HEADER VIRAL PROTEIN 17-JUL-23 8PU6 TITLE STRUCTURE OF IMMATURE HTLV-1 CA-NTD FROM IN VITRO ASSEMBLED MA126-CANC TITLE 2 TUBES: POOLED CLASS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG PROTEIN (FRAGMENT); COMPND 3 CHAIN: A, B, C; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RETROVIRUS, HTLV, IMMATURE CAPSID, CA, CA-NTD, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.OBR,M.PERCIPALLE,D.CHERNIKOVA,H.YANG,A.THADER,G.PINKE,D.PORLEY, AUTHOR 2 L.M.MANSKY,R.A.DICK,F.K.M.SCHUR REVDAT 1 23-AUG-23 8PU6 0 JRNL AUTH M.OBR,M.PERCIPALLE,D.CHERNIKOVA,H.YANG,A.THADER,G.PINKE, JRNL AUTH 2 D.PORLEY,L.M.MANSKY,R.A.DICK,F.K.SCHUR JRNL TITL UNCONVENTIONAL STABILIZATION OF THE HUMAN T-CELL LEUKEMIA JRNL TITL 2 VIRUS TYPE 1 IMMATURE GAG LATTICE. JRNL REF BIORXIV 2023 JRNL REFN ISSN 2692-8205 JRNL PMID 37546793 JRNL DOI 10.1101/2023.07.24.548988 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SUBTOM, WARP, MATLAB, SERIALEM, WARP, REMARK 3 UCSF CHIMERA, UCSF CHIMERAX, COOT, REMARK 3 SERIALEM, CTFFIND, NOVACTF, ISOLDE, REMARK 3 PHENIX, RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1QRJ REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 134000 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 8PU6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292131146. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SUBTOMOGRAM AVERAGING REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : HELICAL ARRAY REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : HUMAN T-CELL LEUKEMIA VIRUS REMARK 245 TYPE I REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : GRIDS COATED WITH 2NM REMARK 245 CONTINUOUS CARBON LAYER 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; FEI TITAN REMARK 245 KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K); GATAN K2 QUANTUM (4K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00; 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00; 3500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70; 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD; BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 350.00; 350.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM; FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 80000; 105000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN; FIELD REMARK 245 EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300; 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 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 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 PRO A 1 REMARK 465 VAL A 2 REMARK 465 MET A 3 REMARK 465 HIS A 4 REMARK 465 PRO A 5 REMARK 465 HIS A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 PRO A 9 REMARK 465 PRO A 10 REMARK 465 ASN A 11 REMARK 465 HIS A 12 REMARK 465 PRO B 1 REMARK 465 VAL B 2 REMARK 465 MET B 3 REMARK 465 HIS B 4 REMARK 465 PRO B 5 REMARK 465 HIS B 6 REMARK 465 GLY B 7 REMARK 465 ALA B 8 REMARK 465 PRO B 9 REMARK 465 PRO B 10 REMARK 465 ASN B 11 REMARK 465 HIS B 12 REMARK 465 PRO C 1 REMARK 465 VAL C 2 REMARK 465 MET C 3 REMARK 465 HIS C 4 REMARK 465 PRO C 5 REMARK 465 HIS C 6 REMARK 465 GLY C 7 REMARK 465 ALA C 8 REMARK 465 PRO C 9 REMARK 465 PRO C 10 REMARK 465 ASN C 11 REMARK 465 HIS C 12 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 H GLN A 16 OD2 ASP A 19 1.59 REMARK 500 NE2 GLN C 74 O ALA C 123 2.16 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 A 104 1.53 -66.54 REMARK 500 GLN B 105 30.34 -95.20 REMARK 500 PRO C 92 1.18 -67.