HEADER ENDOCYTOSIS/EXOCYTOSIS,SIGNALING PROTEIN12-DEC-04 1Y8F TITLE SOLUTION STRUCTURE OF THE MUNC13-1 C1-DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNC-13 HOMOLOG A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C1-DOMAIN (RESIDUES 567-616); COMPND 5 SYNONYM: MUNC13-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: MUNC13-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-KG KEYWDS CYSTEINE-RICH DOMAIN, C1-DOMAIN, ZINC-BINDING DOMAIN, KEYWDS 2 ENDOCYTOSIS/EXOCYTOSIS,SIGNALING PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.SHEN,O.GURYEV,J.RIZO REVDAT 2 24-FEB-09 1Y8F 1 VERSN REVDAT 1 12-APR-05 1Y8F 0 JRNL AUTH N.SHEN,O.GURYEV,J.RIZO JRNL TITL INTRAMOLECULAR OCCLUSION OF THE JRNL TITL 2 DIACYLGLYCEROL-BINDING SITE IN THE C1 DOMAIN OF JRNL TITL 3 MUNC13-1. JRNL REF BIOCHEMISTRY V. 44 1089 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15667202 JRNL DOI 10.1021/BI0476127 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 861 RESTRAINTS WERE USED REMARK 3 FOR THE FINAL CALCULATIONS, INCLUDING 781 NOES (OF WHICH 384 REMARK 3 WERE LONG-RANGE NOES), 30 HYDROGEN BOND RESTRAINTS, 50 TORSION REMARK 3 ANGLE RESTRAINTS AND 18 RESTRAINTS FOR THE TWO ZN2+ BINDING REMARK 3 SITES. THE LATTER WERE DERIVED FROM ANALYSIS OF HIGH REMARK 3 RESOLUTION CRYSTAL STRUCTURES CONTAINING BOUND ZN2+ IONS THAT REMARK 3 ARE COORDINATED BY THREE CYSTEINES AND ONE HISTIDINE REMARK 4 REMARK 4 1Y8F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-04. REMARK 100 THE RCSB ID CODE IS RCSB031246. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5MM MUNC13-1 C1-DOMAIN U- REMARK 210 15N, 40MM HEPES (PH 7.0), REMARK 210 150MM NACL, 50UM ZNCL2; 1.5MM REMARK 210 MUNC13-1 C1-DOMAIN U-15N,13C, REMARK 210 40MM HEPES (PH 7.0), 150MM REMARK 210 NACL, 50UM ZNCL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 3D_15N-SEPARATED_ REMARK 210 NOESY, 3D_13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1C, NMRPIPE 2.3, REMARK 210 NMRVIEW 4.1.2, TALOS REMARK 210 2003.027.13.05 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 2000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH LOWEST NOE REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD TRIPLE REMARK 210 RESONANCE TECHNIQUES 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 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 GLY A 554 REMARK 465 SER A 555 REMARK 465 PRO A 556 REMARK 465 GLY A 557 REMARK 465 ILE A 558 REMARK 465 SER A 559 REMARK 465 GLY A 560 REMARK 465 GLY A 561 REMARK 465 GLY A 562 REMARK 465 GLY A 563 REMARK 465 GLY A 564 REMARK 465 ILE A 565 REMARK 465 LYS A 617 REMARK 465 LEU A 618 REMARK 465 ASN A 619 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 LEU A 587 40.74 -95.04 REMARK 500 1 TRP A 588 -165.06 -108.44 REMARK 500 1 ILE A 590 -61.49 -131.42 REMARK 500 1 GLN A 593 158.68 -42.46 REMARK 500 1 THR A 598 30.75 -98.38 REMARK 500 1 GLU A 599 -39.44 -139.51 REMARK 500 1 ASP A 615 39.65 -176.48 REMARK 500 2 LEU A 587 39.51 -94.01 REMARK 500 2 TRP A 588 -168.58 -108.36 REMARK 500 2 ILE A 590 -62.07 -127.23 REMARK 500 2 GLN A 593 152.40 -42.75 REMARK 500 2 THR A 598 31.30 -99.18 REMARK 500 2 GLU A 599 -40.77 -140.37 REMARK 500 2 ASP A 615 41.76 -161.06 REMARK 500 3 LEU A 587 41.94 -93.73 REMARK 500 3 TRP A 588 -165.91 -111.01 REMARK 500 3 ILE A 590 -61.18 -132.58 REMARK 500 3 GLN A 593 156.15 -41.41 REMARK 500 3 GLU A 599 -41.30 -136.42 REMARK 500 3 ASP A 615 39.67 -161.10 REMARK 500 4 LEU A 587 41.09 -94.38 REMARK 500 4 