HEADER VIRUS LIKE PARTICLE 20-JUL-18 6AB5 TITLE CRYO-EM STRUCTURE OF T=1 PENAEUS VANNAMEI NODAVIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PENAEUS VANNAMEI NODAVIRUS; SOURCE 3 ORGANISM_TAXID: 430911; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NODAVIRIDAE, SHRIMP NODAVIRUS, VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR N.C.CHEN,N.MIYAZAKI,M.YOSHIMURA,H.H.GUAN,C.C.LIN,K.IWASAKI,C.J.CHEN REVDAT 3 27-MAR-24 6AB5 1 REMARK REVDAT 2 06-NOV-19 6AB5 1 CRYST1 SCALE REVDAT 1 20-MAR-19 6AB5 0 JRNL AUTH N.C.CHEN,M.YOSHIMURA,N.MIYAZAKI,H.H.GUAN,P.CHUANKHAYAN, JRNL AUTH 2 C.C.LIN,S.K.CHEN,P.J.LIN,Y.C.HUANG,K.IWASAKI,A.NAKAGAWA, JRNL AUTH 3 S.I.CHAN,C.J.CHEN JRNL TITL THE ATOMIC STRUCTURES OF SHRIMP NODAVIRUSES REVEAL NEW JRNL TITL 2 DIMERIC SPIKE STRUCTURES AND PARTICLE POLYMORPHISM. JRNL REF COMMUN BIOL V. 2 72 2019 JRNL REFN ESSN 2399-3642 JRNL PMID 30820467 JRNL DOI 10.1038/S42003-019-0311-Z REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, RELION, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.700 REMARK 3 NUMBER OF PARTICLES : 70543 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6AB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008343. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : PENAEUS VANNAMEI NODAVIRUS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 6.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2806 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1250.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2750.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 0.01 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 59000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 ICOSAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = I). 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 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 350 BIOMT1 2 0.500000 -0.809017 0.309017 -0.54710 REMARK 350 BIOMT2 2 0.809017 0.309017 -0.500000 0.91143 REMARK 350 BIOMT3 2 0.309017 0.500000 0.809017 0.33813 REMARK 350 BIOMT1 3 -0.309017 -0.500000 0.809017 -1.45353 REMARK 350 BIOMT2 3 0.500000 -0.809017 -0.309017 0.58140 REMARK 350 BIOMT3 3 0.809017 0.309017 0.500000 0.89833 REMARK 350 BIOMT1 4 -0.309017 0.500000 0.809017 -1.46663 REMARK 350 BIOMT2 4 -0.500000 -0.809017 0.309017 -0.53400 REMARK 350 BIOMT3 4 0.809017 -0.309017 0.500000 0.90643 REMARK 350 BIOMT1 5 0.500000 0.809017 0.309017 -0.56830 REMARK 350 BIOMT2 5 -0.809017 0.309017 0.500000 -0.89332 