS A 388 LEU A 395 -1 N HIS A 394 O SER A 408 SHEET 5 B 5 VAL A 373 HIS A 376 -1 N ILE A 375 O LEU A 393 SHEET 1 C 5 GLN B 605 ASP B 608 0 SHEET 2 C 5 LYS A 469 HIS A 478 -1 N GLY A 470 O ILE B 607 SHEET 3 C 5 TYR A 406 MET A 414 -1 N ILE A 407 O MET A 477 SHEET 4 C 5 LYS A 388 LEU A 395 -1 N HIS A 394 O SER A 408 SHEET 5 C 5 PHE A 380 TYR A 381 -1 N PHE A 380 O LEU A 389 CISPEP 1 LYS A 384 PRO A 385 0 -0.16 CISPEP 2 TRP A 424 PRO A 425 0 -0.18 CRYST1 39.879 43.815 101.435 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 0.025076 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009859 0.00000