HEADER VIRAL PROTEIN 24-JAN-25 9N0W TITLE HTLV-1 GAG CAPSID FROM IMMATURE PARTICLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG PROTEIN; COMPND 3 CHAIN: B, C, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN T-CELL LEUKEMIA VIRUS TYPE I; SOURCE 3 ORGANISM_TAXID: 11908; SOURCE 4 STRAIN: B1033-2009; SOURCE 5 GENE: GAG; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: 293T KEYWDS COMPLEX, VIRUS, LATTICE, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR W.G.ARNDT,A.RAMEZANI,B.CHEN,J.R.PERILLA,W.ZHANG,L.M.MANSKY REVDAT 1 24-DEC-25 9N0W 0 JRNL AUTH W.G.ARNDT,A.RAMEZANI,N.TALLEDGE,G.YU,H.YANG,B.CHEN, JRNL AUTH 2 J.R.PERILLA,W.ZHANG,L.M.MANSKY JRNL TITL HIGH-RESOLUTION ANALYSIS OF THE HUMAN T-CELL LEUKEMIA VIRUS JRNL TITL 2 CAPSID PROTEIN REVEALS INSIGHTS INTO IMMATURE PARTICLE JRNL TITL 3 MORPHOLOGY. JRNL REF NAT COMMUN 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41381513 JRNL DOI 10.1038/S41467-025-67129-1 REMARK 2 REMARK 2 RESOLUTION. 3.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, CTFFIND, UCSF CHIMERA, ISOLDE, REMARK 3 RELION, RELION, RELION, RELION, PHENIX 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) : 3.440 REMARK 3 NUMBER OF PARTICLES : 140020 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 9N0W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000291995. 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 : HTLV-1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : LEICA GP2 GRID PLUNGER REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : HTLV-1 VIRUS-LIKE PARTICLES REMARK 245 PRODUCED BY TRANSFECTING 293T CELLS WITH HTLV-1 GAG AND ENVELOPE. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2502 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 750.00 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) : 5000.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C6). 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: B, C, 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 0.500003 -0.866023 0.001283 230.50596 REMARK 350 BIOMT2 2 0.866022 0.500000 -0.002251 -61.40010 REMARK 350 BIOMT3 2 0.001307 0.002237 0.999997 -0.59803 REMARK 350 BIOMT1 3 -0.499990 -0.866023 0.003874 398.93282 REMARK 350 BIOMT2 3 0.866022 -0.500000 -0.002265 107.52454 REMARK 350 BIOMT3 3 0.003898 0.002223 0.999990 -1.03200 REMARK 350 BIOMT1 4 -0.999987 0.000000 0.005181 336.85371 REMARK 350 BIOMT2 4 0.000000 -1.000000 -0.000028 337.84929 REMARK 350 BIOMT3 4 0.005181 -0.000028 0.999987 -0.86794 REMARK 350 BIOMT1 5 -0.499990 0.866022 0.003898 106.34775 REMARK 350 BIOMT2 5 -0.866023 -0.500000 0.002223 399.24939 REMARK 350 BIOMT3 5 0.003874 -0.002265 0.999990 -0.26991 REMARK 350 