PDB Short entry for 2K3H HEADER PROTEIN TRANSPORT 08-MAY-08 2K3H TITLE STRUCTURAL DETERMINANTS FOR CA2+ AND PIP2 BINDING BY THE C2A DOMAIN OF TITLE 2 RABPHILIN-3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: RABPHILIN-3A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2A DOMAIN (UNP RESIDUES 368-570); COMPND 5 SYNONYM: C2 DOMAIN; COMPND 6 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: RPH3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX2T KEYWDS PIP2, C2 DOMAIN, CALCIUM, TAMA MECHANISM, CELL JUNCTION, METAL- KEYWDS 2 BINDING, PHOSPHOPROTEIN, PROTEIN TRANSPORT, SYNAPSE, TRANSPORT, KEYWDS 3 ZINC, ZINC-FINGER EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.COUDEVYLLE,P.MONTAVILLE,A.LEONOV,M.ZWECKSTETTER,S.BECKER REVDAT 5 16-MAR-22 2K3H 1 REMARK LINK REVDAT 4 09-JUN-09 2K3H 1 REVDAT REVDAT 3 24-FEB-09 2K3H 1 VERSN REVDAT 2 30-DEC-08 2K3H 1 JRNL REVDAT 1 21-OCT-08 2K3H 0 JRNL AUTH N.COUDEVYLLE,P.MONTAVILLE,A.LEONOV,M.ZWECKSTETTER,S.BECKER JRNL TITL STRUCTURAL DETERMINANTS FOR CA2+ AND PHOSPHATIDYLINOSITOL JRNL TITL 2 4,5-BISPHOSPHATE BINDING BY THE C2A DOMAIN OF RABPHILIN-3A. JRNL REF J.BIOL.CHEM. V. 283 35918 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18945677 JRNL DOI 10.1074/JBC.M804094200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CARA, X-PLOR NIH REMARK 3 AUTHORS : ROCHUS KELLER (CARA), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K3H COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000100628. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] C2A DOMAIN, REMARK 210 20 MM NA ACETATE, 150 MM NACL, REMARK 210 20 MM CACL2, 1 MM DTT, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLU A 371 REMARK 465 ALA A 372 REMARK 465 ASN A 373 REMARK 465 SER A 374 REMARK 465 TYR A 375 REMARK 465 ASP A 376 REMARK 465 SER A 377 REMARK 465 ASP A 378 REMARK 465 GLU A 379 REMARK 465 ALA A 380 REMARK 465 THR A 381 REMARK 465 THR A 382 REMARK 465 LEU A 383 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H SER A 389 O THR A 402 1.46 REMARK 500 O LYS A 477 H GLY A 479 1.47 REMARK 500 O SER A 389 H THR A 402 1.49 REMARK 500 O ASP A 413 H GLY A 416 1.53 REMARK 500 O LEU A 491 H LEU A 494 1.55 REMARK 500 OE1 GLU A 387 HE ARG A 405 1.56 REMARK 500 REMARK 500 REMARK: NULL 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 ILE A 404 -71.25 -77.07 REMARK 500 1 PRO A 411 143.82 -30.05 REMARK 500 1 MET A 412 -68.33 -128.76 REMARK 500 1 ALA A 418 143.76 -171.42 REMARK 500 1 SER A 431 -4.73 -53.43 REMARK 500 1 SER A 433 19.28 -155.57 REMARK 500 1 ASN A 434 25.31 -73.53 REMARK 500 1 ASN A 443 80.16 35.31 