10 20 30 40 50 60 70 80 1SYJ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER CONTRACTILE PROTEIN 01-APR-04 1SYJ
TITLE MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED TITLE 2 AND THE ELECTRON PARAMAGNETIC RESONANCE (EPR) SPIN PROBE TITLE 3 SSL-NANDP BOUND AT THE NUCLEOTIDE SITE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLARET SEGREGATIONAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MOTOR DOMAIN; COMPND 5 SYNONYM: NCD
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY
KEYWDS NCD, MICROTUBULE MOTOR, SWITCH 1, MOLECULAR MODELING, EPR, KEYWDS 2 ELECTRON PARAMAGNETIC RESONANCE, SPIN PROBE, THEORETICAL KEYWDS 3 MODEL
EXPDTA THEORETICAL MODEL
AUTHOR N.NABER,T.J.MINEHARDT,S.RICE,X.CHEN,J.GRAMMER,M.MATUSKA, AUTHOR 2 R.D.VALE,P.A.KOLLMAN,R.CAR,R.G.YOUNT,R.COOKE,E.PATE
REVDAT 2 18-MAY-04 1SYJ 1 SOURCE REVDAT 1 13-APR-04 1SYJ 0
JRNL AUTH N.NABER,T.J.MINEHARDT,S.RICE,X.CHEN,J.GRAMMER, JRNL AUTH 2 M.MATUSKA,R.D.VALE,P.A.KOLLMAN,R.CAR,R.G.YOUNT, JRNL AUTH 3 R.COOKE,E.PATE JRNL TITL CLOSING OF THE NUCLEOTIDE POCKET OF KINESIN-FAMILY JRNL TITL 2 MOTORS UPON BINDING TO MICROTUBULES JRNL REF SCIENCE V. 300 798 2003 JRNL REFN ASTM SCIEAS US ISSN 0036-8075
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.J.MINEHARDT,R.COOKE,E.PATE,P.A.KOLLMAN REMARK 1 TITL MOLECULAR DYNAMICS STUDY OF THE ENERGETIC, REMARK 1 TITL 2 MECHANISTIC, AND STRUCTURAL IMPLICATIONS OF A REMARK 1 TITL 3 CLOSED PHOSPHATE TUBE IN NCD REMARK 1 REF BIOPHYS.J. V. 80 1151 2001 REMARK 1 REFN ASTM BIOJAU US ISSN 0006-3495
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1SYJ COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-2004. REMARK 100 THE RCSB ID CODE IS RCSB022093.
REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THE MODELED NCD*ADP STRUCTURE WITH SWITCH 1 CLOSED REMARK 220 (ADJACENT TO THE DIPHOSPHATE MOIETY, HOMOLOGOUS TO REMARK 220 SWITCH 1 IN THE ORIGINAL MYOSIN STRUCTURES) IS DESCRIBED REMARK 220 IN MINEHARDT ET AL. 2001. BIOPHYS. J. 80: 1151-1168. SSL REMARK 220 -NANDP (RESIDUE NAME SSL) WAS DOCKED USING THE REMARK 220 PREVIOUSLY OBSERVED NUCLEOTIDE SITE BINDING HOMOLOGY REMARK 220 BETWEEN KINESIN-FAMILY MOTORS AND MYOSIN MOTORS. THE REMARK 220 NANDP BACKBONE OF THESE ADP-ANALOG SPIN PROBES CONSISTS REMARK 220 OF A SUBSTITUTED PHENYL RING AND DIPHOSPHATE ARM REMARK 220 CONNECTED BY AN AMINO ETHYL SPACER (NAKAMAYE ET AL. REMARK 220 1985. BIOCHEMISTRY 24: 5226-5235). THE STRUCTURE OF REMARK 220 MYOSIN BOUND TO THE DNPHAEDP*BEFX COMPLEX (GULICK ET AL. REMARK 220 2000. J. BIOL. CHEM. 275: 398-408) (NANDP WITH THE REMARK 220 PHENYL RING P-N3 GROUP SUSTITUTED WITH A P-NO2 GROUP) REMARK 220 WAS SUPERIMPOSED ON THE NCD*ADP STRUCTURE VIA A LEAST- REMARK 220 SQUARES, P-LOOP DISTANCE MINIMIZATION. THE PREVIOUSLY REMARK 220 OBSERVED BINDING SITE HOMOLOGIES BETWEEN NCD*ADP AND REMARK 220 MYOSIN*ADP, AND MYOSIN*ADP AND MYOSIN*DNPHAEDP, WERE REMARK 220 THEN USED TO DOCK THE NANDP BACKBONE OF SSL-NANDP INTO REMARK 220 THE MODELED NCD*ADP STRUCTURE BINDING SITE. THIS DOCKING REMARK 220 RESULTED IN THE SPIN PROBE MOIETY AUTOMATICALLY REMARK 220 PROJECTING OUT OF THE NUCLEOTIDE POCKET INTO THE SOLVENT REMARK 220 PHASE. THE SPIN PROBE NITROXIDE WAS MODELED IN THE REMARK 220 REDUCED STATE. THE STRUCTURE WAS ENERGY MINIMIZED IN A REMARK 220 FULL BOX OF TIP3P WATERS USING THE AMBER 7 SUITE OF REMARK 220 CODES. EPR PROBE MOBILITY RESULTS REPORTED IN THE REMARK 220 PRIMARY REFERENCE WERE FROM MOLECULAR DYNAMICS REMARK 220 SIMULATIONS USING A HYDRATED SPHERE AT THE NUCLEOTIDE REMARK 220 SITE OF THE ENERGY MINIMIZED STRUCTURE.
REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 580 OD1 - CG - OD2 ANGL. DEV. =-14.3 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 LYS A 509 -26.92 135.26 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 423 ASP A 424 148.88 REMARK 500 ASN A 495 GLU A 496 -149.82 REMARK 500 LYS A 509 ASN A 510 130.35 REMARK 500 VAL A 556 THR A 557 146.14 REMARK 500 LEU A 578 VAL A 579 -143.60
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SYP RELATED DB: PDB REMARK 900 MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED REMARK 900 AND THE ELECTRON PARAMAGNETIC RESONANCE (EPR) SPIN PROBE SL REMARK 900 -NANDP BOUND AT THE NUCLEOTIDE SITE REMARK 900 RELATED ID: 1SZ4 RELATED DB: PDB REMARK 900 MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED REMARK 900 AND THE ELECTRON PARAMAGNETIC RESONANCE (EPR) SPIN PROBE 2' REMARK 900 -SLADP BOUND AT THE NUCLEOTIDE SITE REMARK 900 RELATED ID: 1SZ5 RELATED DB: PDB REMARK 900 MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED REMARK 900 AND THE ELECTRON PARAMAGNETIC RESONANCE (EPR) SPIN PROBE 3' REMARK 900 -SLADP BOUND AT THE NUCLEOTIDE SITE REMARK 900 RELATED ID: 1OZX RELATED DB: PDB REMARK 900 MODEL OF THE MICROTUBULE MOTOR, NCD, WITH SWITCH 1 CLOSED REMARK 900 AND WITH ADP BOUND AT THE NUCLEOTIDE SITE
DBREF 1SYJ A 345 667 UNP P20480 NCD_DROME 345 667
SEQRES 1 A 323 LEU ARG GLY ASN ILE ARG VAL PHE CYS ARG ILE ARG PRO SEQRES 2 A 323 PRO LEU GLU SER GLU GLU ASN ARG MET CYS CYS THR TRP SEQRES 3 A 323 THR TYR HIS ASP GLU SER THR VAL GLU LEU GLN SER ILE SEQRES 4 A 323 ASP ALA GLN ALA LYS SER LYS MET GLY GLN GLN ILE PHE SEQRES 5 A 323 SER PHE ASP GLN VAL PHE HIS PRO LEU SER SER GLN SER SEQRES 6 A 323 ASP ILE PHE GLU MET VAL SER PRO LEU ILE GLN SER ALA SEQRES 7 A 323 LEU ASP GLY TYR ASN ILE CYS ILE PHE ALA TYR GLY GLN SEQRES 8 A 323 THR GLY SER GLY LYS THR TYR THR MET ASP GLY VAL PRO SEQRES 9 A 323 GLU SER VAL GLY VAL ILE PRO ARG THR VAL ASP LEU LEU SEQRES 10 A 323 PHE ASP SER ILE ARG GLY TYR ARG ASN LEU GLY TRP GLU SEQRES 11 A 323 TYR GLU ILE LYS ALA THR PHE LEU GLU ILE TYR ASN GLU SEQRES 12 A 323 VAL LEU TYR ASP LEU LEU SER ASN GLU GLN LYS ASP MET SEQRES 13 A 323 GLU ILE ARG MET ALA LYS ASN ASN LYS ASN ASP ILE TYR SEQRES 14 A 323 VAL SER ASN ILE THR GLU GLU THR VAL LEU ASP PRO ASN SEQRES 15 A 323 HIS LEU ARG HIS LEU MET HIS THR ALA LYS MET ASN ARG