PDB Short entry for 2MJ2 HEADER VIRAL PROTEIN 23-DEC-13 2MJ2 TITLE STRUCTURE OF THE DIMERIZATION DOMAIN OF THE HUMAN POLYOMA, JC VIRUS TITLE 2 AGNOPROTEIN IS AN AMPHIPATHIC ALPHA-HELIX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGNOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 17-52; COMPND 5 SYNONYM: AGNO; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: JC POLYOMAVIRUS; SOURCE 4 ORGANISM_COMMON: JCPYV; SOURCE 5 ORGANISM_TAXID: 10632 KEYWDS AGNOPROTEIN, POLYOMAVIRUS JCV, DNA REPLICATION, PROGRESSIVE KEYWDS 2 MULTIFOCAL LEUKOENCEPHALOPATHY, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR P.CORIC,S.A.SARIBAS,M.ABOU-GHARBIA,W.CHILDERS,M.WHITE,S.BOUAZIZ, AUTHOR 2 M.SAFAK REVDAT 2 14-JUN-23 2MJ2 1 REMARK REVDAT 1 23-APR-14 2MJ2 0 JRNL AUTH P.CORIC,S.A.SARIBAS,M.ABOU-GHARBIA,W.CHILDERS,M.WHITE, JRNL AUTH 2 S.BOUAZIZ,M.SAFAK JRNL TITL THE STRUCTURE OF THE DIMERIZATION DOMAIN OF THE HUMAN JRNL TITL 2 POLYOMA, JC VIRUS AGNOPROTEIN IS AN AMPHIPATHIC ALPHA-HELIX JRNL REF J.VIROL. 2014 JRNL REFN ESSN 1098-5514 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.SAMI SARIBAS,M.ABOU-GHARBIA,W.CHILDERS,I.K.SARIYER, REMARK 1 AUTH 2 M.K.WHITE,M.SAFAK REMARK 1 TITL ESSENTIAL ROLES OF LEU/ILE/PHE-RICH DOMAIN OF JC VIRUS REMARK 1 TITL 2 AGNOPROTEIN IN DIMER/OLIGOMER FORMATION, PROTEIN STABILITY REMARK 1 TITL 3 AND SPLICING OF VIRAL TRANSCRIPTS. REMARK 1 REF VIROLOGY V. 443 161 2013 REMARK 1 REFN ISSN 0042-6822 REMARK 1 PMID 23747198 REMARK 1 DOI 10.1016/J.VIROL.2013.05.003 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.S.SARIBAS,B.T.ARACHEA,M.K.WHITE,R.E.VIOLA,M.SAFAK REMARK 1 TITL HUMAN POLYOMAVIRUS JC SMALL REGULATORY AGNOPROTEIN FORMS REMARK 1 TITL 2 HIGHLY STABLE DIMERS AND OLIGOMERS: IMPLICATIONS FOR THEIR REMARK 1 TITL 3 ROLES IN AGNOPROTEIN FUNCTION. REMARK 1 REF VIROLOGY V. 420 51 2011 REMARK 1 REFN ISSN 0042-6822 REMARK 1 PMID 21920573 REMARK 1 DOI 10.1016/J.VIROL.2011.08.015 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, ARIA 2.3.1 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), LINGE, O'DONOGHUE AND REMARK 3 NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MJ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000103672. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 303; 313 REMARK 210 PH : 3.0; 3.0; 3.0 REMARK 210 IONIC STRENGTH : NO SALTS; NO SALTS; NO SALTS REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM AGNO, 70 V/V H2O, 30 V/V REMARK 210 [U-100% 2H] TFE, WATER WITH 30% REMARK 210 (V/V) TFE (TRIFLUOROETHANOL, REMARK 210 CF3CH2OH) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.2.2, ARIA REMARK 210 2.3.1 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 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: 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 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 29 -164.57 65.40 REMARK 500 1 VAL A 30 49.09 -140.42 REMARK 500 1 LYS A 33 78.43 65.54 REMARK 500 2 ASP A 28 -6.68 -140.89 REMARK 500 2 VAL A 30 79.67 41.07 REMARK 500 2 LYS A 34 38.28 -90.74 REMARK 500 3 ASP A 28 -66.16 -132.40 REMARK 500 3 VAL A 30 71.71 58.32 REMARK 500 4 ASP A 28 52.07 -168.18 REMARK 500 5 THR A 25 -37.39 172.57 REMARK 500 5 SER A 29 -172.39 63.79 REMARK 500 5 VAL A 30 74.22 32.36 REMARK 500 6 SER A 3 84.10 49.39 REMARK 500 6 ASP A 28 41.73 -146.98 REMARK 500 7 THR A 25 -95.38 -94.18 REMARK 500 7 VAL A 30 68.83 -110.99 REMARK 500 8 SER A 29 -165.44 70.03 REMARK 500 8 ARG A 35 27.12 -142.41 REMARK 500 9 TRP A 2 -54.34 -169.71 REMARK 500 9 SER A 3 71.02 -116.79 REMARK 500 9 THR A 25 -78.42 -116.39 REMARK 500 9 ARG A 35 131.95 178.42 REMARK 500 10 THR A 25 -89.70 -140.66 REMARK 500 10 ASP A 28 -60.61 -137.16 REMARK 500 10 SER A 29 -170.14 162.88 REMARK 500 10 ASP A 31 75.77 60.29 REMARK 500 10 LYS A 33 -54.77 -154.68 REMARK 500 11 SER A 3 101.69 -57.89 REMARK 500 11 LYS A 6 38.18 -97.24 REMARK 500 11 CYS A 24 46.28 -95.10 REMARK 500 12 THR A 5 -76.08 -69.67 REMARK 500 12 CYS A 24 36.86 -95.07 REMARK 500 12 ASP A 28 -51.07 -121.76 REMARK 500 12 ASP A 31 -29.12 79.18 REMARK 500 12 LYS A 34 -55.01 -124.65 REMARK 500 13 SER A 3 48.92 -109.88 REMARK 500 13 CYS A 24 41.04 -91.08 REMARK 500 13 VAL A 30 59.01 -113.70 REMARK 500 13 ARG A 35 74.59 58.75 REMARK 500 14 SER A 29 -161.05 -124.70 REMARK 500 14 VAL A 30 97.72 67.63 REMARK 500 14 LYS A 33 97.33 71.90 REMARK 500 15 THR A 5 -64.97 -105.65 REMARK 500 15 SER A 29 -160.21 66.18 REMARK 500 15 ASP A 31 -60.95 -94.87 REMARK 500 16 THR A 25 -61.25 -101.88 REMARK 500 16 SER A 29 177.99 69.57 REMARK 500 16 LYS A 34 50.32 -98.38 REMARK 500 17 TRP A 2 55.83 -145.48 REMARK 500 17 SER A 3 21.36 -147.40 REMARK 500 REMARK 500 THIS ENTRY HAS 52 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19702 RELATED DB: BMRB DBREF 2MJ2 A 1 36 UNP P03086 AGNO_POVJC 17 52 SEQRES 1 A 36 THR TRP SER GLY THR LYS LYS ARG ALA GLN ARG ILE LEU SEQRES 2 A 36 ILE PHE LEU LEU GLU PHE LEU LEU ASP PHE CYS THR GLY SEQRES 3 A 36 GLU ASP SER VAL ASP GLY LYS LYS ARG GLN HELIX 1 1 LYS A 6 CYS A 24 1 19 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