HEADER DE NOVO PROTEIN 05-JAN-20 6VFH TITLE DE NOVO DESIGNED TETRAHEDRAL NANOPARTICLE T33_DN10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: T33_DN10A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: T33_DN10B; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DE NOVO, NANOPARTICLE, DE NOVO PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.ANTANASIJEVIC,A.B.WARD REVDAT 3 06-MAR-24 6VFH 1 REMARK REVDAT 2 19-AUG-20 6VFH 1 JRNL REVDAT 1 12-AUG-20 6VFH 0 JRNL AUTH G.UEDA,A.ANTANASIJEVIC,J.A.FALLAS,W.SHEFFLER,J.COPPS, JRNL AUTH 2 D.ELLIS,G.B.HUTCHINSON,A.MOYER,A.YASMEEN,Y.TSYBOVSKY, JRNL AUTH 3 Y.J.PARK,M.J.BICK,B.SANKARAN,R.A.GILLESPIE,P.J.BROUWER, JRNL AUTH 4 P.H.ZWART,D.VEESLER,M.KANEKIYO,B.S.GRAHAM,R.W.SANDERS, JRNL AUTH 5 J.P.MOORE,P.J.KLASSE,A.B.WARD,N.P.KING,D.BAKER JRNL TITL TAILORED DESIGN OF PROTEIN NANOPARTICLE SCAFFOLDS FOR JRNL TITL 2 MULTIVALENT PRESENTATION OF VIRAL GLYCOPROTEIN ANTIGENS. JRNL REF ELIFE V. 9 2020 JRNL REFN ESSN 2050-084X JRNL PMID 32748788 JRNL DOI 10.7554/ELIFE.57659 REMARK 2 REMARK 2 RESOLUTION. 3.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, LEGINON, RELION, UCSF REMARK 3 CHIMERA, RELION, RELION, RELION, RELION, REMARK 3 ROSETTA REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : TETRAHEDRAL NANOPARTICLE T33_DN10 MODEL WAS REMARK 3 DOCKED INTO THE RECONSTRUCTED MAP USING UCSF CHIMERA. THE MODEL REMARK 3 WAS THEN RELAXED USING A COMBINATION OF ROSETTA RELAXED REMARK 3 REFINEMENT AND MANUAL REFINEMENT IN COOT. 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) : 3.860 REMARK 3 NUMBER OF PARTICLES : 49961 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6VFH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246113. 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 : DE NOVO DESIGNED TETRAHEDRAL REMARK 245 NANOPARTICLE T33_DN10 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 4.20 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : 0.06MM DDM DETERGENT (FROM AN REMARK 245 8X STOCK) ADDED IMMEDIATELY REMARK 245 BEFORE FREEZING REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : SELF-ASSEMBLING NANOPARTICLE REMARK 245 WITH TETRAHEDRAL SYMMETRY REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 502 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) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5040.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 29000 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 TETRAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = T). 