REMARK 350 BIOMT3 5 0.309017 -0.500000 0.809017 0.35123 REMARK 350 BIOMT1 6 0.309017 0.500000 0.809017 -0.77938 REMARK 350 BIOMT2 6 0.500000 -0.809017 0.309017 0.57800 REMARK 350 BIOMT3 6 0.809017 0.309017 -0.500000 0.90384 REMARK 350 BIOMT1 7 0.809017 0.309017 0.500000 -0.21918 REMARK 350 BIOMT2 7 -0.309017 -0.500000 0.809017 -0.32843 REMARK 350 BIOMT3 7 0.500000 -0.809017 -0.309017 0.57381 REMARK 350 BIOMT1 8 0.809017 -0.309017 0.500000 -0.21108 REMARK 350 BIOMT2 8 -0.309017 0.500000 0.809017 -0.34153 REMARK 350 BIOMT3 8 -0.500000 -0.809017 0.309017 -0.54159 REMARK 350 BIOMT1 9 0.309017 -0.500000 0.809017 -0.76627 REMARK 350 BIOMT2 9 0.500000 0.809017 0.309017 0.55680 REMARK 350 BIOMT3 9 -0.809017 0.309017 0.500000 -0.90092 REMARK 350 BIOMT1 10 0.000000 0.000000 1.000000 -1.11750 REMARK 350 BIOMT2 10 1.000000 0.000000 0.000000 1.12510 REMARK 350 BIOMT3 10 0.000000 1.000000 0.000000 -0.00759 REMARK 350 BIOMT1 11 -0.809017 0.309017 -0.500000 -2.01291 REMARK 350 BIOMT2 11 0.309017 -0.500000 -0.809017 0.36774 REMARK 350 BIOMT3 11 -0.500000 -0.809017 0.309017 -0.54159 REMARK 350 BIOMT1 12 -0.309017 0.500000 -0.809017 -1.45772 REMARK 350 BIOMT2 12 -0.500000 -0.809017 -0.309017 -0.53059 REMARK 350 BIOMT3 12 -0.809017 0.309017 0.500000 -0.90092 REMARK 350 BIOMT1 13 0.000000 0.000000 -1.000000 -1.10649 REMARK 350 BIOMT2 13 -1.000000 0.000000 0.000000 -1.09889 REMARK 350 BIOMT3 13 0.000000 1.000000 0.000000 -0.00759 REMARK 350 BIOMT1 14 -0.309017 -0.500000 -0.809017 -1.44461 REMARK 350 BIOMT2 14 -0.500000 0.809017 -0.309017 -0.55179 REMARK 350 BIOMT3 14 0.809017 0.309017 -0.500000 0.90384 REMARK 350 BIOMT1 15 -0.809017 -0.309017 -0.500000 -2.00482 REMARK 350 BIOMT2 15 0.309017 0.500000 -0.809017 0.35463 REMARK 350 BIOMT3 15 0.500000 -0.809017 -0.309017 0.57381 REMARK 350 BIOMT1 16 -0.500000 -0.809017 -0.309017 -1.65569 REMARK 350 BIOMT2 16 -0.809017 0.309017 0.500000 -0.89332 REMARK 350 BIOMT3 16 -0.309017 0.500000 -0.809017 -0.34021 REMARK 350 BIOMT1 17 -1.000000 0.000000 0.000000 -2.22399 REMARK 350 BIOMT2 17 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 17 0.000000 0.000000 -1.000000 0.01102 REMARK 350 BIOMT1 18 -0.500000 0.809017 -0.309017 -1.67689 REMARK 350 BIOMT2 18 0.809017 0.309017 -0.500000 0.91143 REMARK 350 BIOMT3 18 -0.309017 -0.500000 -0.809017 -0.32711 REMARK 350 BIOMT1 19 0.309017 0.500000 -0.809017 -0.77047 REMARK 350 BIOMT2 19 0.500000 -0.809017 -0.309017 0.58140 REMARK 350 BIOMT3 19 -0.809017 -0.309017 -0.500000 -0.88731 REMARK 350 BIOMT1 20 0.309017 -0.500000 -0.809017 -0.75736 REMARK 350 BIOMT2 20 -0.500000 -0.809017 0.309017 -0.53400 REMARK 350 BIOMT3 20 -0.809017 0.309017 -0.500000 -0.89541 REMARK 350 BIOMT1 21 -0.500000 -0.809017 0.309017 -1.65909 REMARK 350 BIOMT2 21 0.809017 -0.309017 0.500000 0.91402 REMARK 350 BIOMT3 21 -0.309017 0.500000 0.809017 -0.34912 REMARK 350 BIOMT1 22 -0.809017 0.309017 0.500000 -2.01842 REMARK 350 BIOMT2 22 0.309017 -0.500000 0.809017 0.35882 REMARK 350 BIOMT3 22 0.500000 0.809017 0.309017 0.54920 REMARK 350 BIOMT1 23 0.000000 1.000000 0.000000 -1.12510 REMARK 350 BIOMT2 23 0.000000 0.000000 1.000000 0.00759 REMARK 350 BIOMT3 23 1.000000 0.000000 0.000000 1.11750 REMARK 350 BIOMT1 24 0.809017 0.309017 -0.500000 -0.21367 REMARK 350 BIOMT2 24 0.309017 0.500000 0.809017 0.34572 REMARK 350 BIOMT3 24 0.500000 -0.809017 0.309017 0.57040 REMARK 350 BIOMT1 25 0.500000 -0.809017 -0.309017 -0.54370 REMARK 350 BIOMT2 25 0.809017 0.309017 0.500000 0.90592 REMARK 350 BIOMT3 25 -0.309017 -0.500000 0.809017 -0.33602 REMARK 350 BIOMT1 26 -0.309017 0.500000 -0.809017 -1.45772 REMARK 350 BIOMT2 26 0.500000 0.809017 0.309017 0.55680 REMARK 350 BIOMT3 26 0.809017 -0.309017 -0.500000 0.91193 REMARK 350 BIOMT1 27 0.000000 0.000000 -1.000000 -1.10649 REMARK 350 BIOMT2 27 1.000000 0.000000 0.000000 1.12510 REMARK 350 BIOMT3 27 0.000000 -1.000000 0.000000 0.01861 REMARK 350 BIOMT1 28 -0.309017 -0.500000 -0.809017 -1.44461 REMARK 350 BIOMT2 28 0.500000 -0.809017 0.309017 0.57800 REMARK 350 BIOMT3 28 -0.809017 -0.309017 0.500000 -0.89282 REMARK 350 BIOMT1 29 -0.809017 -0.309017 -0.500000 -2.00482 REMARK 350 BIOMT2 29 -0.309017 -0.500000 0.809017 -0.32843 REMARK 350 BIOMT3 29 -0.500000 0.809017 0.309017 -0.56279 REMARK 350 BIOMT1 30 -0.809017 0.309017 -0.500000 -2.01291 REMARK 350 BIOMT2 30 -0.309017 0.500000 0.809017 -0.34153 REMARK 350 BIOMT3 30 0.500000 0.809017 -0.309017 0.55261 REMARK 350 BIOMT1 31 0.000000 0.000000 1.000000 -1.11750 REMARK 350 BIOMT2 31 -1.000000 0.000000 0.000000 -1.09889 REMARK 350 BIOMT3 31 0.000000 -1.000000 0.000000 0.01861 REMARK 350 BIOMT1 32 0.309017 0.500000 0.809017 -0.77938 REMARK 350 BIOMT2 32 -0.500000 0.809017 -0.309017 -0.55179 REMARK 350 BIOMT3 32 -0.809017 -0.309017 0.500000 -0.89282 REMARK 350 BIOMT1 33 0.809017 0.309017 0.500000 -0.21918 REMARK 350 BIOMT2 33 0.309017 0.500000 -0.809017 0.35463 REMARK 350 BIOMT3 33 -0.500000 0.809017 0.309017 -0.56279 REMARK 350 BIOMT1 34 