PDB Short entry for 1Y8F 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, ENDOCYTOSIS- KEYWDS 3 EXOCYTOSIS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.SHEN,O.GURYEV,J.RIZO REVDAT 3 02-MAR-22 1Y8F 1 REMARK SEQADV LINK 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 DIACYLGLYCEROL-BINDING SITE JRNL TITL 2 IN THE C1 DOMAIN OF MUNC13-1. JRNL REF BIOCHEMISTRY V. 44 1089 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15667202 JRNL DOI 10.1021/BI0476127 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CNS 0.9 REMARK 3 AUTHORS : VARIAN (VNMR), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 861 RESTRAINTS WERE USED FOR REMARK 3 THE FINAL CALCULATIONS, INCLUDING 781 NOES (OF WHICH 384 WERE REMARK 3 LONG-RANGE NOES), 30 HYDROGEN BOND RESTRAINTS, 50 TORSION ANGLE REMARK 3 RESTRAINTS AND 18 RESTRAINTS FOR THE TWO ZN2+ BINDING SITES. THE REMARK 3 LATTER WERE DERIVED FROM ANALYSIS OF HIGH RESOLUTION CRYSTAL REMARK 3 STRUCTURES CONTAINING BOUND ZN2+ IONS THAT ARE COORDINATED BY REMARK 3 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 DEPOSITION ID IS D_1000031246. 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-15N, REMARK 210 40MM HEPES (PH 7.0), 150MM NACL, REMARK 210 50UM ZNCL2; 1.5MM MUNC13-1 C1- REMARK 210 DOMAIN U-15N,13C, 40MM HEPES (PH REMARK 210 7.0), 150MM NACL, 50UM ZNCL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 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 : NMRPIPE 2.3, NMRVIEW 4.1.2, REMARK 210 TALOS 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 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 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: 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 O MET A 595 H CYS A 604 1.59 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 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 REMARK 500 THIS ENTRY HAS 133 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 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 567 ND1 REMARK 620 2 CYS A 597 SG 105.1 REMARK 620 3 CYS A 600 SG 100.9 120.0 REMARK 620 4 CYS A 616 SG 114.4 111.8 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 580 SG REMARK 620 2 CYS A 583 SG 110.5 REMARK 620 3 HIS A 605 ND1 100.4 115.2 REMARK 620 4 CYS A 608 SG 103.9 99.9 126.1 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 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 ND1 HIS A 567 ZN ZN A 701 1555 1555 2.30 LINK SG CYS A 580 ZN ZN A 702 1555 1555 2.37 LINK SG CYS A 583 ZN ZN A 702 1555 1555 2.51 LINK SG CYS A 597 ZN ZN A 701 1555 1555 2.50 LINK SG CYS A 600 ZN ZN A 701 1555 1555 2.36 LINK ND1 HIS A 605 ZN ZN A 702 1555 1555 2.29 LINK SG CYS A 608 ZN ZN A 702 1555 1555 2.31 LINK SG CYS A 616 ZN ZN A 701 1555 1555 2.50 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