HEADER VIRAL PROTEIN 17-SEP-24 9DND TITLE PSEUDOSYMMETRIC PROTEIN NANOCAGE GI4 -F7 (LOCAL REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOSYMMETRIC PROTEIN NANOCAGES GI4 A CHAIN; COMPND 3 CHAIN: D, A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PSEUDOSYMMETRIC PROTEIN NANOCAGES GI4 C CHAIN; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PSEUDOSYMMETRIC PROTEIN NANOCAGES GI4 B CHAIN; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI #1/H766; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 1354003; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FUSION PROTEIN, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS KEYWDS 2 CENTER FOR INFECTIOUS DISEASE, SSGCID, PSEUDOSYMMETRIC PROTEIN KEYWDS 3 NANOCAGES, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.J.PARK,Q.M.DOWLING,SEATTLE STRUCTURAL GENOMICS CENTER FOR AUTHOR 2 INFECTIOUS DISEASE (SSGCID),N.P.KING,D.VEESLER REVDAT 3 26-FEB-25 9DND 1 JRNL REVDAT 2 01-JAN-25 9DND 1 JRNL REVDAT 1 18-DEC-24 9DND 0 JRNL AUTH Q.M.DOWLING,Y.J.PARK,C.N.FRIES,N.C.GERSTENMAIER,S.OLS, JRNL AUTH 2 E.C.YANG,A.J.WARGACKI,A.DOSEY,Y.HSIA,R.RAVICHANDRAN, JRNL AUTH 3 C.D.WALKEY,A.L.BURRELL,D.VEESLER,D.BAKER,N.P.KING JRNL TITL HIERARCHICAL DESIGN OF PSEUDOSYMMETRIC PROTEIN NANOCAGES. JRNL REF NATURE V. 638 553 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 39695230 JRNL DOI 10.1038/S41586-024-08360-6 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : LEGINON, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 984020 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 9DND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1000284245. 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 : PSEUDOSYMMETRIC PROTEIN REMARK 245 NANOCAGES: GI4-F7 NANOCAGE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, C, 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. (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 GLY D 1 REMARK 465 SER D 2 REMARK 465 HIS D 3 REMARK 465 HIS D 4 REMARK 465 HIS D 5 REMARK 465 HIS D 6 REMARK 465 HIS D 7 REMARK 465 HIS D 8 REMARK 465 GLY D 9 REMARK 465 SER D 10 REMARK 465 GLU D 11 REMARK 465 LYS D 12 REMARK 465 ALA D 13 REMARK 465 ALA D 14 REMARK 465 LYS D 15 REMARK 465 ALA D 16 REMARK 465 GLU D 17 REMARK 465 GLU D 18 REMARK 465 ALA D 19 REMARK 465 THR D 224 REMARK 465 GLU D 225 REMARK 465 MET C 1 REMARK 465 GLU C 205 REMARK 465 GLY C 206 REMARK 465 SER C 207 REMARK 465 LEU C 208 REMARK 465 GLU C 209 REMARK 465 HIS C 210 REMARK 465 HIS C 211 REMARK 465 HIS C 212 REMARK 465 HIS C 213 REMARK 465 HIS C 214 REMARK 465 HIS C 215 REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 GLU A 11 REMARK 465 LYS A 12 REMARK 465 ALA A 13 REMARK 465 ALA A 14 REMARK 465 LYS A 15 REMARK 465 ALA A 16 REMARK 465 GLU A 17 REMARK 465 GLU A 18 REMARK 465 ALA A 19 REMARK 465 THR A 224 REMARK 465 GLU A 225 REMARK 465 MET B 1 REMARK 465 THR B 204 REMARK 465 GLU B 205 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 ARG D 21 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 22 CG CD CE NZ REMARK 470 ASN D 39 CG OD1 ND2 REMARK 470 SER D 40 OG REMARK 470 GLU D 42 CG CD OE1 OE2 REMARK 470 LYS D 46 CG CD CE NZ REMARK 470 THR D 64 OG1 CG2 REMARK 470 ASP D 67 CG OD1 OD2 REMARK 470 ASP D 69 CG OD1 OD2 REMARK 470 THR D 70 OG1 CG2 REMARK 470 SER D 76 OG REMARK 470 GLU D 80 CG CD OE1 OE2 REMARK 470 THR D 91 OG1 CG2 REMARK 470 SER D 92 OG REMARK 470 GLU D 94 CG CD OE1 OE2 REMARK 470 GLU D 98 CG CD OE1 OE2 REMARK 470 GLU D 101 CG CD OE1 OE2 REMARK 470 SER D 102 OG REMARK 470 SER D 109 OG REMARK 470 ASP D 113 CG OD1 OD2 REMARK 470 GLU D 114 CG CD OE1 OE2 REMARK 470 GLU D 115 CG CD OE1 OE2 REMARK 470 GLN D 118 CG CD OE1 NE2 REMARK 470 GLU D 122 CG CD OE1 OE2 REMARK 470 GLU D 123 CG CD OE1 OE2 REMARK 470 LYS D 142 CG CD CE NZ REMARK 470 THR D 146 OG1 CG2 REMARK 470 GLU D 162 CG CD OE1 OE2 REMARK 470 ASN D 170 CG OD1 ND2 REMARK 470 LYS D 172 CG CD CE NZ REMARK 470 THR D 176 OG1 CG2 REMARK 470 ASP D 182 CG OD1 OD2 REMARK 470 GLU D 189 CG CD OE1 OE2 REMARK 470 SER D 199 OG REMARK 470 GLU D 203 CG CD OE1 OE2 REMARK 470 THR D 205 OG1 CG2 REMARK 470 VAL D 207 CG1 CG2 REMARK 470 GLU D 208 CG CD OE1 OE2 REMARK 470 GLU D 211 CG CD OE1 OE2 REMARK 470 GLU D 218 CG CD OE1 OE2 REMARK 470 GLU D 221 CG CD OE1 OE2 REMARK 470 GLU C 4 CG CD OE1 OE2 REMARK 470 GLU C 5 CG CD OE1 OE2 REMARK 470 LYS C 8 CG CD CE NZ REMARK 470 GLU C 9 CG CD OE1 OE2 REMARK 470 ASN C 19 CG OD1 ND2 REMARK 470 SER C 20 OG REMARK 470 GLU C 22 CG CD OE1 OE2 REMARK 470 GLU C 26 CG CD OE1 OE2 REMARK 470 THR C 44 OG1 CG2 REMARK 470 ASP C 47 CG OD1 OD2 REMARK 470 ASP C 49 CG OD1 OD2 REMARK 470 GLU C 50 CG CD OE1 OE2 REMARK 470 ARG C 54 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 56 CG CD OE1 OE2 REMARK 470 THR C 69 OG1 CG2 REMARK 470 SER C 72 OG REMARK 470 GLU C 81 CG CD OE1 OE2 REMARK 470 ASP C 93 CG OD1 OD2 REMARK 470 GLU C 94 CG CD OE1 OE2 REMARK 470 GLU C 95 CG CD OE1 OE2 REMARK 470 GLU C 102 CG CD OE1 OE2 REMARK 470 GLU C 103 CG CD OE1 OE2 REMARK 470 VAL C 105 CG1 CG2 REMARK 470 THR C 126 OG1 CG2 REMARK 470 GLU C 142 CG CD OE1 OE2 REMARK 470 ASN C 150 CG OD1 ND2 REMARK 470 ASN C 160 CG OD1 ND2 REMARK 470 ASP C 162 CG OD1 OD2 REMARK 