0.809017 -0.309017 0.500000 -0.21108 REMARK 350 BIOMT2 34 0.309017 -0.500000 -0.809017 0.36774 REMARK 350 BIOMT3 34 0.500000 0.809017 -0.309017 0.55261 REMARK 350 BIOMT1 35 0.309017 -0.500000 0.809017 -0.76627 REMARK 350 BIOMT2 35 -0.500000 -0.809017 -0.309017 -0.53059 REMARK 350 BIOMT3 35 0.809017 -0.309017 -0.500000 0.91193 REMARK 350 BIOMT1 36 0.809017 0.309017 -0.500000 -0.21367 REMARK 350 BIOMT2 36 -0.309017 -0.500000 -0.809017 -0.31952 REMARK 350 BIOMT3 36 -0.500000 0.809017 -0.309017 -0.55939 REMARK 350 BIOMT1 37 0.500000 -0.809017 -0.309017 -0.54370 REMARK 350 BIOMT2 37 -0.809017 -0.309017 -0.500000 -0.87972 REMARK 350 BIOMT3 37 0.309017 0.500000 -0.809017 0.34704 REMARK 350 BIOMT1 38 -0.500000 -0.809017 0.309017 -1.65909 REMARK 350 BIOMT2 38 -0.809017 0.309017 -0.500000 -0.88782 REMARK 350 BIOMT3 38 0.309017 -0.500000 -0.809017 0.36014 REMARK 350 BIOMT1 39 -0.809017 0.309017 0.500000 -2.01842 REMARK 350 BIOMT2 39 -0.309017 0.500000 -0.809017 -0.33262 REMARK 350 BIOMT3 39 -0.500000 -0.809017 -0.309017 -0.53819 REMARK 350 BIOMT1 40 0.000000 1.000000 0.000000 -1.12510 REMARK 350 BIOMT2 40 0.000000 0.000000 -1.000000 0.01861 REMARK 350 BIOMT3 40 -1.000000 0.000000 0.000000 -1.10649 REMARK 350 BIOMT1 41 -0.500000 0.809017 -0.309017 -1.67689 REMARK 350 BIOMT2 41 -0.809017 -0.309017 0.500000 -0.88523 REMARK 350 BIOMT3 41 0.309017 0.500000 0.809017 0.33813 REMARK 350 BIOMT1 42 0.309017 0.500000 -0.809017 -0.77047 REMARK 350 BIOMT2 42 -0.500000 0.809017 0.309017 -0.55520 REMARK 350 BIOMT3 42 0.809017 0.309017 0.500000 0.89833 REMARK 350 BIOMT1 43 0.309017 -0.500000 -0.809017 -0.75736 REMARK 350 BIOMT2 43 0.500000 0.809017 -0.309017 0.56020 REMARK 350 BIOMT3 43 0.809017 -0.309017 0.500000 0.90643 REMARK 350 BIOMT1 44 -0.500000 -0.809017 -0.309017 -1.65569 REMARK 350 BIOMT2 44 0.809017 -0.309017 -0.500000 0.91953 REMARK 350 BIOMT3 44 0.309017 -0.500000 0.809017 0.35123 REMARK 350 BIOMT1 45 -1.000000 0.000000 0.000000 -2.22399 REMARK 350 BIOMT2 45 0.000000 -1.000000 0.000000 0.02621 REMARK 350 BIOMT3 45 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 46 0.000000 -1.000000 0.000000 -1.09889 REMARK 350 BIOMT2 46 0.000000 0.000000 -1.000000 0.01861 REMARK 350 BIOMT3 46 1.000000 0.000000 0.000000 1.11750 REMARK 350 BIOMT1 47 -0.809017 -0.309017 0.500000 -2.01032 REMARK 350 BIOMT2 47 -0.309017 -0.500000 -0.809017 -0.31952 REMARK 350 BIOMT3 47 0.500000 -0.809017 0.309017 0.57040 REMARK 350 BIOMT1 48 -0.500000 0.809017 0.309017 -1.68030 REMARK 350 BIOMT2 48 -0.809017 -0.309017 -0.500000 -0.87972 REMARK 350 BIOMT3 48 -0.309017 -0.500000 0.809017 -0.33602 REMARK 350 BIOMT1 49 0.500000 0.809017 -0.309017 -0.56490 REMARK 350 BIOMT2 49 -0.809017 0.309017 -0.500000 -0.88782 REMARK 350 BIOMT3 49 -0.309017 0.500000 0.809017 -0.34912 REMARK 350 BIOMT1 50 0.809017 -0.309017 -0.500000 -0.20557 REMARK 350 BIOMT2 50 -0.309017 0.500000 -0.809017 -0.33262 REMARK 350 BIOMT3 50 0.500000 0.809017 0.309017 0.54920 REMARK 350 BIOMT1 51 0.809017 -0.309017 -0.500000 -0.20557 REMARK 350 BIOMT2 51 0.309017 -0.500000 0.809017 0.35882 REMARK 350 BIOMT3 51 -0.500000 -0.809017 -0.309017 -0.53819 REMARK 350 BIOMT1 52 0.000000 -1.000000 0.000000 -1.09889 REMARK 350 BIOMT2 52 0.000000 0.000000 1.000000 0.00759 REMARK 350 BIOMT3 52 -1.000000 0.000000 0.000000 -1.10649 REMARK 350 BIOMT1 53 -0.809017 -0.309017 0.500000 -2.01032 REMARK 350 BIOMT2 53 0.309017 0.500000 0.809017 0.34572 REMARK 350 BIOMT3 53 -0.500000 0.809017 -0.309017 -0.55939 REMARK 350 BIOMT1 54 -0.500000 0.809017 0.309017 -1.68030 REMARK 350 BIOMT2 54 0.809017 0.309017 0.500000 0.90592 REMARK 350 BIOMT3 54 0.309017 0.500000 -0.809017 0.34704 REMARK 350 BIOMT1 55 0.500000 0.809017 -0.309017 -0.56490 REMARK 350 BIOMT2 55 0.809017 -0.309017 0.500000 0.91402 REMARK 350 BIOMT3 55 0.309017 -0.500000 -0.809017 0.36014 REMARK 350 BIOMT1 56 -0.309017 0.500000 0.809017 -1.46663 REMARK 350 BIOMT2 56 0.500000 0.809017 -0.309017 0.56020 REMARK 350 BIOMT3 56 -0.809017 0.309017 -0.500000 -0.89541 REMARK 350 BIOMT1 57 0.500000 0.809017 0.309017 -0.56830 REMARK 350 BIOMT2 57 0.809017 -0.309017 -0.500000 0.91953 REMARK 350 BIOMT3 57 -0.309017 0.500000 -0.809017 -0.34021 REMARK 350 BIOMT1 58 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 58 0.000000 -1.000000 0.000000 0.02621 REMARK 350 BIOMT3 58 0.000000 0.000000 -1.000000 0.01102 REMARK 350 BIOMT1 59 0.500000 -0.809017 0.309017 -0.54710 REMARK 350 BIOMT2 59 -0.809017 -0.309017 0.500000 -0.88523 REMARK 350 BIOMT3 59 -0.309017 -0.500000 -0.809017 -0.32711 REMARK 350 BIOMT1 60 -0.309017 -0.500000 0.809017 -1.45353 REMARK 350 BIOMT2 60 -0.500000 0.809017 0.309017 -0.55520 REMARK 350 BIOMT3 60 -0.809017 -0.309017 -0.500000 -0.88731 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 ARG A 3 REMARK 465 LYS A 4 REMARK 465 PRO A 5 REMARK 465 ASN A 6 REMARK 465 SER A 7 REMARK 465 ASN A 8 REMARK 465 GLN A 9 REMARK 465 ASN A 10 REMARK 465 ASN A 11 REMARK 465 ASN A 12 REMARK 465 