TRP A 588 -166.74 -108.82 REMARK 500 4 ILE A 590 -61.75 -125.07 REMARK 500 4 GLN A 593 157.20 -43.56 REMARK 500 4 THR A 598 31.31 -99.02 REMARK 500 4 GLU A 599 -40.39 -140.05 REMARK 500 4 ASN A 613 -168.04 -61.25 REMARK 500 4 ASP A 615 39.47 -167.39 REMARK 500 5 LEU A 587 38.88 -94.55 REMARK 500 5 ILE A 590 -69.02 68.86 REMARK 500 5 THR A 598 31.41 -98.92 REMARK 500 5 GLU A 599 -41.36 -139.95 REMARK 500 5 ASP A 615 59.62 -170.49 REMARK 500 6 LEU A 587 39.75 -94.62 REMARK 500 6 TRP A 588 -165.69 -109.20 REMARK 500 6 ILE A 590 -61.98 -126.00 REMARK 500 6 GLN A 593 156.66 -43.04 REMARK 500 6 THR A 598 30.35 -98.65 REMARK 500 6 GLU A 599 -40.79 -141.29 REMARK 500 6 ASN A 613 -177.82 -60.72 REMARK 500 6 ASP A 615 39.57 -157.39 REMARK 500 7 ALA A 574 109.43 -59.30 REMARK 500 7 LEU A 587 39.22 -94.03 REMARK 500 7 ILE A 590 -65.76 69.34 REMARK 500 7 GLN A 593 156.43 -37.83 REMARK 500 7 THR A 598 31.03 -99.01 REMARK 500 7 GLU A 599 -40.01 -140.12 REMARK 500 7 ASP A 615 39.84 -171.26 REMARK 500 8 LEU A 587 38.93 -94.02 REMARK 500 8 ILE A 590 -60.46 -139.98 REMARK 500 8 GLU A 599 -40.28 -136.73 REMARK 500 8 ASP A 615 39.85 -177.30 REMARK 500 9 LEU A 587 39.58 -93.34 REMARK 500 9 ILE A 590 -68.58 68.98 REMARK 500 9 GLN A 593 154.29 -44.98 REMARK 500 9 THR A 598 30.56 -97.75 REMARK 500 9 GLU A 599 -40.03 -138.33 REMARK 500 9 ASN A 613 -171.61 -60.86 REMARK 500 9 ASP A 615 39.56 -170.69 REMARK 500 10 LEU A 587 40.00 -93.66 REMARK 500 10 TRP A 588 -166.00 -111.03 REMARK 500 10 ILE A 590 -60.50 -133.85 REMARK 500 10 GLN A 593 153.60 -42.41 REMARK 500 10 THR A 598 30.79 -98.82 REMARK 500 10 GLU A 599 -40.69 -140.78 REMARK 500 10 ASP A 615 38.67 -154.77 REMARK 500 11 LEU A 587 39.12 -94.67 REMARK 500 11 ILE A 590 -69.13 68.31 REMARK 500 11 GLN A 593 159.98 -40.63 REMARK 500 11 THR A 598 30.50 -98.16 REMARK 500 11 GLU A 599 -40.26 -138.32 REMARK 500 11 ASN A 613 -178.14 -67.15 REMARK 500 11 ASP A 615 53.94 -165.41 REMARK 500 12 LEU A 587 38.62 -94.06 REMARK 500 12 ILE A 590 -67.55 69.20 REMARK 500 12 GLN A 593 154.02 -45.23 REMARK 500 12 THR A 598 31.39 -98.83 REMARK 500 12 GLU A 599 -39.72 -139.75 REMARK 500 12 ASP A 615 40.06 -176.04 REMARK 500 13 LEU A 587 39.46 -93.98 REMARK 500 13 ILE A 590 -69.18 68.73 REMARK 500 13 GLN A 593 155.63 -45.00 REMARK 500 13 THR A 598 30.61 -98.46 REMARK 500 13 GLU A 599 -40.37 -139.14 REMARK 500 13 ASP A 615 40.68 -176.64 REMARK 500 14 LEU A 587 38.88 -94.12 REMARK 500 14 TRP A 588 -167.89 -108.65 REMARK 500 14 ILE A 590 -61.69 -129.28 REMARK 500 14 GLN A 593 154.48 -43.14 REMARK 500 14 THR A 598 30.97 -98.49 REMARK 500 14 GLU A 599 -40.01 -139.37 REMARK 500 14 ASN A 613 -174.15 -65.50 REMARK 500 14 ASP A 615 39.57 -176.18 REMARK 500 15 LEU A 587 42.72 -93.48 REMARK 500 15 ILE A 590 -66.91 69.32 REMARK 500 15 GLN A 593 152.60 -45.02 REMARK 500 15 THR A 598 30.52 -97.85 REMARK 500 15 GLU A 599 -40.93 -137.72 REMARK 500 15 ASP A 615 39.51 -176.41 REMARK 500 16 LEU A 587 44.80 -93.03 REMARK 500 16 TRP A 588 -165.45 -113.03 REMARK 500 16 ILE A 590 -61.09 -130.42 REMARK 500 16 GLN A 593 153.36 -41.23 REMARK 500 16 GLU A 599 -42.01 -137.98 REMARK 500 16 ASP A 615 39.80 -176.93 REMARK 500 17 LEU A 587 39.30 -94.11 REMARK 500 17 ILE A 590 -69.31 68.63 REMARK 500 17 GLN A 593 153.38 -45.22 REMARK 500 17 THR A 598 30.85 -98.96 REMARK 500 17 GLU A 599 -40.37 -140.89 REMARK 500 17 ASN A 613 -171.35 -60.50 REMARK 500 17 ASP A 615 39.48 -156.00 REMARK 500 18 LEU A 587 43.03 -94.27 REMARK 500 18 TRP A 588 -165.80 -111.86 REMARK 500 18 ILE A 590 -60.68 -133.77 REMARK 500 18 GLN A 593 155.82 -41.35 REMARK 500 18 THR A 598 30.92 -97.27 REMARK 500 18 GLU A 599 -40.86 -136.95 REMARK 500 18 ASN A 613 -174.26 -62.42 REMARK 500 18 ASP A 615 39.92 -165.45 REMARK 500 19 LEU A 587 39.88 -95.43 REMARK 500 19 TRP A 588 -167.81 -109.23 REMARK 500 19 ILE A 590 -61.14 -129.95 REMARK 500 19 GLN A 593 153.82 -42.99 REMARK 500 19 THR A 598 32.15 -99.61 REMARK 500 19 GLU A 599 -41.20 -139.25 REMARK 500 19 ASP A 615 39.45 -168.98 REMARK 500 20 LEU A 587 39.62 -94.53 REMARK 500 20 ILE A 590 -68.93 68.68 REMARK 500 20 GLN A 593 154.76 -45.62 REMARK 500 20 THR A 598 31.32 -98.38 REMARK 500 20 GLU A 599 -40.76 -139.42 REMARK 500 20 ASP A 615 39.89 -172.38 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 1 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 567 ND1 REMARK 620 2 CYS A 600 SG 100.9 REMARK 620 3 CYS A 597 SG 105.1 120.0 REMARK 620 4 CYS A 616 SG 114.4 104.5 111.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 605 ND1 REMARK 620 2 CYS A 608 SG 126.1 REMARK 620 3 CYS A 583 SG 115.2 99.9 REMARK 620 4 CYS A 580 SG 100.4 103.9 110.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 701 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 702 DBREF 1Y8F A 567 616 UNP Q62768 UN13A_RAT 567 616 SEQADV 1Y8F GLY A 554 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F SER A 555 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F PRO A 556 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F GLY A 557 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F ILE A 558 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F SER A 559 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F GLY A 560 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F GLY A 561 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F GLY A 562 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F GLY A 563 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F GLY A 564 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F ILE A 565 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F GLN A 566 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F LYS A 617 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F LEU A 618 UNP Q62768 CLONING ARTIFACT SEQADV 1Y8F ASN A 619 UNP Q62768 CLONING ARTIFACT SEQRES 1 A 66 GLY SER PRO GLY ILE SER GLY GLY GLY GLY GLY ILE GLN SEQRES 2 A 66 HIS ASN PHE GLU VAL TRP THR ALA THR THR PRO THR TYR SEQRES 3 A 66 CYS TYR GLU CYS GLU GLY LEU LEU TRP GLY ILE ALA ARG SEQRES 4 A 66 GLN GLY MET ARG CYS THR GLU CYS GLY VAL LYS CYS HIS SEQRES 5 A 66 GLU LYS CYS GLN ASP LEU LEU ASN ALA ASP CYS LYS LEU SEQRES 6 A 66 ASN HET ZN A 701 1 HET ZN A 702 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 LYS A 607 LEU A 612 1 6 SHEET 1 A 3 PHE A 569 THR A 573 0 SHEET 2 A 3 GLN A 593 CYS A 597 -1 O ARG A 596 N GLU A 570 SHEET 3 A 3 LYS A 603 CYS A 604 -1 O CYS A 604 N MET A 595 LINK ZN ZN A 701 ND1 HIS A 567 1555 1555 2.30 LINK ZN ZN A 702 ND1 HIS A 605 1555 1555 2.29 LINK ZN ZN A 701 SG CYS A 600 1555 1555 2.36 LINK ZN ZN A 701 SG CYS A 597 1555 1555 2.50 LINK ZN ZN A 701 SG CYS A 616 1555 1555 2.50 LINK ZN ZN A 702 SG CYS A 608 1555 1555 2.31 LINK ZN ZN A 702 SG CYS A 583 1555 1555 2.51 LINK ZN ZN A 702 SG CYS A 580 1555 1555 2.37 SITE 1 AC1 5 HIS A 567 CYS A 597 GLU A 599 CYS A 600 SITE 2 AC1 5 CYS A 616 SITE 1 AC2 4 CYS A 580 CYS A 583 HIS A 605 CYS 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 263 0 2 1 3 0 3 6 0 0 0 6 END