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, 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 -1.000000 0.000000 0.000000 308.99999 REMARK 350 BIOMT2 2 0.000000 0.333334 -0.942809 247.69291 REMARK 350 BIOMT3 2 0.000000 -0.942809 -0.333334 350.29076 REMARK 350 BIOMT1 3 0.000000 -0.577350 -0.816497 369.00839 REMARK 350 BIOMT2 3 -0.577350 -0.666667 0.471405 274.35411 REMARK 350 BIOMT3 3 -0.816497 0.471405 -0.333333 257.94347 REMARK 350 BIOMT1 4 0.000000 0.577350 0.816497 -60.00840 REMARK 350 BIOMT2 4 0.577350 -0.666667 0.471404 95.95292 REMARK 350 BIOMT3 4 0.816497 0.471404 -0.333333 5.64604 REMARK 350 BIOMT1 5 0.500000 -0.288675 0.816497 -3.45746 REMARK 350 BIOMT2 5 -0.866025 -0.166667 0.471405 241.70441 REMARK 350 BIOMT3 5 0.000000 -0.942809 -0.333333 350.29077 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 365.55092 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 97.94909 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 -0.500000 0.288675 -0.816497 312.45745 REMARK 350 BIOMT2 7 -0.288675 0.833333 0.471405 -1.99618 REMARK 350 BIOMT3 7 0.816497 0.471405 -0.333333 5.64602 REMARK 350 BIOMT1 8 0.500000 0.866025 0.000000 -56.55093 REMARK 350 BIOMT2 8 0.288675 -0.166667 -0.942809 280.34263 REMARK 350 BIOMT3 8 -0.816497 0.471405 -0.333333 257.94348 REMARK 350 BIOMT1 9 0.500000 -0.866025 0.000000 211.05093 REMARK 350 BIOMT2 9 -0.288675 -0.166667 -0.942809 369.54326 REMARK 350 BIOMT3 9 0.816497 0.471405 -0.333333 5.64606 REMARK 350 BIOMT1 10 -0.500000 -0.288675 0.816497 151.04252 REMARK 350 BIOMT2 10 0.288675 0.833333 0.471405 -91.19681 REMARK 350 BIOMT3 10 -0.816497 0.471405 -0.333333 257.94344 REMARK 350 BIOMT1 11 0.500000 0.288675 -0.816497 157.95747 REMARK 350 BIOMT2 11 0.866025 -0.166667 0.471405 -25.89743 REMARK 350 BIOMT3 11 0.000000 -0.942809 -0.333333 350.29073 REMARK 350 BIOMT1 12 -0.500000 0.866025 0.000000 97.94906 REMARK 350 BIOMT2 12 -0.866025 -0.500000 0.000000 365.55092 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 0.00004 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 GLY A 0 REMARK 465 MET B 0 REMARK 465 ARG B 278 REMARK 465 THR B 279 REMARK 465 LEU B 280 REMARK 465 GLU B 281 REMARK 465 HIS B 282 REMARK 465 HIS B 283 REMARK 465 HIS B 284 REMARK 465 HIS B 285 REMARK 465 HIS B 286 REMARK 465 HIS B 287 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 45 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 211 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES 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 ASN B 91 -119.45 58.04 REMARK 500 THR B 93 1.88 59.96 REMARK 500 SER B 218 67.96 -162.38 REMARK 500 GLU B 250 -55.02 68.