ASN A 13 REMARK 465 ASN A 14 REMARK 465 ARG A 15 REMARK 465 GLY A 16 REMARK 465 ASN A 17 REMARK 465 GLY A 18 REMARK 465 ASN A 19 REMARK 465 GLY A 20 REMARK 465 LEU A 21 REMARK 465 ARG A 22 REMARK 465 ARG A 23 REMARK 465 VAL A 24 REMARK 465 ARG A 25 REMARK 465 GLY A 26 REMARK 465 GLY A 27 REMARK 465 ARG A 28 REMARK 465 VAL A 29 REMARK 465 SER A 30 REMARK 465 ARG A 31 REMARK 465 ARG A 32 REMARK 465 ARG A 33 REMARK 465 VAL A 34 REMARK 465 VAL A 35 REMARK 465 ILE A 36 REMARK 465 ASN A 37 REMARK 465 GLN A 38 REMARK 465 SER A 39 REMARK 465 ASN A 40 REMARK 465 GLN A 41 REMARK 465 SER A 42 REMARK 465 MET A 43 REMARK 465 PRO A 44 REMARK 465 VAL A 45 REMARK 465 THR A 46 REMARK 465 SER A 47 REMARK 465 ASN A 48 REMARK 465 GLY A 49 REMARK 465 ALA A 50 REMARK 465 PRO A 51 REMARK 465 LEU A 52 REMARK 465 GLN A 53 REMARK 465 ALA A 54 REMARK 465 LEU A 55 REMARK 465 THR A 56 REMARK 465 SER A 57 REMARK 465 TYR A 58 REMARK 465 SER A 59 REMARK 465 ARG A 60 REMARK 465 PRO A 61 REMARK 465 ASN A 62 REMARK 465 VAL A 63 REMARK 465 ASN A 64 REMARK 465 LYS A 65 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 NH2 ARG A 188 CB GLN A 192 1.95 REMARK 500 NH2 ARG A 188 CG GLN A 192 2.18 REMARK 500 O PHE A 299 NZ LYS A 355 2.19 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 LYS A 200 -158.71 -88.71 REMARK 500 ASN A 221 -166.70 -119.88 REMARK 500 LEU A 241 111.35 -160.49 REMARK 500 ILE A 246 80.62 60.05 REMARK 500 ASN A 250 81.87 61.70 REMARK 500 PRO A 251 -174.66 -66.14 REMARK 500 GLU A 296 62.28 61.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-6999 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF T=1 PENAEUS VANNAMEI NODAVIRUS REMARK 900 RELATED ID: EMD-9576 RELATED DB: EMDB DBREF 6AB5 A 1 368 UNP A5H7Q8 A5H7Q8_9VIRU 1 368 SEQRES 1 A 368 MET LYS ARG LYS PRO ASN SER ASN GLN ASN ASN ASN ASN SEQRES 2 A 368 ASN ARG GLY ASN GLY ASN GLY LEU ARG ARG VAL ARG GLY SEQRES 3 A 368 GLY ARG VAL SER ARG ARG ARG VAL VAL ILE ASN GLN SER SEQRES 4 A 368 ASN GLN SER MET PRO VAL THR SER ASN GLY ALA PRO LEU SEQRES 5 A 368 GLN ALA LEU THR SER TYR SER ARG PRO ASN VAL ASN LYS SEQRES 6 A 368 ILE SER ARG LEU GLY PRO ASP SER ASP PHE LEU THR SER SEQRES 7 A 368 VAL VAL ALA LYS ALA SER THR SER ILE VAL THR PRO ALA SEQRES 8 A 368 ASP ARG ILE LEU VAL LYS GLN PRO LEU SER ALA SER SER SEQRES 9 A 368 PHE PRO GLY THR ARG ILE THR GLY LEU SER SER TYR TRP SEQRES 10 A 368 GLU ARG TYR LYS TRP LEU SER ALA VAL ALA ARG TYR VAL SEQRES 11 A 368 PRO ALA VAL PRO ASN THR VAL ALA