HEADER VIRUS LIKE PARTICLE 01-DEC-20 7B3Y TITLE STRUCTURE OF A NANOPARTICLE FOR A COVID-19 VACCINE CANDIDATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRONECTIN BINDING PROTEIN,2-DEHYDRO-3- COMPND 3 DEOXYPHOSPHOGLUCONATE ALDOLASE/4-HYDROXY-2-OXOGLUTARATE ALDOLASE; COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: MODEL JUST CONTAINS MI3 CAGE COMPONENT OF VLP. NOTE COMPND 7 THAT THE SPY AND RBD (SPY TAG AND RBD ARE OMITTED FROM THE SEQUENCE) COMPND 8 ARE ARE NOT INCLUDED IN THE MODEL. THE SPYCATCHER003-MI3 CAN BE FOUND COMPND 9 ON GENBANK WITH CODE MT945417 AND THAT OF THE SPYTAG-RBD AT COMPND 10 MT945427.,MODEL JUST CONTAINS MI3 CAGE COMPONENT OF VLP. NOTE THAT COMPND 11 THE SPY AND RBD (SPY TAG AND RBD ARE OMITTED FROM THE SEQUENCE) ARE COMPND 12 ARE NOT INCLUDED IN THE MODEL. THE SPYCATCHER003-MI3 CAN BE FOUND ON COMPND 13 GENBANK WITH CODE MT945417 AND THAT OF THE SPYTAG-RBD AT MT945427. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES SEROTYPE M49 (STRAIN SOURCE 3 NZ131), THERMOTOGA MARITIMA (STRAIN ATCC 43589 / MSB8 / DSM 3109 / SOURCE 4 JCM 10099); SOURCE 5 ORGANISM_TAXID: 471876, 243274; SOURCE 6 STRAIN: NZ131, ATCC 43589 / MSB8 / DSM 3109 / JCM 10099; SOURCE 7 GENE: PRTF, SPY49_0119, TM_0066; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, SPYTAG, VLP, RECEPTOR-BINDING DOMAIN, VACCINE, COVID-19, KEYWDS 2 SPYCATCHER, NANOCAGE, ICOSAHEDRAL, NANOPARTICLE, CORONAVIRUS, MI3, KEYWDS 3 VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR H.M.E.DUYVESTEYN,D.I.STUART REVDAT 2 03-FEB-21 7B3Y 1 JRNL REVDAT 1 13-JAN-21 7B3Y 0 JRNL AUTH T.K.TAN,P.RIJAL,R.RAHIKAINEN,A.H.KEEBLE,L.SCHIMANSKI, JRNL AUTH 2 S.HUSSAIN,R.HARVEY,J.W.P.HAYES,J.C.EDWARDS,R.K.MCLEAN, JRNL AUTH 3 V.MARTINI,M.PEDRERA,N.THAKUR,C.CONCEICAO,I.DIETRICH, JRNL AUTH 4 H.SHELTON,A.LUDI,G.WILSDEN,C.BROWNING,A.K.ZAGRAJEK,D.BIALY, JRNL AUTH 5 S.BHAT,P.STEVENSON-LEGGETT,P.HOLLINGHURST,M.TULLY,K.MOFFAT, JRNL AUTH 6 C.CHIU,R.WATERS,A.GRAY,M.AZHAR,V.MIOULET,J.NEWMAN,A.S.ASFOR, JRNL AUTH 7 A.BURMAN,S.CROSSLEY,J.A.HAMMOND,E.TCHILIAN,B.CHARLESTON, JRNL AUTH 8 D.BAILEY,T.J.TUTHILL,S.P.GRAHAM,H.M.E.DUYVESTEYN, JRNL AUTH 9 T.MALINAUSKAS,J.HUO,J.A.TREE,K.R.BUTTIGIEG,R.J.OWENS, JRNL AUTH10 M.W.CARROLL,R.S.DANIELS,J.W.MCCAULEY,D.I.STUART,K.A.HUANG, JRNL AUTH11 M.HOWARTH,A.R.TOWNSEND JRNL TITL A COVID-19 VACCINE CANDIDATE USING SPYCATCHER JRNL TITL 2 MULTIMERIZATION OF THE SARS-COV-2 SPIKE PROTEIN JRNL TITL 3 RECEPTOR-BINDING DOMAIN INDUCES POTENT NEUTRALISING ANTIBODY JRNL TITL 4 RESPONSES. JRNL REF NAT COMMUN V. 12 542 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33483491 JRNL DOI 10.1038/S41467-020-20654-7 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CRYOSPARC, UCSF REMARK 3 CHIMERA, COOT, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 5KP9 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 9.400 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 : 150785 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 7B3Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292112567. 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 : RBD-SPYCATCHER-MI3 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.90 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 7393 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 48.10 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : 165000 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 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: 60-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT2 2 -0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT3 2 0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT1 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT2 4 0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT3 4 0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 5 -0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT2 5 0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT3 5 -0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT1 6 -0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT2 6 0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT3 6 -0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT1 7 -0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 7 -0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT3 7 0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT1 8 0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT2 8 0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT3 