REMARK 500 1 ARG A 445 -11.22 -147.17 REMARK 500 1 ASN A 446 60.61 -155.60 REMARK 500 1 ASP A 476 -134.89 -119.98 REMARK 500 1 PHE A 478 51.44 -65.45 REMARK 500 2 ILE A 404 -71.65 -77.85 REMARK 500 2 PRO A 411 149.11 -32.29 REMARK 500 2 MET A 412 -67.04 -128.63 REMARK 500 2 ALA A 418 142.48 -170.32 REMARK 500 2 SER A 431 -7.32 -50.92 REMARK 500 2 SER A 433 18.61 -156.82 REMARK 500 2 ASN A 434 24.36 -73.35 REMARK 500 2 ASN A 443 80.36 36.07 REMARK 500 2 ARG A 445 -12.90 -148.96 REMARK 500 2 ASN A 446 71.10 -153.52 REMARK 500 2 ARG A 465 -34.12 -146.51 REMARK 500 2 ASP A 476 -133.52 -122.71 REMARK 500 2 PHE A 478 52.06 -65.36 REMARK 500 2 ILE A 484 -70.07 -84.59 REMARK 500 2 ARG A 508 115.67 -160.67 REMARK 500 2 VAL A 509 126.41 -172.61 REMARK 500 3 ILE A 404 -71.89 -78.72 REMARK 500 3 PRO A 411 136.28 -26.04 REMARK 500 3 MET A 412 -75.52 -117.83 REMARK 500 3 SER A 414 -19.01 -49.65 REMARK 500 3 LEU A 417 -169.70 -113.76 REMARK 500 3 SER A 431 -0.41 -56.52 REMARK 500 3 SER A 433 22.27 -158.57 REMARK 500 3 ASN A 434 30.77 -72.56 REMARK 500 3 ASN A 443 81.23 37.83 REMARK 500 3 ARG A 445 -10.33 -149.50 REMARK 500 3 ASN A 446 69.30 -156.45 REMARK 500 3 GLN A 464 33.67 -96.47 REMARK 500 3 ARG A 465 -32.29 -154.38 REMARK 500 3 ASP A 476 -134.08 -128.11 REMARK 500 3 PHE A 478 51.56 -65.97 REMARK 500 3 VAL A 509 125.83 -172.57 REMARK 500 4 ILE A 404 -71.97 -79.62 REMARK 500 4 PRO A 411 136.56 -26.05 REMARK 500 4 MET A 412 -76.05 -118.54 REMARK 500 4 LEU A 417 -169.17 -110.15 REMARK 500 4 SER A 431 -7.40 -51.56 REMARK 500 4 SER A 433 19.32 -155.38 REMARK 500 REMARK 500 THIS ENTRY HAS 272 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 413 OD1 REMARK 620 2 ASP A 413 OD2 45.2 REMARK 620 3 ASP A 419 N 148.4 111.9 REMARK 620 4 ASP A 419 OD1 123.8 83.5 58.5 REMARK 620 5 ASP A 474 OD1 119.1 146.8 65.8 116.8 REMARK 620 6 GLU A 475 O 122.5 131.8 88.9 70.8 81.1 REMARK 620 7 ASP A 476 OD1 53.5 93.2 154.9 128.0 93.3 73.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 2 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 412 O REMARK 620 2 ASP A 413 OD1 87.7 REMARK 620 3 ASP A 474 OD2 124.3 84.2 REMARK 620 4 ASP A 476 OD1 137.7 50.1 57.9 REMARK 620 5 ASP A 476 OD2 143.8 82.9 89.5 47.2 REMARK 620 6 GLU A 482 OE1 61.7 148.9 116.8 160.5 117.