CYS GLN PHE VAL MET SEQRES 12 A 368 TYR ILE ASP THR ASP PRO LEU ASP ASP PRO SER ASN ILE SEQRES 13 A 368 SER ASP ASP ASN GLN ILE VAL ARG GLN ALA VAL SER GLN SEQRES 14 A 368 ALA GLY SER ASN GLN PHE ASN PHE ASN THR SER LYS THR SEQRES 15 A 368 VAL PRO LEU ILE VAL ARG ALA ASP ASN GLN TYR TYR TYR SEQRES 16 A 368 THR GLY VAL ASP LYS GLN ASN LEU ARG PHE SER LEU GLN SEQRES 17 A 368 GLY ILE LEU TYR ILE ILE GLN VAL THR ASP LEU ILE ASN SEQRES 18 A 368 PHE ASN GLY GLU LEU ILE THR GLN ASP LEU THR CYS GLY SEQRES 19 A 368 SER LEU PHE LEU ASP TRP LEU VAL ASN PHE SER ILE PRO SEQRES 20 A 368 GLN ILE ASN PRO THR SER LEU THR ASP VAL ARG VAL ASP SEQRES 21 A 368 LYS ALA VAL ASN PHE ILE LYS PRO GLU VAL SER GLY VAL SEQRES 22 A 368 ALA GLU ILE GLN THR VAL THR GLY LEU SER PRO SER THR SEQRES 23 A 368 SER TYR LEU LEU THR PRO ALA PHE LEU GLU GLN ASN PHE SEQRES 24 A 368 GLN SER GLU ALA GLY ILE TYR ILE LEU SER ALA THR PRO SEQRES 25 A 368 VAL GLU GLY GLU GLY THR ILE SER ILE ASN MET ASP PRO SEQRES 26 A 368 THR VAL THR THR VAL SER GLY PHE ILE LYS VAL LYS THR SEQRES 27 A 368 ASP THR PHE GLY THR PHE ASP LEU SER VAL VAL LEU THR SEQRES 28 A 368 THR ALA SER LYS LYS GLN THR THR GLY PHE ASN ILE ILE SEQRES 29 A 368 ALA ALA THR SER HELIX 1 AA1 THR A 89 ASP A 92 5 4 HELIX 2 AA2 THR A 108 SER A 115 1 8 HELIX 3 AA3 ASP A 152 ILE A 156 5 5 HELIX 4 AA4 ASN A 160 GLN A 169 1 10 HELIX 5 AA5 ASN A 202 SER A 206 5 5 SHEET 1 AA1 4 SER A 67 ALA A 81 0 SHEET 2 AA1 4 LEU A 231 PHE A 244 -1 O LEU A 236 N LEU A 76 SHEET 3 AA1 4 ALA A 127 PRO A 131 -1 N ARG A 128 O PHE A 237 SHEET 4 AA1 4 LYS A 181 VAL A 183 -1 O VAL A 183 N ALA A 127 SHEET 1 AA2 4 ILE A 94 PRO A 99 0 SHEET 2 AA2 4 ILE A 210 GLN A 215 -1 O LEU A 211 N GLN A 98 SHEET 3 AA2 4 GLN A 140 ASP A 146 -1 N VAL A 142 O ILE A 214 SHEET 4 AA2 4 ASN A 173 ASN A 176 -1 O PHE A 175 N PHE A 141 SHEET 1 AA3 2 ARG A 119 TYR A 120 0 SHEET 2 AA3 2 TYR A 194 TYR A 195 -1 O TYR A 194 N TYR A 120 SHEET 1 AA4 8 VAL A 257 ASN A 264 0 SHEET 2 AA4 8 GLY A 360 ALA A 366 -1 O ILE A 363 N ASP A 260 SHEET 3 AA4 8 SER A 287 PRO A 292 -1 N THR A 291 O ASN A 362 SHEET 4 AA4 8 THR A 328 LYS A 337 -1 O ILE A 334 N LEU A 290 SHEET 5 AA4 8 GLU A 316 MET A 323 -1 N GLU A 316 O LYS A 335 SHEET 6 AA4 8 ILE A 307 PRO A 312 -1 N LEU A 308 O ILE A 321 SHEET 7 AA4 8 PHE A 344 LEU A 350 -1 O SER A 347 N THR A 311 SHEET 8 AA4 8 GLU A 275 VAL A 279 -1 N GLU A 275 O VAL A 348 CISPEP 1 GLY A 70 PRO A 71 0 1.03 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