470 GLU C 166 CG CD OE1 OE2 REMARK 470 GLU C 169 CG CD OE1 OE2 REMARK 470 SER C 179 OG REMARK 470 GLU C 183 CG CD OE1 OE2 REMARK 470 SER C 187 OG REMARK 470 GLU C 188 CG CD OE1 OE2 REMARK 470 GLU C 191 CG CD OE1 OE2 REMARK 470 THR C 204 OG1 CG2 REMARK 470 ARG A 21 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 22 CG CD CE NZ REMARK 470 GLU A 24 CG CD OE1 OE2 REMARK 470 GLU A 25 CG CD OE1 OE2 REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 ASN A 39 CG OD1 ND2 REMARK 470 SER A 40 OG REMARK 470 VAL A 41 CG1 CG2 REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 GLU A 43 CG CD OE1 OE2 REMARK 470 THR A 64 OG1 CG2 REMARK 470 ASP A 67 CG OD1 OD2 REMARK 470 ASP A 69 CG OD1 OD2 REMARK 470 THR A 70 OG1 CG2 REMARK 470 SER A 76 OG REMARK 470 GLU A 80 CG CD OE1 OE2 REMARK 470 THR A 89 OG1 CG2 REMARK 470 THR A 91 OG1 CG2 REMARK 470 SER A 92 OG REMARK 470 GLU A 94 CG CD OE1 OE2 REMARK 470 GLU A 98 CG CD OE1 OE2 REMARK 470 GLU A 101 CG CD OE1 OE2 REMARK 470 SER A 102 OG REMARK 470 ASP A 113 CG OD1 OD2 REMARK 470 GLU A 114 CG CD OE1 OE2 REMARK 470 GLU A 115 CG CD OE1 OE2 REMARK 470 GLN A 118 CG CD OE1 NE2 REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 LYS A 142 CG CD CE NZ REMARK 470 THR A 146 OG1 CG2 REMARK 470 ASN A 170 CG OD1 ND2 REMARK 470 ASP A 182 CG OD1 OD2 REMARK 470 GLU A 189 CG CD OE1 OE2 REMARK 470 SER A 199 OG REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 THR A 205 OG1 CG2 REMARK 470 GLU A 208 CG CD OE1 OE2 REMARK 470 GLU A 211 CG CD OE1 OE2 REMARK 470 GLU A 221 CG CD OE1 OE2 REMARK 470 LYS B 2 CG CD CE NZ REMARK 470 GLU B 5 CG CD OE1 OE2 REMARK 470 LYS B 8 CG CD CE NZ REMARK 470 GLU B 9 CG CD OE1 OE2 REMARK 470 SER B 20 OG REMARK 470 GLU B 22 CG CD OE1 OE2 REMARK 470 GLU B 23 CG CD OE1 OE2 REMARK 470 SER B 26 OG REMARK 470 THR B 44 OG1 CG2 REMARK 470 VAL B 45 CG1 CG2 REMARK 470 ASP B 47 CG OD1 OD2 REMARK 470 ASP B 49 CG OD1 OD2 REMARK 470 GLU B 54 CG CD OE1 OE2 REMARK 470 GLU B 56 CG CD OE1 OE2 REMARK 470 GLU B 60 CG CD OE1 OE2 REMARK 470 SER B 72 OG REMARK 470 GLU B 74 CG CD OE1 OE2 REMARK 470 ASP B 93 CG OD1 OD2 REMARK 470 GLU B 94 CG CD OE1 OE2 REMARK 470 GLU B 95 CG CD OE1 OE2 REMARK 470 GLN B 98 CG CD OE1 NE2 REMARK 470 GLU B 103 CG CD OE1 OE2 REMARK 470 THR B 126 OG1 CG2 REMARK 470 GLU B 142 CG CD OE1 OE2 REMARK 470 THR B 156 OG1 CG2 REMARK 470 ASP B 162 CG OD1 OD2 REMARK 470 GLU B 166 CG CD OE1 OE2 REMARK 470 GLU B 169 CG CD OE1 OE2 REMARK 470 SER B 179 OG REMARK 470 GLU B 183 CG CD OE1 OE2 REMARK 470 GLU B 185 CG CD OE1 OE2 REMARK 470 GLU B 191 CG CD OE1 OE2 REMARK 470 GLU B 198 