HEADER VIRUS LIKE PARTICLE 03-DEC-23 8RB5 TITLE STRUCTURE OF THE THREE-FOLD CAPSOMER OF THE PNMA2 CAPSID COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARANEOPLASTIC ANTIGEN MA2 HOMOLOG; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PNMA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENDOGENOUS RETROVIRUS. PNMA2, PNMA, PARANEOPLASTIC SYNDROME, KEYWDS 2 PARANEOPLASTIC ANTIGEN MA2, VLP., VIRUS LIKE PARTICLE EXPDTA ELECTRON MICROSCOPY AUTHOR S.ERLENDSSON,J.XU,J.D.SHEPHERD,J.A.G.BRIGGS REVDAT 2 28-FEB-24 8RB5 1 JRNL REVDAT 1 14-FEB-24 8RB5 0 JRNL AUTH J.XU,S.ERLENDSSON,M.SINGH,G.A.HOLLING,M.REGIER,I.IBIRICU, JRNL AUTH 2 J.EINSTEIN,M.P.HANTAK,G.S.DAY,A.L.PIQUET,T.L.SMITH, JRNL AUTH 3 S.L.CLARDY,A.M.WHITELEY,C.FESCHOTTE,J.A.G.BRIGGS, JRNL AUTH 4 J.D.SHEPHERD JRNL TITL PNMA2 FORMS IMMUNOGENIC NON-ENVELOPED VIRUS-LIKE CAPSIDS JRNL TITL 2 ASSOCIATED WITH PARANEOPLASTIC NEUROLOGICAL SYNDROME. JRNL REF CELL V. 187 831 2024 JRNL REFN ISSN 1097-4172 JRNL PMID 38301645 JRNL DOI 10.1016/J.CELL.2024.01.009 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, CTFFIND, UCSF CHIMERAX, REMARK 3 RELION, RELION, RELION, COOT, PHENIX, REMARK 3 UCSF CHIMERAX, ISOLDE REMARK 3 RECONSTRUCTION SCHEMA : NULL 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 : 105.000 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 972807 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 8RB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292135065. 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 : STRUCTURE OF THE THREE-FOLD REMARK 245 CAPSOMER OF THE PNMA2 CAPSID REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 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 : 3005 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) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 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) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 96000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: 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 GLU A 232 CD GLU A 232 OE2 -0.071 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 ARG A 166 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 204 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 294 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 332 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 166 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 294 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 311 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 332 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG C 166 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG C 277 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG C 277 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG C 294 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG C 332 NE - CZ - NH2 ANGL. DEV. = 3.1 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 SER A 169 -22.01 -141.77 REMARK 500 ALA A 173 49.21 -77.61 REMARK 500 ASN B 225 87.09 -158.28 REMARK 500 ASN B 306 -102.07 45.45 REMARK 500 LYS C 161 57.59 -100.14 REMARK 500 ASN C 225 89.15 -155.31 REMARK 500 ASN C 306 -132.19 51.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 162 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-19026 RELATED DB: EMDB REMARK 900 STRUCTURE OF THE THREE-FOLD CAPSOMER OF THE PNMA2 CAPSID DBREF 8RB5 A 157 336 UNP Q8BHK0 PNMA2_MOUSE 157 336 DBREF 8RB5 B 157 336 UNP Q8BHK0 PNMA2_MOUSE 157 336 DBREF 8RB5 C 157 336 UNP Q8BHK0 PNMA2_MOUSE 157 336 SEQRES 1 A 180 LEU LEU PRO VAL LYS TYR CYS LYS MET ARG ILE PHE SER SEQRES 2 A 180 GLY SER THR ALA ALA ALA PRO GLU GLU GLU PRO PHE GLU SEQRES 3 A 180 VAL TRP LEU GLU GLN ALA THR GLU ILE ALA LYS GLU TRP SEQRES 4 A 180 PRO ILE PRO GLU