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17930 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17931 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17932 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17933 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17934 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17935 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17936 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17937 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17940 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17942 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17943 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17938 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17939 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17941 RELATED DB: EMDB REMARK 900 THE DEPOSITION ID NEEDS TO BE REPLACED BY THE EMDB ACCESSION CODE, REMARK 900 ONCE AVAILABLE REMARK 900 RELATED ID: EMD-17929 RELATED DB: EMDB REMARK 900 STRUCTURE OF IMMATURE HTLV-1 CA-NTD FROM IN VITRO ASSEMBLED MA126- REMARK 900 CANC TUBES: POOLED CLASS DBREF 8PU6 A 1 125 UNP X5GX59 X5GX59_9DELA 28 152 DBREF 8PU6 B 1 125 UNP X5GX59 X5GX59_9DELA 28 152 DBREF 8PU6 C 1 125 UNP X5GX59 X5GX59_9DELA 28 152 SEQRES 1 A 125 PRO VAL MET HIS PRO HIS GLY ALA PRO PRO ASN HIS ARG SEQRES 2 A 125 PRO TRP GLN MET LYS ASP LEU GLN ALA ILE LYS GLN GLU SEQRES 3 A 125 VAL SER GLN ALA ALA PRO GLY SER PRO GLN PHE MET GLN SEQRES 4 A 125 THR ILE ARG LEU ALA VAL GLN GLN PHE ASP PRO THR ALA SEQRES 5 A 125 LYS ASP LEU GLN ASP LEU LEU GLN TYR LEU CYS SER SER SEQRES 6 A 125 LEU VAL ALA SER LEU HIS HIS GLN GLN LEU ASP SER LEU SEQRES 7 A 125 ILE SER GLU ALA GLU THR ARG GLY ILE THR GLY TYR ASN SEQRES 8 A 125 PRO LEU ALA GLY PRO LEU ARG VAL GLN ALA ASN ASN PRO SEQRES 9 A 125 GLN GLN GLN GLY LEU ARG ARG GLU TYR GLN GLN LEU TRP SEQRES 10 A 125 LEU ALA ALA PHE ALA ALA LEU PRO SEQRES 1 B 125 PRO VAL MET HIS PRO HIS GLY ALA PRO PRO ASN HIS ARG SEQRES 2 B 125 PRO TRP GLN MET LYS ASP LEU GLN ALA ILE LYS GLN GLU SEQRES 3 B 125 VAL SER GLN ALA ALA PRO GLY SER PRO GLN PHE MET GLN SEQRES 4 B 125 THR ILE ARG LEU ALA VAL GLN GLN PHE ASP PRO THR ALA SEQRES 5 B 125 LYS ASP LEU GLN ASP LEU LEU GLN TYR LEU CYS SER SER SEQRES 6 B 125 LEU VAL ALA SER LEU HIS HIS GLN GLN LEU ASP SER LEU SEQRES 7 B 125 ILE SER GLU ALA GLU THR ARG GLY ILE THR GLY TYR ASN SEQRES 8 B 125 PRO LEU ALA GLY PRO LEU ARG VAL GLN ALA ASN ASN PRO SEQRES 9 B 125 GLN GLN GLN GLY LEU ARG ARG GLU TYR GLN GLN LEU TRP SEQRES 10 B 125 LEU ALA ALA PHE ALA ALA LEU PRO SEQRES 1 C 125 PRO VAL MET HIS PRO HIS GLY ALA PRO PRO ASN HIS ARG SEQRES 2 C 125 PRO TRP GLN MET LYS ASP LEU GLN ALA ILE LYS GLN GLU SEQRES 3 C 125 VAL SER GLN ALA ALA PRO GLY SER PRO GLN PHE MET GLN SEQRES 4 C 125 THR ILE ARG LEU ALA VAL GLN GLN PHE ASP PRO THR ALA SEQRES 5 C 125 LYS ASP LEU GLN ASP LEU LEU GLN TYR LEU CYS SER SER SEQRES 6 C 125 LEU VAL ALA SER LEU HIS HIS GLN GLN LEU ASP SER LEU SEQRES 7 C 125 ILE SER GLU ALA GLU THR ARG GLY ILE THR GLY TYR ASN SEQRES 8 C 125 PRO LEU ALA GLY PRO LEU ARG VAL GLN ALA ASN ASN PRO SEQRES 9 C 125 GLN GLN GLN GLY LEU ARG ARG GLU TYR GLN GLN LEU TRP SEQRES 10 C 125 LEU ALA ALA PHE ALA ALA LEU PRO HELIX 1 AA1 GLN A 16 VAL A 27 1 12 HELIX 2 AA2 SER A 34 ASP A 49 1 16 HELIX 3 AA3 THR A 51 CYS A 63 1 13 HELIX 4 AA4 SER A 64 GLY A 86 1 23 HELIX 5 AA5 PRO A 96 ALA A 101 1 6 HELIX 6 AA6 GLN A 106 ALA A 123 1 18 HELIX 7 AA7 GLN B 16 VAL B 27 1 12 HELIX 8 AA8 SER B 34 ASP B 49 1 16 HELIX 9 AA9 THR B 51 CYS B 63 1 13 HELIX 10 AB1 SER B 64 GLY B 86 1 23 HELIX 11 AB2 PRO B 96 ALA B 101 1 6 HELIX 12 AB3 GLN B 106 ALA B 123 1 18 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 ASN C 103 1 8 HELIX 19 AC1 GLN C 106 ALA C 123 1 18 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