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO C 90 CD PRO C 90 N -0.118 REMARK 500 REMARK 500 REMARK: NULL 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 LEU D 49 CD1 - CG - CD2 ANGL. DEV. = 21.8 DEGREES REMARK 500 PRO D 66 N - CA - C ANGL. DEV. = 24.8 DEGREES REMARK 500 ASP D 67 N - CA - CB ANGL. DEV. = -14.2 DEGREES REMARK 500 ASP D 67 N - CA - C ANGL. DEV. = -17.3 DEGREES REMARK 500 PRO C 90 C - N - CD ANGL. DEV. = -17.3 DEGREES REMARK 500 PRO C 90 CA - N - CD ANGL. DEV. = 10.0 DEGREES REMARK 500 VAL C 182 CA - CB - CG2 ANGL. DEV. = 17.1 DEGREES REMARK 500 LEU A 53 CD1 - CG - CD2 ANGL. DEV. = 21.6 DEGREES REMARK 500 LEU B 29 CB - CG - CD2 ANGL. DEV. = 17.0 DEGREES REMARK 500 SER B 82 N - CA - CB ANGL. DEV. = 10.3 DEGREES REMARK 500 VAL B 164 CA - CB - CG2 ANGL. DEV. = 17.0 DEGREES REMARK 500 VAL B 177 CA - CB - CG2 ANGL. DEV. = 17.2 DEGREES REMARK 500 VAL B 182 N - CA - C ANGL. DEV. = 24.8 DEGREES REMARK 500 GLU B 183 N - CA - CB ANGL. DEV. = -19.7 DEGREES REMARK 500 GLU B 183 N - CA - C ANGL. DEV. = 22.6 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 PRO D 66 -66.53 -16.36 REMARK 500 THR D 89 51.29 39.28 REMARK 500 VAL D 156 -63.75 -91.57 REMARK 500 PRO D 158 2.64 -68.48 REMARK 500 VAL D 184 -43.43 -13.49 REMARK 500 GLU D 203 148.83 -177.63 REMARK 500 SER C 179 -71.93 62.42 REMARK 500 VAL A 184 -29.84 -39.76 REMARK 500 ASP B 47 -104.09 62.87 REMARK 500 ALA B 48 -57.12 71.60 REMARK 500 SER B 179 -51.93 64.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY C 34 11.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-47036 RELATED DB: EMDB REMARK 900 PSEUDOSYMMETRIC PROTEIN NANOCAGE GI4 -F7 (LOCAL REFINEMENT) DBREF 9DND D 1 225 PDB 9DND 9DND 1 225 DBREF 9DND C 1 215 PDB 9DND 9DND 1 215 DBREF 9DND A 1 225 PDB 9DND 9DND 1 225 DBREF 9DND B 1 205 PDB 9DND 9DND 1 205 SEQRES 1 D 225 GLY SER HIS HIS HIS HIS HIS HIS GLY SER GLU LYS ALA SEQRES 2 D 225 ALA LYS ALA GLU GLU ALA ALA ARG LYS MET GLU GLU LEU SEQRES 3 D 225 PHE LYS GLU HIS LYS ILE VAL ALA VAL LEU ARG ALA ASN SEQRES 4 D 225 SER VAL GLU GLU ALA LYS LYS LYS ALA LEU ALA VAL PHE SEQRES 5 D 225 LEU GLY GLY VAL HIS LEU ILE GLU ILE THR PHE THR VAL SEQRES 6 D 225 PRO ASP ALA ASP THR VAL ILE LYS GLU LEU SER PHE LEU SEQRES 7 D 225 LYS GLU MET GLY ALA ILE ILE GLY ALA GLY THR VAL THR SEQRES 8 D 225 SER VAL GLU GLN CYS ARG GLU ALA VAL GLU SER GLY ALA SEQRES 9 D 225 GLU PHE ILE VAL SER PRO HIS LEU ASP GLU GLU ILE SER SEQRES 10 D 225 GLN PHE CYS LYS GLU GLU GLY VAL PHE TYR MET PRO GLY SEQRES 11 D 225 VAL MET THR PRO THR GLU LEU TYR LYS ALA MET LYS LEU SEQRES 12 D 225 GLY HIS THR ILE LEU LYS