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-21172 RELATED DB: EMDB REMARK 900 DE NOVO DESIGNED TETRAHEDRAL NANOPARTICLE T33_DN10 DBREF 6VFH A -1 119 PDB 6VFH 6VFH -1 119 DBREF 6VFH B 0 287 PDB 6VFH 6VFH 0 287 SEQRES 1 A 121 MET GLY GLU GLU ALA GLU LEU ALA TYR LEU LEU GLY GLU SEQRES 2 A 121 LEU ALA TYR LYS LEU GLY GLU TYR ARG ILE ALA ILE ARG SEQRES 3 A 121 ALA TYR ARG ILE ALA LEU LYS ARG ASP PRO ASN ASN ALA SEQRES 4 A 121 GLU ALA TRP TYR ASN LEU GLY ASN ALA TYR TYR LYS GLN SEQRES 5 A 121 GLY ASP TYR ASP GLU ALA ILE GLU TYR TYR GLN LYS ALA SEQRES 6 A 121 LEU GLU LEU ASP PRO ASN ASN ALA GLU ALA TRP TYR ASN SEQRES 7 A 121 LEU GLY ASN ALA TYR TYR LYS GLN GLY ASP TYR ASP GLU SEQRES 8 A 121 ALA ILE GLU TYR TYR GLU LYS ALA LEU GLU LEU ASP PRO SEQRES 9 A 121 GLU ASN LEU GLU ALA LEU GLN ASN LEU LEU ASN ALA MET SEQRES 10 A 121 ASP LYS GLN GLY SEQRES 1 B 288 MET ILE GLU GLU VAL VAL ALA GLU MET ILE ASP ILE LEU SEQRES 2 B 288 ALA GLU SER SER LYS LYS SER ILE GLU GLU LEU ALA ARG SEQRES 3 B 288 ALA ALA ASP ASN LYS THR THR GLU LYS ALA VAL ALA GLU SEQRES 4 B 288 ALA ILE GLU GLU ILE ALA ARG LEU ALA THR ALA ALA ILE SEQRES 5 B 288 GLN LEU ILE GLU ALA LEU ALA LYS ASN LEU ALA SER GLU SEQRES 6 B 288 GLU PHE MET ALA ARG ALA ILE SER ALA ILE ALA GLU LEU SEQRES 7 B 288 ALA LYS LYS ALA ILE GLU ALA ILE TYR ARG LEU ALA ASP SEQRES 8 B 288 ASN HIS THR THR ASP THR PHE MET ALA ARG ALA ILE ALA SEQRES 9 B 288 ALA ILE ALA ASN LEU ALA VAL THR ALA ILE LEU ALA ILE SEQRES 10 B 288 ALA ALA LEU ALA SER ASN HIS THR THR GLU GLU PHE MET SEQRES 11 B 288 ALA ARG ALA ILE SER ALA ILE ALA GLU LEU ALA LYS LYS SEQRES 12 B 288 ALA ILE GLU ALA ILE TYR ARG LEU ALA ASP ASN HIS THR SEQRES 13 B 288 THR ASP LYS PHE MET ALA ALA ALA ILE GLU ALA ILE ALA SEQRES 14 B 288 LEU LEU ALA THR LEU ALA ILE LEU ALA ILE ALA LEU LEU SEQRES 15 B 288 ALA SER ASN HIS THR THR GLU LYS PHE MET ALA ARG ALA SEQRES 16 B 288 ILE MET ALA ILE ALA ILE LEU ALA ALA LYS ALA ILE GLU SEQRES 17 B 288 ALA ILE TYR ARG LEU ALA ASP ASN HIS THR SER PRO THR SEQRES 18 B 288 TYR ILE GLU LYS ALA ILE GLU ALA ILE GLU LYS ILE ALA SEQRES 19 B 288 ARG LYS ALA ILE LYS ALA ILE GLU MET LEU ALA LYS ASN SEQRES 20 B 288 ILE THR THR GLU GLU TYR LYS GLU LYS ALA LYS LYS ILE SEQRES 21 B 288 ILE ASP ILE ILE ARG LYS LEU ALA LYS MET ALA ILE LYS SEQRES 22 B 288 LYS LEU GLU ASP ASN ARG THR LEU GLU HIS HIS HIS HIS SEQRES 23 B 288 HIS HIS HELIX 1 AA1 GLU A 1 LEU A 16 1 16 HELIX 2 AA2 GLU A 18 ASP A 33 1 16 HELIX 3 AA3 ASN A 36 GLN A 50 1 15 HELIX 4 AA4 ASP A 52 ASP A 67 1 16 HELIX 5 AA5 ASN A 70 GLN A 84 1 15 HELIX 6 AA6 ASP A 86 ASP A 101 1 16 HELIX 7 AA7 ASN A 104 GLN A 118 1 15 HELIX 8 AA8 GLU B 2 ASN B 29 1 28 HELIX 9 AA9 THR B 32 LYS B 59 1 28 HELIX 10 AB1 SER B 63 ALA B 89 1 27 HELIX 11 AB2 ASN B 91 ASP B 95 5 5 HELIX 12 AB3 PHE B 97 SER B 121 1 25 HELIX 13 AB4 THR B 125 ASP B 152 1 28 HELIX 14 AB5 PHE B 159 SER B 183 1 25 HELIX 15 AB6 THR B 187 ASP B 214 1 28 HELIX 16 AB7 SER B 218 LYS B 245 1 28 HELIX 17 AB8 GLU B 250 ASN B 277 1 28 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