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6787 RELATED DB: BMRB DBREF 2K3H A 371 510 UNP P47708 RP3A_MOUSE 368 507 SEQRES 1 A 140 GLU ALA ASN SER TYR ASP SER ASP GLU ALA THR THR LEU SEQRES 2 A 140 GLY ALA LEU GLU PHE SER LEU LEU TYR ASP GLN ASP ASN SEQRES 3 A 140 SER ASN LEU GLN CYS THR ILE ILE ARG ALA LYS GLY LEU SEQRES 4 A 140 LYS PRO MET ASP SER ASN GLY LEU ALA ASP PRO TYR VAL SEQRES 5 A 140 LYS LEU HIS LEU LEU PRO GLY ALA SER LYS SER ASN LYS SEQRES 6 A 140 LEU ARG THR LYS THR LEU ARG ASN THR ARG ASN PRO VAL SEQRES 7 A 140 TRP ASN GLU THR LEU GLN TYR HIS GLY ILE THR GLU GLU SEQRES 8 A 140 ASP MET GLN ARG LYS THR LEU ARG ILE SER VAL CYS ASP SEQRES 9 A 140 GLU ASP LYS PHE GLY HIS ASN GLU PHE ILE GLY GLU THR SEQRES 10 A 140 ARG PHE SER LEU LYS LYS LEU LYS ALA ASN GLN ARG LYS SEQRES 11 A 140 ASN PHE ASN ILE CYS LEU GLU ARG VAL ILE HET CA A 1 1 HET CA A 2 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 THR A 459 GLN A 464 1 6 HELIX 2 2 LYS A 492 LEU A 494 5 3 SHEET 1 A 4 VAL A 448 HIS A 456 0 SHEET 2 A 4 ASN A 398 LYS A 407 -1 N CYS A 401 O LEU A 453 SHEET 3 A 4 ALA A 385 ASP A 393 -1 N SER A 389 O THR A 402 SHEET 4 A 4 GLN A 498 CYS A 505 -1 O PHE A 502 N PHE A 388 SHEET 1 B 4 LYS A 435 THR A 440 0 SHEET 2 B 4 PRO A 420 LEU A 427 -1 N VAL A 422 O THR A 438 SHEET 3 B 4 THR A 467 GLU A 475 -1 O SER A 471 N LYS A 423 SHEET 4 B 4 ASN A 481 SER A 490 -1 O GLY A 485 N VAL A 472 LINK CA CA A 1 OD1 ASP A 413 1555 1555 2.80 LINK CA CA A 1 OD2 ASP A 413 1555 1555 2.80 LINK CA CA A 1 N ASP A 419 1555 1555 2.91 LINK CA CA A 1 OD1 ASP A 419 1555 1555 2.80 LINK CA CA A 1 OD1 ASP A 474 1555 1555 2.80 LINK CA CA A 1 O GLU A 475 1555 1555 2.80 LINK CA CA A 1 OD1 ASP A 476 1555 1555 2.41 LINK CA CA A 2 O MET A 412 1555 1555 2.76 LINK CA CA A 2 OD1 ASP A 413 1555 1555 2.80 LINK CA CA A 2 OD2 ASP A 474 1555 1555 2.80 LINK CA CA A 2 OD1 ASP A 476 1555 1555 2.80 LINK CA CA A 2 OD2 ASP A 476 1555 1555 2.55 LINK CA CA A 2 OE1 GLU A 482 1555 1555 2.80 CISPEP 1 LEU A 427 PRO A 428 1 -0.99 CISPEP 2 LEU A 427 PRO A 428 2 -0.99 CISPEP 3 LEU A 427 PRO A 428 3 -1.04 CISPEP 4 LEU A 427 PRO A 428 4 -1.06 CISPEP 5 LEU A 427 PRO A 428 5 -1.05 CISPEP 6 LEU A 427 PRO A 428 6 -1.18 CISPEP 7 LEU A 427 PRO A 428 7 -1.32 CISPEP 8 LEU A 427 PRO A 428 8 -0.94 CISPEP 9 LEU A 427 PRO A 428 9 -0.75 CISPEP 10 LEU A 427 PRO A 428 10 -1.09 CISPEP 11 LEU A 427 PRO A 428 11 -0.96 CISPEP 12 LEU A 427 PRO A 428 12 -1.11 CISPEP 13 LEU A 427 PRO A 428 13 -0.85 CISPEP 14 LEU A 427 PRO A 428 14 -1.00 CISPEP 15 LEU A 427 PRO A 428 15 -1.04 CISPEP 16 LEU A 427 PRO A 428 16 -0.53 CISPEP 17 LEU A 427 PRO A 428 17 -0.55 CISPEP 18 LEU A 427 PRO A 428 18 -1.45 CISPEP 19 LEU A 427 PRO A 428 19 -0.85 CISPEP 20 LEU A 427 PRO A 428 20 -0.88 SITE 1 AC1 5 MET A 412 ASP A 413 ALA A 418 ASP A 419 SITE 2 AC1 5 ASP A 476 SITE 1 AC2 4 PRO A 411 MET A 412 ASP A 474 ASP A 476 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