LEU PHE PRO GLY GLU VAL VAL SEQRES 13 D 225 GLY PRO GLN PHE VAL GLU ALA MET LYS GLY PRO PHE PRO SEQRES 14 D 225 ASN VAL LYS PHE VAL PRO THR GLY GLY VAL ASN LEU ASP SEQRES 15 D 225 ASN VAL CYS GLU TRP PHE GLU ALA GLY VAL LEU ALA VAL SEQRES 16 D 225 GLY VAL GLY SER ALA LEU VAL GLU GLY THR PRO VAL GLU SEQRES 17 D 225 VAL ALA GLU LYS ALA LYS ALA PHE VAL GLU LYS ILE GLU SEQRES 18 D 225 GLY CYS THR GLU SEQRES 1 C 215 MET LYS MET GLU GLU LEU PHE LYS GLU HIS LYS ILE VAL SEQRES 2 C 215 ALA VAL LEU ARG ALA ASN SER ARG GLU GLU ALA ILE GLU SEQRES 3 C 215 ILE ALA LEU ALA VAL PHE ALA GLY GLY VAL HIS LEU ILE SEQRES 4 C 215 GLU ILE THR PHE THR VAL PRO ASP ALA ASP GLU VAL ILE SEQRES 5 C 215 LYS ARG LEU GLU MET LEU LYS ARG ALA GLY ALA ILE ILE SEQRES 6 C 215 GLY ALA GLY THR VAL THR SER VAL GLU GLN CYS ARG GLU SEQRES 7 C 215 ALA VAL GLU SER GLY ALA GLU PHE ILE VAL SER PRO HIS SEQRES 8 C 215 LEU ASP GLU GLU ILE SER GLN PHE CYS LYS GLU GLU GLY SEQRES 9 C 215 VAL PHE TYR MET PRO GLY VAL MET THR PRO THR GLU LEU SEQRES 10 C 215 VAL LYS ALA MET LYS LEU GLY HIS THR ILE LEU LYS LEU SEQRES 11 C 215 PHE PRO GLY GLU VAL VAL GLY PRO GLN PHE VAL GLU ALA SEQRES 12 C 215 MET LYS GLY PRO PHE PRO ASN VAL LYS PHE VAL PRO THR SEQRES 13 C 215 GLY GLY VAL ASN LEU ASP ASN VAL CYS GLU TRP PHE GLU SEQRES 14 C 215 ALA GLY VAL LEU ALA VAL GLY VAL GLY SER ALA LEU VAL SEQRES 15 C 215 GLU GLY LYS PRO SER GLU VAL ALA GLU LYS ALA ARG ARG SEQRES 16 C 215 PHE VAL LYS LYS ILE ARG GLY CYS THR GLU GLY SER LEU SEQRES 17 C 215 GLU HIS HIS HIS HIS HIS HIS SEQRES 1 A 225 GLY SER HIS HIS HIS HIS HIS HIS GLY SER GLU LYS ALA SEQRES 2 A 225 ALA LYS ALA GLU GLU ALA ALA ARG LYS MET GLU GLU LEU SEQRES 3 A 225 PHE LYS GLU HIS LYS ILE VAL ALA VAL LEU ARG ALA ASN SEQRES 4 A 225 SER VAL GLU GLU ALA LYS LYS LYS ALA LEU ALA VAL PHE SEQRES 5 A 225 LEU GLY GLY VAL HIS LEU ILE GLU ILE THR PHE THR VAL SEQRES 6 A 225 PRO ASP ALA ASP THR VAL ILE LYS GLU LEU SER PHE LEU SEQRES 7 A 225 LYS GLU MET GLY ALA ILE ILE GLY ALA GLY THR VAL THR SEQRES 8 A 225 SER VAL GLU GLN CYS ARG GLU ALA VAL GLU SER GLY ALA SEQRES 9 A 225 GLU PHE ILE VAL SER PRO HIS LEU ASP GLU GLU ILE SER SEQRES 10 A 225 GLN PHE CYS LYS GLU GLU GLY VAL PHE TYR MET PRO GLY SEQRES 11 A 225 VAL MET THR PRO THR GLU LEU TYR LYS ALA MET LYS LEU SEQRES 12 A 225 GLY HIS THR ILE LEU LYS LEU PHE PRO GLY GLU VAL VAL SEQRES 13 A 225 GLY PRO GLN PHE VAL GLU ALA MET LYS GLY PRO PHE PRO SEQRES 14 A 225 ASN VAL LYS PHE VAL PRO THR GLY GLY VAL ASN LEU ASP SEQRES 15 A 225 ASN VAL CYS GLU TRP PHE GLU ALA GLY VAL LEU ALA VAL SEQRES 16 A 225 GLY VAL GLY SER ALA LEU VAL GLU GLY