ALA GLU LYS LYS ARG TRP VAL ALA GLU SEQRES 5 A 180 SER LEU ARG GLY PRO ALA LEU ASP LEU MET HIS ILE VAL SEQRES 6 A 180 GLN ALA ASP ASN PRO SER ILE SER VAL GLY GLU CYS LEU SEQRES 7 A 180 GLU ALA PHE LYS GLN VAL PHE GLY SER THR GLU SER ARG SEQRES 8 A 180 ARG THR SER GLN VAL LYS TYR LEU ARG THR TYR GLN GLN SEQRES 9 A 180 GLU GLY GLU LYS ILE SER ALA TYR VAL LEU ARG LEU GLU SEQRES 10 A 180 THR LEU LEU ARG ARG ALA VAL GLU LYS ARG ALA ILE PRO SEQRES 11 A 180 ARG ASN ILE ALA ASP GLN VAL ARG LEU GLU GLN VAL MET SEQRES 12 A 180 ALA GLY ALA ASN LEU GLY ASN VAL LEU TRP CYS ARG LEU SEQRES 13 A 180 GLN GLU LEU LYS ASP GLN GLY PRO LEU PRO THR PHE LEU SEQRES 14 A 180 GLN LEU MET LYS VAL ILE ARG GLU GLU GLU GLU SEQRES 1 B 180 LEU LEU PRO VAL LYS TYR CYS LYS MET ARG ILE PHE SER SEQRES 2 B 180 GLY SER THR ALA ALA ALA PRO GLU GLU GLU PRO PHE GLU SEQRES 3 B 180 VAL TRP LEU GLU GLN ALA THR GLU ILE ALA LYS GLU TRP SEQRES 4 B 180 PRO ILE PRO GLU ALA GLU LYS LYS ARG TRP VAL ALA GLU SEQRES 5 B 180 SER LEU ARG GLY PRO ALA LEU ASP LEU MET HIS ILE VAL SEQRES 6 B 180 GLN ALA ASP ASN PRO SER ILE SER VAL GLY GLU CYS LEU SEQRES 7 B 180 GLU ALA PHE LYS GLN VAL PHE GLY SER THR GLU SER ARG SEQRES 8 B 180 ARG THR SER GLN VAL LYS TYR LEU ARG THR TYR GLN GLN SEQRES 9 B 180 GLU GLY GLU LYS ILE SER ALA TYR VAL LEU ARG LEU GLU SEQRES 10 B 180 THR LEU LEU ARG ARG ALA VAL GLU LYS ARG ALA ILE PRO SEQRES 11 B 180 ARG ASN ILE ALA ASP GLN VAL ARG LEU GLU GLN VAL MET SEQRES 12 B 180 ALA GLY ALA ASN LEU GLY ASN VAL LEU TRP CYS ARG LEU SEQRES 13 B 180 GLN GLU LEU LYS ASP GLN GLY PRO LEU PRO THR PHE LEU SEQRES 14 B 180 GLN LEU MET LYS VAL ILE ARG GLU GLU GLU GLU SEQRES 1 C 180 LEU LEU PRO VAL LYS TYR CYS LYS MET ARG ILE PHE SER SEQRES 2 C 180 GLY SER THR ALA ALA ALA PRO GLU GLU GLU PRO PHE GLU SEQRES 3 C 180 VAL TRP LEU GLU GLN ALA THR GLU ILE ALA LYS GLU TRP SEQRES 4 C 180 PRO ILE PRO GLU ALA GLU LYS LYS ARG TRP VAL ALA GLU SEQRES 5 C 180 SER LEU ARG GLY PRO ALA LEU ASP LEU MET HIS ILE VAL SEQRES 6 C 180 GLN ALA ASP ASN PRO SER ILE SER VAL GLY GLU CYS LEU SEQRES 7 C 180 GLU ALA PHE LYS GLN VAL PHE GLY SER THR GLU SER ARG SEQRES 8 C 180 ARG THR SER GLN VAL LYS TYR LEU ARG THR TYR GLN GLN SEQRES 9 C 180 GLU GLY GLU LYS ILE SER ALA TYR VAL LEU ARG LEU GLU SEQRES 10 C 180 THR LEU LEU ARG ARG ALA VAL GLU LYS ARG ALA ILE PRO SEQRES 11 C 180 ARG ASN ILE ALA ASP GLN VAL ARG LEU GLU GLN VAL MET SEQRES 12 C 180 ALA GLY ALA ASN LEU GLY ASN VAL LEU TRP CYS ARG LEU SEQRES 13 C 180 GLN GLU LEU LYS ASP GLN GLY PRO LEU PRO THR PHE LEU SEQRES 14 C 180 GLN LEU MET LYS VAL ILE ARG GLU GLU GLU GLU HELIX 1 AA1 PRO A 180 GLU A 194 1 15 HELIX 2 AA2 PRO A 198 GLU A 208 1 11 HELIX 3 AA3 ARG A 211 ASN A 225 1 15 HELIX 4 AA4 SER A 229 GLY A 242 1 14 HELIX 5 AA5 SER A 246 ARG A 256 1 11 HELIX 6 AA6 LYS A 264 LYS A 282 1 19 HELIX 7 AA7 PRO A 286 ASN A 288 5 3 HELIX 8 AA8 ILE A 289 ALA A 302 1 14 HELIX 9 AA9 GLY A 305 GLN A 318 1 14 HELIX 10 AB1 THR A 323 GLU A 333 1 11 HELIX 11 AB2 PRO B 180 GLU B 194 1 15 HELIX 12 AB3 PRO B 198 GLU B 208 1 11 HELIX 13 AB4 ARG B 211 ASN B 225 1 15 HELIX 14 AB5 SER B 229 GLY B 242 1 14 HELIX 15 AB6 SER B 246 ARG B 256 1 11 HELIX 16 AB7 LYS B 264 LYS B 282 1 19 HELIX 17 AB8 PRO B 286 ASN B 288 5 3 HELIX 18 AB9 ILE B 289 ALA B 302 1 14 HELIX 19 AC1 GLY B 305 GLN B 318 1 14 HELIX 20 AC2 THR B 323 GLU B 333 1 11 HELIX 21 AC3 PRO C 180 GLU C 194 1 15 HELIX 22 AC4 PRO C 198 GLU C 208 1 11 HELIX 23 AC5 ARG C 211 ASN C 225 1 15 HELIX 24 AC6 SER C 229 GLY C 242 1 14 HELIX 25 AC7 SER C 246 ARG C 256 1 11 HELIX 26 AC8 LYS C 264 LYS C 282 1 19 HELIX 27 AC9 PRO C 286 ASN C 288 5 3 HELIX 28 AD1 ILE C 289 ALA C 302 1 14 HELIX 29 AD2 GLY C 305 GLN C 318 1 14 HELIX 30 AD3 THR C 323 GLU C 333 1 11 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