BIOMT1 6 0.500003 0.866022 0.001308 -62.07911 REMARK 350 BIOMT2 6 -0.866023 0.500000 0.002237 230.32474 REMARK 350 BIOMT3 6 0.001283 -0.002251 0.999997 0.16406 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 O PRO B 50 NE2 GLN B 114 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 PRO B 96 -176.54 -69.54 REMARK 500 ALA C 94 33.53 -98.89 REMARK 500 ASP A 130 72.85 51.98 REMARK 500 PRO A 194 172.98 -59.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48795 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-48796 RELATED DB: EMDB REMARK 900 HTLV-1 GAG CAPSID FROM IMMATURE PARTICLES DBREF 9N0W B 15 207 UNP Q82230 Q82230_9DELA 145 337 DBREF 9N0W C 15 207 UNP Q82230 Q82230_9DELA 145 337 DBREF 9N0W A 15 207 UNP Q82230 Q82230_9DELA 145 337 SEQRES 1 B 193 TRP GLN MET LYS ASP LEU GLN ALA ILE LYS GLN GLU VAL SEQRES 2 B 193 SER GLN ALA ALA PRO GLY SER PRO GLN PHE MET GLN THR SEQRES 3 B 193 ILE ARG LEU ALA VAL GLN GLN PHE ASP PRO THR ALA LYS SEQRES 4 B 193 ASP LEU GLN ASP LEU LEU GLN TYR LEU CYS SER SER LEU SEQRES 5 B 193 VAL ALA SER LEU HIS HIS GLN GLN LEU ASP SER LEU ILE SEQRES 6 B 193 SER GLU ALA GLU THR ARG GLY ILE THR GLY TYR ASN PRO SEQRES 7 B 193 LEU ALA GLY PRO LEU ARG VAL GLN ALA ASN ASN PRO GLN SEQRES 8 B 193 GLN GLN GLY LEU ARG ARG GLU TYR GLN GLN LEU TRP LEU SEQRES 9 B 193 ALA ALA PHE ALA ALA LEU PRO GLY SER ALA LYS ASP PRO SEQRES 10 B 193 SER TRP ALA SER ILE LEU GLN GLY LEU GLU GLU PRO TYR SEQRES 11 B 193 HIS ALA PHE VAL GLU ARG LEU ASN ILE ALA LEU ASP ASN SEQRES 12 B 193 GLY LEU PRO GLU GLY THR PRO LYS ASP PRO ILE LEU ARG SEQRES 13 B 193 SER LEU ALA TYR SER ASN ALA ASN LYS GLU CYS GLN LYS SEQRES 14 B 193 LEU LEU GLN ALA ARG GLY HIS THR ASN SER PRO LEU GLY SEQRES 15 B 193 ASP MET LEU ARG ALA CYS GLN THR TRP THR PRO SEQRES 1 C 193 TRP GLN MET LYS ASP LEU GLN ALA ILE LYS GLN GLU VAL SEQRES 2 C 193 SER GLN ALA ALA PRO GLY SER PRO GLN PHE MET GLN THR SEQRES 3 C 193 ILE ARG LEU ALA VAL GLN GLN PHE ASP PRO THR ALA LYS SEQRES 4 C 193 ASP LEU GLN ASP LEU LEU GLN TYR LEU CYS SER SER LEU SEQRES 5 C 193 VAL ALA SER LEU HIS HIS GLN GLN LEU ASP SER LEU ILE SEQRES 6 C 193 SER GLU ALA GLU THR ARG GLY ILE THR GLY TYR ASN PRO SEQRES 7 C 193 LEU ALA GLY PRO LEU ARG VAL GLN ALA ASN ASN PRO GLN SEQRES 8 C 193 GLN GLN GLY LEU ARG ARG GLU TYR GLN GLN LEU TRP LEU SEQRES 9 C 193 ALA ALA PHE ALA ALA LEU PRO GLY SER ALA LYS ASP PRO SEQRES 10 C 193 SER TRP ALA SER ILE LEU GLN GLY LEU GLU GLU PRO TYR SEQRES 11 C 193 HIS ALA PHE VAL GLU ARG LEU ASN ILE ALA LEU ASP ASN SEQRES 12 C 193 GLY LEU PRO GLU GLY THR PRO LYS ASP PRO ILE LEU ARG SEQRES 13 C 193 SER LEU ALA TYR SER ASN ALA ASN LYS GLU CYS GLN LYS SEQRES 14 C 193 LEU LEU GLN ALA ARG