SEQRES 16 A 323 ALA THR ALA SER THR ALA GLY ASN GLU ARG SER SER ARG SEQRES 17 A 323 SER HIS ALA VAL THR LYS LEU GLU LEU ILE GLY ARG HIS SEQRES 18 A 323 ALA GLU LYS GLN GLU ILE SER VAL GLY SER ILE ASN LEU SEQRES 19 A 323 VAL ASP LEU ALA GLY SER GLU SER PRO LYS THR SER THR SEQRES 20 A 323 ARG MET THR GLU THR LYS ASN ILE ASN ARG SER LEU SER SEQRES 21 A 323 GLU LEU THR ASN VAL ILE LEU ALA LEU LEU GLN LYS GLN SEQRES 22 A 323 ASP HIS ILE PRO TYR ARG ASN SER LYS LEU THR HIS LEU SEQRES 23 A 323 LEU MET PRO SER LEU GLY GLY ASN SER LYS THR LEU MET SEQRES 24 A 323 PHE ILE ASN VAL SER PRO PHE GLN ASP CYS PHE GLN GLU SEQRES 25 A 323 SER VAL LYS SER LEU ARG PHE ALA ALA SER VAL
HET MG 669 1 HET NA 670 1 HET NA 671 1 HET NA 672 1 HET NA 673 1 HET NA 674 1 HET SSL 668 66
HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM SSL (3-{[2-(DIHYDROXYAMINO)-4-(2LAMBDA~5~-TRIAZA-1,2- HETNAM 2 SSL DIENYL)PHENYL]AMINO}-9-HYDROXY-8,8,10,10-TETRAMETHYL- HETNAM 3 SSL 1,5-DIOXA-9-AZASPIRO[5.5]UNDEC-3-YL)METHYL HETNAM 4 SSL TRIHYDROGEN DIPHOSPHATE
FORMUL 2 MG MG 2+ FORMUL 3 NA 5(NA 1+) FORMUL 8 SSL C19 H30 N6 O12 P2 FORMUL 9 HOH *1232(H2 O1)
HELIX 1 1 LEU A 359 GLU A 363 5 5 HELIX 2 2 ASP A 384 LYS A 388 5 5 HELIX 3 3 SER A 407 MET A 414 1 8 HELIX 4 4 SER A 416 GLY A 425 1 10 HELIX 5 5 LYS A 440 MET A 444 5 5 HELIX 6 6 GLY A 452 ARG A 469 1 18 HELIX 7 7 ASP A 524 ASN A 538 1 15 HELIX 8 8 ASN A 600 LYS A 616 1 17 HELIX 9 9 LYS A 626 MET A 632 1 7 HELIX 10 10 PRO A 633 LEU A 635 5 3 HELIX 11 11 CYS A 653 PHE A 663 1 11
SHEET 1 A 8 VAL A 401 PHE A 402 0 SHEET 2 A 8 ILE A 349 ARG A 354 1 N CYS A 353 O PHE A 402 SHEET 3 A 8 THR A 641 ILE A 645 1 O ILE A 645 N PHE A 352 SHEET 4 A 8 ASN A 427 TYR A 433 1 N PHE A 431 O LEU A 642 SHEET 5 A 8 ILE A 571 VAL A 579 1 O SER A 575 N ILE A 428 SHEET 6 A 8 HIS A 554 ARG A 564 -1 N LEU A 559 O ILE A 576 SHEET 7 A 8 GLU A 474 ILE A 484 -1 N ILE A 484 O HIS A 554 SHEET 8 A 8 LEU A 489 ASP A 491 -1 O TYR A 490 N GLU A 483 SHEET 1 B 3 THR A 369 TYR A 372 0 SHEET 2 B 3 THR A 377 GLN A 381 -1 O GLN A 381 N THR A 369 SHEET 3 B 3 PHE A 396 SER A 397 -1 O PHE A 396 N VAL A 378 SHEET 1 C 2 ILE A 502 MET A 504 0 SHEET 2 C 2 ILE A 512 VAL A 514 -1 O TYR A 513 N ARG A 503 SHEET 1 D 2 THR A 589 ARG A 592 0 SHEET 2 D 2 GLU A 595 ASN A 598 -1 O LYS A 597 N SER A 590
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