PDB Short entry for 1ZUB HEADER ENDOCYTOSIS/EXOCYTOSIS 30-MAY-05 1ZUB TITLE SOLUTION STRUCTURE OF THE RIM1ALPHA PDZ DOMAIN IN COMPLEX WITH AN TITLE 2 ELKS1B C-TERMINAL PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN; COMPND 5 SYNONYM: RAB3-INTERACTING MOLECULE 1, RIM 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ELKS1B; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: ERC PROTEIN 1, ERC1, CAZ-ASSOCIATED STRUCTURAL PROTEIN 2, COMPND 11 CAST2, RAB6 INTERACTING PROTEIN 2, C-TERMINAL PEPTIDE; COMPND 12 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: RIMS1, RIM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODON+; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-KT; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 13 ORGANISM_COMMON: NORWAY RAT; SOURCE 14 ORGANISM_TAXID: 10116; SOURCE 15 GENE: RAB6IP2, CAST2, ELKS, ERC1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PTMHA KEYWDS PDZ DOMAIN, COMPLEX, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.LU,H.LI,Y.WANG,T.C.SUDHOF,J.RIZO REVDAT 4 02-MAR-22 1ZUB 1 REMARK SEQADV REVDAT 3 24-FEB-09 1ZUB 1 VERSN REVDAT 2 13-SEP-05 1ZUB 1 JRNL REVDAT 1 30-AUG-05 1ZUB 0 JRNL AUTH J.LU,H.LI,Y.WANG,T.C.SUDHOF,J.RIZO JRNL TITL SOLUTION STRUCTURE OF THE RIM1ALPHA PDZ DOMAIN IN COMPLEX JRNL TITL 2 WITH AN ELKS1B C-TERMINAL PEPTIDE JRNL REF J.MOL.BIOL. V. 352 455 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16095618 JRNL DOI 10.1016/J.JMB.2005.07.047 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZUB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033127. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM RIM1ALPHA PDZ DOMAIN U REMARK 210 -15N, 0.75MM ELKS1B C-TERMINAL REMARK 210 PEPTIDE, 20MM MES BUFFER, 90% REMARK 210 H2O, 10% D2O; 0.5MM RIM1ALPHA REMARK 210 PDZ DOMAIN U-15N, 13C, 0.75MM REMARK 210 ELKS1B C-TERMINAL PEPTIDE, 20MM REMARK 210 MES BUFFER, 90% H2O, 10% D2O; REMARK 210 0.5MM RIM1ALPHA PDZ DOMAIN U-15N, REMARK 210 10%-13C, 0.75MM ELKS1B C- REMARK 210 TERMINAL PEPTIDE, 20MM MES REMARK 210 BUFFER, 90% H2O, 10% D2O; 0.5MM REMARK 210 ELKS1B C-TERMINAL PEPTIDE U-15N, REMARK 210 0.75MM RIM1ALPHA PDZ DOMAIN, REMARK 210 20MM MES BUFFER, 90% H2O, 10% REMARK 210 D2O; 0.5MM ELKS1B C-TERMINAL REMARK 210 PEPTIDE U-15N, 13C, 0.75MM REMARK 210 RIM1ALPHA PDZ DOMAIN, 20MM MES REMARK 210 BUFFER, 90% H2O, 10% D2O; 0.5MM REMARK 210 ELKS1B C-TERMINAL PEPTIDE U-15N, REMARK 210 10%-13C, 0.75MM RIM1ALPHA PDZ REMARK 210 DOMAIN, 20MM MES BUFFER, 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 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 5.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: DIMERIC 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. (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 592 REMARK 465 SER A 593 REMARK 465 PRO A 594 REMARK 465 GLY A 595 REMARK 465 SER A 596 REMARK 465 CYS B 938 REMARK 465 ASP B 939 REMARK 465 GLN B 940 REMARK 465 ASP B 941 REMARK 465 GLU B 942 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 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 SER A 604 -175.48 -64.87 REMARK 500 1 THR A 621 31.87 -163.54 REMARK 500 1 GLU A 625 -92.90 -174.16 REMARK 500 1 ALA A 628 -56.61 -169.12 REMARK 500 1 LEU A 629 -89.77 -119.05 REMARK 500 1 LYS A 654 108.21 -54.89 REMARK 500 2 GLU A 625 -80.66 177.76 REMARK 500 2 ALA A 628 -80.50 -97.10 REMARK 500 2 LEU A 629 -95.11 -117.88 REMARK 500 2 LYS A 654 103.94 -57.70 REMARK 500 2 HIS A 663 61.77 72.87 REMARK 500 2 PRO A 679 114.62 -39.45 REMARK 500 3 THR A 620 19.09 57.61 REMARK 500 3 THR A 621 65.26 -157.89 REMARK 500 3 GLU A 625 -82.06 -145.17 REMARK 500 3 SER A 626 -45.43 178.17 REMARK 500 3 LEU A 629 -91.32 -126.55 REMARK 500 3 MET A 639 104.53 -58.54 REMARK 500 3 LYS A 654 103.72 -59.74 REMARK 500 3 HIS A 663 66.89 68.21 REMARK 500 3 GLU B 944 -177.19 -59.83 REMARK 500 4 GLU A 625 -39.94 178.72 REMARK 500 4 ALA A 628 -84.06 -63.40 REMARK 500 4 LEU A 629 -89.58 -117.84 REMARK 500 4 LEU A 630 -59.85 -125.24 REMARK 500 4 LYS A 654 102.83 -57.79 REMARK 500 4 HIS A 663 62.12 71.04 REMARK 500 5 SER A 604 -175.42 -65.38 REMARK 500 5 THR A 621 -169.55 56.86 REMARK 500 5 GLU A 625 151.02 178.03 REMARK 500 5 ALA A 628 -71.55 -174.29 REMARK 500 5 LEU A 629 -85.40 -120.35 REMARK 500 5 LEU A 630 -57.59 -120.60 REMARK 500 5 LYS A 651 148.68 -170.57 REMARK 500 5 LYS A 654 101.99 -56.18 REMARK 500 5 HIS A 663 57.61 70.77 REMARK 500 6 GLU A 606 17.58 -69.75 REMARK 500 6 ASP A 608 74.79 65.67 REMARK 500 6 GLU A 625 -81.47 -143.28 REMARK 500 6 SER A 626 -43.33 -161.77 REMARK 500 6 ALA A 628 -60.99 -154.59 REMARK 500 6 LEU A 629 -91.90 -116.59 REMARK 500 6 LYS A 654 101.00 -57.52 REMARK 500 6 HIS A 663 65.00 70.30 REMARK 500 7 SER A 604 -177.14 -61.01 REMARK 500 7 THR A 621 156.16 57.41 REMARK 500 7 GLU A 625 -79.14 -89.85 REMARK 500 7 SER A 626 -68.35 -163.23 REMARK 500 7 ALA A 628 -86.51 -69.45 REMARK 500 7 LEU A 629 -77.46 -122.83 REMARK 500 REMARK 500 THIS ENTRY HAS 150 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1ZUB A 597 705 UNP Q9JIR4 RIMS1_RAT 597 705 DBREF 1ZUB B 939 948 UNP Q811U3 RB6I2_RAT 939 948 SEQADV 1ZUB GLY A 592 UNP Q9JIR4 CLONING ARTIFACT SEQADV 1ZUB SER A 593 UNP Q9JIR4 CLONING ARTIFACT SEQADV 1ZUB PRO A 594 UNP Q9JIR4 CLONING ARTIFACT SEQADV 1ZUB GLY A 595 UNP Q9JIR4 CLONING ARTIFACT SEQADV 1ZUB SER A 596 UNP Q9JIR4 CLONING ARTIFACT SEQADV 1ZUB CYS B 938 UNP Q811U3 CLONING ARTIFACT SEQRES 1 A 114 GLY SER PRO GLY SER HIS PRO VAL THR TRP GLN PRO SER SEQRES 2 A 114 LYS GLU GLY ASP ARG LEU ILE GLY ARG VAL ILE LEU ASN SEQRES 3 A 114 LYS ARG THR THR MET PRO LYS GLU SER GLY ALA LEU LEU SEQRES 4 A 114 GLY LEU LYS VAL VAL GLY GLY LYS MET THR ASP LEU GLY SEQRES 5 A 114 ARG LEU GLY ALA PHE ILE THR LYS VAL LYS LYS GLY SER SEQRES 6 A 114 LEU ALA ASP VAL VAL GLY HIS LEU ARG ALA GLY ASP GLU SEQRES 7 A 114 VAL LEU GLU TRP ASN GLY LYS PRO LEU PRO GLY ALA THR SEQRES 8 A 114 ASN GLU GLU VAL TYR ASN ILE ILE LEU GLU SER LYS SER SEQRES 9 A 114 GLU PRO GLN VAL GLU ILE ILE VAL SER ARG SEQRES 1 B 11 CYS ASP GLN ASP GLU GLU GLU GLY ILE TRP ALA HELIX 1 1 SER A 656 VAL A 661 1 6 HELIX 2 2 THR A 682 SER A 695 1 14 SHEET 1 A 5 THR A 600 PRO A 603 0 SHEET 2 A 5 LEU A 610 LEU A 616 -1 O ILE A 611 N GLN A 602 SHEET 3 A 5 VAL A 699 VAL A 703 -1 O ILE A 701 N VAL A 614 SHEET 4 A 5 VAL A 670 TRP A 673 -1 N GLU A 672 O ILE A 702 SHEET 5 A 5 LYS A 676 PRO A 677 -1 O LYS A 676 N TRP A 673 SHEET 1 B 2 LEU A 632 GLY A 636 0 SHEET 2 B 2 ALA A 647 VAL A 652 -1 O PHE A 648 N VAL A 635 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