GLY HIS THR ASN SER PRO LEU GLY SEQRES 15 C 193 ASP MET LEU ARG ALA CYS GLN THR TRP THR PRO SEQRES 1 A 193 TRP GLN MET LYS ASP LEU GLN ALA ILE LYS GLN GLU VAL SEQRES 2 A 193 SER GLN ALA ALA PRO GLY SER PRO GLN PHE MET GLN THR SEQRES 3 A 193 ILE ARG LEU ALA VAL GLN GLN PHE ASP PRO THR ALA LYS SEQRES 4 A 193 ASP LEU GLN ASP LEU LEU GLN TYR LEU CYS SER SER LEU SEQRES 5 A 193 VAL ALA SER LEU HIS HIS GLN GLN LEU ASP SER LEU ILE SEQRES 6 A 193 SER GLU ALA GLU THR ARG GLY ILE THR GLY TYR ASN PRO SEQRES 7 A 193 LEU ALA GLY PRO LEU ARG VAL GLN ALA ASN ASN PRO GLN SEQRES 8 A 193 GLN GLN GLY LEU ARG ARG GLU TYR GLN GLN LEU TRP LEU SEQRES 9 A 193 ALA ALA PHE ALA ALA LEU PRO GLY SER ALA LYS ASP PRO SEQRES 10 A 193 SER TRP ALA SER ILE LEU GLN GLY LEU GLU GLU PRO TYR SEQRES 11 A 193 HIS ALA PHE VAL GLU ARG LEU ASN ILE ALA LEU ASP ASN SEQRES 12 A 193 GLY LEU PRO GLU GLY THR PRO LYS ASP PRO ILE LEU ARG SEQRES 13 A 193 SER LEU ALA TYR SER ASN ALA ASN LYS GLU CYS GLN LYS SEQRES 14 A 193 LEU LEU GLN ALA ARG GLY HIS THR ASN SER PRO LEU GLY SEQRES 15 A 193 ASP MET LEU ARG ALA CYS GLN THR TRP THR PRO HELIX 1 AA1 GLN B 16 SER B 28 1 13 HELIX 2 AA2 SER B 34 ASP B 49 1 16 HELIX 3 AA3 THR B 51 CYS B 63 1 13 HELIX 4 AA4 SER B 64 GLY B 86 1 23 HELIX 5 AA5 PRO B 96 ASN B 103 1 8 HELIX 6 AA6 GLN B 106 ALA B 128 1 23 HELIX 7 AA7 PRO B 131 ILE B 136 5 6 HELIX 8 AA8 PRO B 143 LEU B 159 1 17 HELIX 9 AA9 LYS B 165 ASN B 176 1 12 HELIX 10 AB1 ASN B 178 GLY B 189 1 12 HELIX 11 AB2 PRO B 194 CYS B 202 1 9 HELIX 12 AB3 GLN B 203 TRP B 205 5 3 HELIX 13 AB4 GLN C 16 VAL C 27 1 12 HELIX 14 AB5 SER C 34 ASP C 49 1 16 HELIX 15 AB6 THR C 51 CYS C 63 1 13 HELIX 16 AB7 SER C 64 GLY C 86 1 23 HELIX 17 AB8 ASN C 91 GLY C 95 5 5 HELIX 18 AB9 PRO C 96 ALA C 101 1 6 HELIX 19 AC1 GLN C 106 ALA C 123 1 18 HELIX 20 AC2 LEU C 124 ALA C 128 5 5 HELIX 21 AC3 PRO C 143 LEU C 159 1 17 HELIX 22 AC4 PRO C 164 ASN C 176 1 13 HELIX 23 AC5 ASN C 178 GLY C 189 1 12 HELIX 24 AC6 PRO C 194 CYS C 202 1 9 HELIX 25 AC7 GLN C 203 TRP C 205 5 3 HELIX 26 AC8 GLN A 16 SER A 28 1 13 HELIX 27 AC9 SER A 34 ASP A 49 1 16 HELIX 28 AD1 THR A 51 CYS A 63 1 13 HELIX 29 AD2 SER A 64 GLY A 86 1 23 HELIX 30 AD3 ASN A 91 GLY A 95 5 5 HELIX 31 AD4 PRO A 96 ASN A 103 1 8 HELIX 32 AD5 GLN A 106 PHE A 121 1 16 HELIX 33 AD6 ALA A 122 SER A 127 1 6 HELIX 34 AD7 PRO A 131 ILE A 136 5 6 HELIX 35 AD8 PRO A 143 LEU A 159 1 17 HELIX 36 AD9 PRO A 164 ASN A 176 1 13 HELIX 37 AE1 GLU A 180 ARG A 188 1 9 HELIX 38 AE2 PRO A 194 CYS A 202 1 9 HELIX 39 AE3 GLN A 203 TRP A 205 5 3 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 TER 1508 PRO B 207 TER 3016 PRO C 207 TER 4524 PRO A 207 MASTER 147 0 0 39 0 0 0 6 4521 3 0 45 END