THR PRO VAL GLU SEQRES 17 A 225 VAL ALA GLU LYS ALA LYS ALA PHE VAL GLU LYS ILE GLU SEQRES 18 A 225 GLY CYS THR GLU SEQRES 1 B 205 MET LYS MET GLU GLU LEU PHE LYS GLU HIS LYS ILE VAL SEQRES 2 B 205 ALA VAL LEU ARG ALA ASN SER VAL GLU GLU ALA ILE SER SEQRES 3 B 205 LYS ALA LEU ALA VAL PHE ALA GLY GLY VAL HIS LEU ILE SEQRES 4 B 205 GLU ILE THR PHE THR VAL PRO ASP ALA ASP GLN VAL ILE SEQRES 5 B 205 LYS GLU LEU GLU PHE LEU LYS GLU ALA GLY ALA ILE ILE SEQRES 6 B 205 GLY ALA GLY THR VAL THR SER VAL GLU GLN CYS ARG GLU SEQRES 7 B 205 ALA VAL GLU SER GLY ALA GLU PHE ILE VAL SER PHE HIS SEQRES 8 B 205 LEU ASP GLU GLU ILE SER GLN PHE CYS LYS GLU GLU GLY SEQRES 9 B 205 VAL PHE TYR MET PRO GLY VAL MET THR PRO THR GLU LEU SEQRES 10 B 205 VAL LYS ALA MET LYS LEU GLY HIS THR ILE LEU LYS LEU SEQRES 11 B 205 VAL PRO GLY GLU VAL VAL GLY PRO GLN PHE VAL GLU ALA SEQRES 12 B 205 MET LYS GLY PRO PHE PRO ASN VAL LYS PHE VAL PRO THR SEQRES 13 B 205 GLY GLY VAL ASN LEU ASP ASN VAL CYS GLU TRP PHE GLU SEQRES 14 B 205 ALA GLY VAL LEU ALA VAL GLY VAL GLY SER ALA LEU VAL SEQRES 15 B 205 GLU GLY GLU PRO ALA GLU VAL ALA GLU LEU ALA ILE ARG SEQRES 16 B 205 PHE VAL GLU LYS ILE ARG GLY CYS THR GLU HELIX 1 AA1 ARG D 21 LYS D 31 1 11 HELIX 2 AA2 SER D 40 GLY D 54 1 15 HELIX 3 AA3 ASP D 67 ILE D 72 1 6 HELIX 4 AA4 LEU D 75 GLU D 80 1 6 HELIX 5 AA5 SER D 92 SER D 102 1 11 HELIX 6 AA6 ASP D 113 GLY D 124 1 12 HELIX 7 AA7 THR D 133 LYS D 142 1 10 HELIX 8 AA8 ASN D 183 GLU D 189 1 7 HELIX 9 AA9 THR D 205 CYS D 223 1 19 HELIX 10 AB1 MET C 3 LYS C 11 1 9 HELIX 11 AB2 SER C 20 GLY C 35 1 16 HELIX 12 AB3 ASP C 47 LEU C 55 1 9 HELIX 13 AB4 LEU C 55 ARG C 60 1 6 HELIX 14 AB5 SER C 72 GLY C 83 1 12 HELIX 15 AB6 ASP C 93 GLY C 104 1 12 HELIX 16 AB7 THR C 113 LYS C 122 1 10 HELIX 17 AB8 PRO C 132 GLY C 137 1 6 HELIX 18 AB9 GLY C 137 MET C 144 1 8 HELIX 19 AC1 ASN C 163 GLY C 171 1 9 HELIX 20 AC2 LYS C 185 THR C 204 1 20 HELIX 21 AC3 ARG A 21 LYS A 31 1 11 HELIX 22 AC4 SER A 40 GLY A 54 1 15 HELIX 23 AC5 ASP A 67 LEU A 75 1 9 HELIX 24 AC6 LEU A 75 GLU A 80 1 6 HELIX 25 AC7 SER A 92 SER A 102 1 11 HELIX 26 AC8 ASP A 113 GLY A 124 1 12 HELIX 27 AC9 THR A 133 LYS A 142 1 10 HELIX 28 AD1 PRO A 152 GLY A 157 1 6 HELIX 29 AD2 GLY A 157 MET A 164 1 8 HELIX 30 AD3 ASN A 183 PHE A 188 1 6 HELIX 31 AD4 THR A 205 CYS A 223 1 19 HELIX 32 AD5 MET B 3 LYS B 11 1 9 HELIX 33 AD6 SER B 20 GLY B 34 1 15 HELIX 34 AD7 ALA B 48 LEU B 55 1 8 HELIX 35 AD8 GLU B 56 GLY B 62 1 7 HELIX 36 AD9 SER B 72 SER B 82 1 11 HELIX 37 AE1 ASP B 93 GLY B 104 1 12 HELIX 38 AE2 THR B 113 LYS B 122 1 10 HELIX 39 AE3 PRO B 132 