8 0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT1 9 -0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT2 9 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT3 9 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 10 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 10 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT1 11 -0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT2 11 -0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT3 11 -0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT1 12 -0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT2 12 -0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 12 0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT1 13 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 13 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 13 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 14 -0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT2 14 0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT3 14 0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT1 15 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 15 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT3 15 0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT1 16 -0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT2 16 0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT3 16 0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT1 17 0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT2 17 0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT3 17 -0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 18 -0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 18 -0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT3 18 -0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT1 19 -0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT2 19 -0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT3 19 -0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT1 20 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT2 20 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 20 -0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT1 21 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 21 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 21 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 22 0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT2 22 0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 22 -0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT1 23 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 23 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 23 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 24 0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT2 24 -0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT3 24 -0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT1 25 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 25 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 25 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 26 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 26 -0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 26 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT1 27 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 27 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 27 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 28 -0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT2 28 -0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 28 -0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT1 29 -0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT2 29 -0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT3 29 0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT1 30 0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT2 30 -0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 30 -0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT1 31 0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT2 31 0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 31 0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT1 32 0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT2 32 0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 32 -0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT1 33 0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT2 33 -0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 33 0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT1 34 0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 34 -0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 34 0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT1 35 -0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT2 35 -0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT3 35 -0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 36 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 36 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 36 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT1 37 0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT2 37 0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT3 37 -0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT1 38 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT2 38 0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT3 38 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 39 0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT2 39 0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT3 39 0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT1 40 0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT2 40 -0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT3 40 -0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT1 41 -0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT2 41 0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT3 41 -0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 42 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT2 42 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT3 42 -0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT1 43 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 43 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 43 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 44 0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT2 44 -0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT3 44 0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 45 0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT2 45 -0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT3 45 -0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 46 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 46 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 46 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 47 0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 47 0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT3 47 -0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT1 48 -0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT2 48 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT3 48 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT1 49 0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT2 49 0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT3 49 -0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT1 50 -0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT2 50 0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT3 50 0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT1 51 0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT2 51 -0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT3 51 0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT1 52 0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT2 52 -0.809017 0.500000 0.309017 0.00000 REMARK 350 BIOMT3 52 0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT1 53 0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT2 53 0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 53 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT1 54 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 54 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 54 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 55 -0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT2 55 0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 55 0.500000 0.309017 0.809017 0.00000 REMARK 350 BIOMT1 56 -0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT2 56 -0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 56 0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT1 57 -0.309017 0.809017 0.500000 0.00000 REMARK 350 BIOMT2 57 -0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT3 57 0.500000 -0.309017 0.809017 0.00000 REMARK 350 BIOMT1 58 -0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 58 0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 58 -0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT1 59 -0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 59 0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 59 0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT1 60 -0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT2 60 -0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 60 -0.500000 0.309017 0.809017 0.00000 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 B -130 REMARK 465 GLY B -129 REMARK 465 SER B -128 REMARK 465 SER B -127 REMARK 465 VAL B -126 REMARK 465 THR B -125 REMARK 465 THR B -124 REMARK 465 LEU B -123 REMARK 465 SER B -122 REMARK 465 GLY B -121 REMARK 465 LEU B -120 REMARK 465 SER B -119 REMARK 465 GLY B -118 REMARK 465 GLU B -117 REMARK 465 GLN B -116 REMARK 465 GLY B -115 REMARK 465 PRO B -114 REMARK 465 SER B -113 REMARK 465 GLY B -112 REMARK 465 ASP B -111 REMARK 465 MET B -110 REMARK 465 THR B -109 REMARK 465 THR B -108 REMARK 465 GLU B -107 REMARK 465 GLU B -106 REMARK 465 ASP B -105 REMARK 465 SER B -104 REMARK 465 ALA B -103 REMARK 465 THR B -102 REMARK 465 HIS B -101 REMARK 465 ILE B -100 REMARK 465 LYS B -99 REMARK 465 PHE B -98 REMARK 465 SER B -97 REMARK 465 LYS B -96 REMARK 465 ARG B -95 REMARK 465 ASP B -94 REMARK 465 GLU B -93 REMARK 465 ASP B -92 REMARK 465 GLY B -91 REMARK 465 ARG B -90 REMARK 465 GLU B -89 REMARK 465 LEU B -88 REMARK 465 ALA B -87 REMARK 465 GLY B -86 REMARK 465 ALA B -85 REMARK 465 THR B -84 REMARK 465 MET B -83 REMARK 465 GLU B -82 REMARK 465 LEU B -81 REMARK 465 ARG B -80 REMARK 465 ASP B -79 REMARK 465 SER B -78 REMARK 465 SER B -77 REMARK 465 GLY B -76 REMARK 465 LYS B -75 REMARK 465 THR B -74 REMARK 465 ILE B -73 REMARK 465 SER B -72 REMARK 465 THR B -71 REMARK 465 TRP B -70 REMARK 465 ILE B -69 REMARK 465 SER B -68 REMARK 465 ASP B -67 REMARK 465 GLY B -66 REMARK 465 HIS B -65 REMARK 465 VAL B -64 REMARK 465 LYS B -63 REMARK 465 ASP B -62 REMARK 465 PHE B -61 REMARK 465 TYR B -60 REMARK 465 LEU B -59 REMARK 465 TYR B -58 REMARK 465 PRO B -57 REMARK 465 GLY B -56 REMARK 465 LYS B -55 REMARK 465 TYR B -54 REMARK 465 THR B -53 REMARK 465 PHE B -52 REMARK 465 VAL B -51 REMARK 465 GLU B -50 REMARK 465 THR B -49 REMARK 465 ALA B -48 REMARK 465 ALA B -47 REMARK 465 PRO B -46 REMARK 465 ASP B -45 REMARK 465 GLY B -44 REMARK 465 TYR B -43 REMARK 465 GLU B -42 REMARK 465 VAL B -41 REMARK 465 ALA B -40 REMARK 465 THR B -39 REMARK 465 PRO B -38 REMARK 465 ILE B -37 REMARK 465 GLU B -36 REMARK 465 PHE B -35 REMARK 465 THR B -34 REMARK 465 VAL B -33 REMARK 465 ASN B -32 REMARK 465 GLU B -31 REMARK 465 ASP B -30 REMARK 465 GLY B -29 REMARK 465 GLN B -28 REMARK 465 VAL B -27 REMARK 465 THR B -26 REMARK 465 VAL B -25 REMARK 465 ASP B -24 REMARK 465 GLY B -23 REMARK 465 GLU B -22 REMARK 465 ALA B -21 REMARK 465 THR B -20 REMARK 465 GLU B -19 REMARK 465 GLY B -18 REMARK 465 ASP B -17 REMARK 465 ALA B -16 REMARK 465 HIS B -15 REMARK 465 THR B -14 REMARK 465 GLY B -13 REMARK 465 GLY B -12 REMARK 465 SER B -11 REMARK 465 GLY B -10 REMARK 465 GLY B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 GLY B -6 REMARK 465 SER B -5 REMARK 465 GLY B -4 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 MET B -1 REMARK 465 THR B 202 REMARK 465 GLU B 203 REMARK 465 GLY B 204 REMARK 465 SER B 205 REMARK 465 GLY B 206 REMARK 465 GLU B 207 REMARK 465 PRO B 208 REMARK 465 GLU B 209 REMARK 465 ALA B 210 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS B 0 CB CG CD CE NZ REMARK 470 MET B 1 CB CG SD CE 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 B 9 -7.27 70.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-11997 RELATED DB: EMDB REMARK 900 STRUCTURE OF A NANOPARTICLE FOR A COVID-19 VACCINE CANDIDATE DBREF1 7B3Y B -127 -15 UNP A0A0H3BX48_STRPZ DBREF2 7B3Y B A0A0H3BX48 866 978 DBREF 7B3Y B -1 203 UNP Q9WXS1 Q9WXS1_THEMA 1 205 SEQADV 7B3Y MET B -130 UNP A0A0H3BX4 INITIATING METHIONINE SEQADV 7B3Y GLY B -129 UNP A0A0H3BX4 EXPRESSION TAG SEQADV 7B3Y SER B -128 UNP A0A0H3BX4 EXPRESSION TAG SEQADV 7B3Y THR B -125 UNP A0A0H3BX4 ASP 868 CONFLICT SEQADV 7B3Y GLY B -118 UNP A0A0H3BX4 SER 875 CONFLICT SEQADV 7B3Y PRO B -114 UNP A0A0H3BX4 GLN 879 CONFLICT SEQADV 7B3Y THR B -108 UNP A0A0H3BX4 ILE 885 CONFLICT SEQADV 7B3Y GLU B -93 UNP A0A0H3BX4 ILE 900 CONFLICT SEQADV 7B3Y ARG B -90 UNP A0A0H3BX4 LYS 903 CONFLICT SEQADV 7B3Y HIS B -65 UNP A0A0H3BX4 GLN 928 CONFLICT SEQADV 7B3Y TYR B -58 UNP A0A0H3BX4 MET 935 CONFLICT SEQADV 7B3Y VAL B -41 UNP