GLY B 137 1 6 HELIX 40 AE4 GLY B 137 LYS B 145 1 9 HELIX 41 AE5 ASN B 163 GLY B 171 1 9 HELIX 42 AE6 GLU B 185 GLY B 202 1 18 SHEET 1 AA1 4 ILE D 84 GLY D 88 0 SHEET 2 AA1 4 LEU D 58 THR D 62 1 N ILE D 61 O GLY D 86 SHEET 3 AA1 4 ILE D 32 LEU D 36 1 N ALA D 34 O LEU D 58 SHEET 4 AA1 4 VAL D 195 VAL D 197 1 O VAL D 197 N VAL D 33 SHEET 1 AA2 2 PHE D 106 VAL D 108 0 SHEET 2 AA2 2 PHE D 126 MET D 128 1 O PHE D 126 N ILE D 107 SHEET 1 AA3 3 GLY D 130 VAL D 131 0 SHEET 2 AA3 3 ILE D 147 LEU D 150 1 O LYS D 149 N VAL D 131 SHEET 3 AA3 3 LYS D 172 PRO D 175 1 O LYS D 172 N LEU D 148 SHEET 1 AA4 4 ILE C 64 GLY C 68 0 SHEET 2 AA4 4 LEU C 38 THR C 42 1 N ILE C 39 O GLY C 66 SHEET 3 AA4 4 ILE C 12 LEU C 16 1 N LEU C 16 O GLU C 40 SHEET 4 AA4 4 VAL C 175 VAL C 177 1 O VAL C 177 N VAL C 13 SHEET 1 AA5 2 PHE C 86 VAL C 88 0 SHEET 2 AA5 2 PHE C 106 MET C 108 1 O PHE C 106 N ILE C 87 SHEET 1 AA6 3 GLY C 110 VAL C 111 0 SHEET 2 AA6 3 ILE C 127 LEU C 130 1 O LYS C 129 N VAL C 111 SHEET 3 AA6 3 LYS C 152 PHE C 153 1 O LYS C 152 N LEU C 128 SHEET 1 AA7 4 ILE A 84 GLY A 88 0 SHEET 2 AA7 4 LEU A 58 THR A 62 1 N ILE A 59 O ILE A 84 SHEET 3 AA7 4 ILE A 32 LEU A 36 1 N ALA A 34 O GLU A 60 SHEET 4 AA7 4 VAL A 195 VAL A 197 1 O VAL A 197 N VAL A 33 SHEET 1 AA8 2 PHE A 106 VAL A 108 0 SHEET 2 AA8 2 PHE A 126 MET A 128 1 O PHE A 126 N ILE A 107 SHEET 1 AA9 3 GLY A 130 VAL A 131 0 SHEET 2 AA9 3 ILE A 147 LEU A 150 1 O LYS A 149 N VAL A 131 SHEET 3 AA9 3 LYS A 172 PRO A 175 1 O LYS A 172 N LEU A 148 SHEET 1 AB1 4 ILE B 64 GLY B 68 0 SHEET 2 AB1 4 LEU B 38 THR B 42 1 N ILE B 39 O ILE B 64 SHEET 3 AB1 4 ILE B 12 LEU B 16 1 N ALA B 14 O GLU B 40 SHEET 4 AB1 4 VAL B 175 VAL B 177 1 O VAL B 177 N VAL B 13 SHEET 1 AB2 2 PHE B 86 VAL B 88 0 SHEET 2 AB2 2 PHE B 106 MET B 108 1 O PHE B 106 N ILE B 87 SHEET 1 AB3 3 GLY B 110 VAL B 111 0 SHEET 2 AB3 3 ILE B 127 LEU B 130 1 O LYS B 129 N VAL B 111 SHEET 3 AB3 3 LYS B 152 PRO B 155 1 O LYS B 152 N LEU B 128 SSBOND 1 CYS D 185 CYS D 223 1555 1555 2.04 SSBOND 2 CYS C 165 CYS C 203 1555 1555 2.04 SSBOND 3 CYS A 185 CYS A 223 1555 1555 2.06 SSBOND 4 CYS B 165 CYS B 203 1555 1555 2.03 CISPEP 1 PHE D 151 PRO D 152 0 -10.60 CISPEP 2 PHE C 131 PRO C 132 0 -10.39 CISPEP 3 PHE A 151 PRO A 152 0 -11.94 CISPEP 4 VAL B 131 PRO B 132 0 -22.29 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 TER 1419 CYS D 223 TER 2848 THR C 204 TER 4272 CYS A 223 TER 5691 CYS B 203 CONECT 1172 1418 CONECT 1418 1172 CONECT 2578 2842 CONECT 2842 2578 CONECT 4019 4271 CONECT 4271 4019 CONECT 5434 5690 CONECT 5690 5434 MASTER 411 0 0 42 36 0 0 6 5687 4 8 69 END