A0A0H3BX4 ILE 952 CONFLICT SEQADV 7B3Y PRO B -38 UNP A0A0H3BX4 ALA 955 CONFLICT SEQADV 7B3Y GLU B -36 UNP A0A0H3BX4 THR 957 CONFLICT SEQADV 7B3Y ASP B -30 UNP A0A0H3BX4 GLN 963 CONFLICT SEQADV 7B3Y ASP B -24 UNP A0A0H3BX4 ASN 969 CONFLICT SEQADV 7B3Y GLU B -22 UNP A0A0H3BX4 LYS 971 CONFLICT SEQADV 7B3Y GLU B -19 UNP A0A0H3BX4 LYS 974 CONFLICT SEQADV 7B3Y THR B -14 UNP A0A0H3BX4 LINKER SEQADV 7B3Y GLY B -13 UNP A0A0H3BX4 LINKER SEQADV 7B3Y GLY B -12 UNP A0A0H3BX4 LINKER SEQADV 7B3Y SER B -11 UNP A0A0H3BX4 LINKER SEQADV 7B3Y GLY B -10 UNP A0A0H3BX4 LINKER SEQADV 7B3Y GLY B -9 UNP A0A0H3BX4 LINKER SEQADV 7B3Y SER B -8 UNP A0A0H3BX4 LINKER SEQADV 7B3Y GLY B -7 UNP A0A0H3BX4 LINKER SEQADV 7B3Y GLY B -6 UNP A0A0H3BX4 LINKER SEQADV 7B3Y SER B -5 UNP A0A0H3BX4 LINKER SEQADV 7B3Y GLY B -4 UNP A0A0H3BX4 LINKER SEQADV 7B3Y GLY B -3 UNP A0A0H3BX4 LINKER SEQADV 7B3Y SER B -2 UNP A0A0H3BX4 LINKER SEQADV 7B3Y LYS B 24 UNP Q9WXS1 GLU 26 CONFLICT SEQADV 7B3Y LEU B 31 UNP Q9WXS1 GLU 33 CONFLICT SEQADV 7B3Y MET B 59 UNP Q9WXS1 LYS 61 CONFLICT SEQADV 7B3Y ALA B 74 UNP Q9WXS1 CYS 76 CONFLICT SEQADV 7B3Y ALA B 98 UNP Q9WXS1 CYS 100 CONFLICT SEQADV 7B3Y VAL B 185 UNP Q9WXS1 ASP 187 CONFLICT SEQADV 7B3Y ALA B 188 UNP Q9WXS1 ARG 190 CONFLICT SEQADV 7B3Y GLY B 204 UNP Q9WXS1 EXPRESSION TAG SEQADV 7B3Y SER B 205 UNP Q9WXS1 EXPRESSION TAG SEQADV 7B3Y GLY B 206 UNP Q9WXS1 EXPRESSION TAG SEQADV 7B3Y GLU B 207 UNP Q9WXS1 EXPRESSION TAG SEQADV 7B3Y PRO B 208 UNP Q9WXS1 EXPRESSION TAG SEQADV 7B3Y GLU B 209 UNP Q9WXS1 EXPRESSION TAG SEQADV 7B3Y ALA B 210 UNP Q9WXS1 EXPRESSION TAG SEQRES 1 B 341 MET GLY SER SER VAL THR THR LEU SER GLY LEU SER GLY SEQRES 2 B 341 GLU GLN GLY PRO SER GLY ASP MET THR THR GLU GLU ASP SEQRES 3 B 341 SER ALA THR HIS ILE LYS PHE SER LYS ARG ASP GLU ASP SEQRES 4 B 341 GLY ARG GLU LEU ALA GLY ALA THR MET GLU LEU ARG ASP SEQRES 5 B 341 SER SER GLY LYS THR ILE SER THR TRP ILE SER ASP GLY SEQRES 6 B 341 HIS VAL LYS ASP PHE TYR LEU TYR PRO GLY LYS TYR THR SEQRES 7 B 341 PHE VAL GLU THR ALA ALA PRO ASP GLY TYR GLU VAL ALA SEQRES 8 B 341 THR PRO ILE GLU PHE THR VAL ASN GLU ASP GLY GLN VAL SEQRES 9 B 341 THR VAL ASP GLY GLU ALA THR GLU GLY ASP ALA HIS THR SEQRES 10 B 341 GLY GLY SER GLY GLY SER GLY GLY SER GLY GLY SER MET SEQRES 11 B 341 LYS MET GLU GLU LEU PHE LYS LYS HIS LYS ILE VAL ALA SEQRES 12 B 341 VAL LEU ARG ALA ASN SER VAL GLU GLU ALA LYS LYS LYS SEQRES 13 B 341 ALA LEU ALA VAL PHE LEU GLY GLY VAL HIS LEU ILE GLU SEQRES 14 B 341 ILE THR PHE THR VAL PRO ASP ALA ASP THR VAL ILE LYS SEQRES 15 B 341 GLU LEU SER PHE LEU LYS GLU MET GLY ALA ILE ILE GLY SEQRES 16 B 341 ALA GLY THR VAL THR SER VAL GLU GLN ALA ARG LYS ALA SEQRES 17 B 341 VAL GLU SER GLY ALA GLU PHE ILE VAL SER PRO HIS LEU SEQRES 18 B 341 ASP GLU GLU ILE SER GLN PHE ALA LYS GLU LYS GLY VAL SEQRES 19 B 341 PHE TYR MET PRO GLY VAL MET THR PRO THR GLU LEU VAL SEQRES 20 B 341 LYS ALA MET LYS LEU GLY HIS THR ILE LEU LYS LEU PHE SEQRES 21 B 341 PRO GLY GLU VAL VAL GLY PRO GLN PHE VAL LYS ALA MET SEQRES 22 B 341 LYS GLY PRO PHE PRO ASN VAL LYS PHE VAL PRO THR GLY SEQRES 23 B 341 GLY VAL ASN LEU ASP ASN VAL CYS GLU TRP PHE LYS ALA SEQRES 24 B 341 GLY VAL LEU ALA VAL GLY VAL GLY SER ALA LEU VAL LYS SEQRES 25 B 341 GLY THR PRO VAL GLU VAL ALA GLU LYS ALA LYS ALA PHE SEQRES 26 B 341 VAL GLU LYS ILE ARG GLY CYS THR GLU GLY SER GLY GLU SEQRES 27 B 341 PRO GLU ALA HELIX 1 AA1 LYS B 0 LYS B 9 1 10 HELIX 2 AA2 SER B 18 GLY B 32 1 15 HELIX 3 AA3 ASP B 45 SER B 54 1 10 HELIX 4 AA4 PHE B 55 GLY B 60 5 6 HELIX 5 AA5 SER B 70 SER B 80 1 11 HELIX 6 AA6 ASP B 91 GLY B 102 1 12 HELIX 7 AA7 THR B 111 LEU B 121 1 11 HELIX 8 AA8 PRO B 130 GLY B 135 1 6 HELIX 9 AA9 GLY B 135 GLY B 144 1 10 HELIX 10 AB1 ASN B 161 GLY B 169 1 9 HELIX 11 AB2 GLY B 176 LYS B 181 1 6 HELIX 12 AB3 THR B 183 GLY B 200 1 18 SHEET 1 AA1 4 ILE B 62 GLY B 66 0 SHEET 2 AA1 4 LEU B 36 THR B 40 1 N ILE B 37 O ILE B 62 SHEET 3 AA1 4 ILE B 10 LEU B 14 1 N ALA B 12 O GLU B 38 SHEET 4 AA1 4 VAL B 173 VAL B 175 1 O VAL B 175 N VAL B 11 SHEET 1 AA2 2 PHE B 84 VAL B 86 0 SHEET 2 AA2 2 PHE B 104 MET B 106 1 O MET B 106 N ILE B 85 SHEET 1 AA3 3 GLY B 108 VAL B 109 0 SHEET 2 AA3 3 ILE B 125 LEU B 128 1 O LYS B 127 N VAL B 109 SHEET 3 AA3 3 LYS B 150 PRO B 153 1 O LYS B 150 N LEU B 126 SSBOND 1 CYS B 163 CYS B 201 1555 1555 2.06 CISPEP 1 PHE B 129 PRO B 130 0 1.14 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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