HEADER VIRAL PROTEIN/RNA 26-MAR-20 6WAZ TITLE +1 EXTENDED HIV-1 REVERSE TRANSCRIPTASE INITIATION COMPLEX CORE (PRE- TITLE 2 TRANSLOCATION STATE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: REVERSE TRANSCRIPTASE/RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PR160GAG-POL; COMPND 5 EC: 2.7.7.49,2.7.7.7,3.1.26.13; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: REVERSE TRANSCRIPTASE P51 SUBUNIT; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: HIV-1 VIRAL RNA GENOME FRAGMENT; COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: TRNA LYSINE 3; COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11678; SOURCE 5 STRAIN: ISOLATE BH10; SOURCE 6 GENE: GAG-POL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 11 ORGANISM_COMMON: HIV-1; SOURCE 12 ORGANISM_TAXID: 11676; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 18 ORGANISM_COMMON: HIV-1; SOURCE 19 ORGANISM_TAXID: 11676; SOURCE 20 MOL_ID: 4; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_TAXID: 9606 KEYWDS REVERSE TRANSCRIPTASE, RNA, COMPLEX, PROTEIN-RNA COMPLEX, TRNA, KEYWDS 2 POLYMERASE, VIRAL PROTEIN, VIRAL PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR K.P.LARSEN,L.N.JACKSON,K.KAPPEL,J.ZHANG,E.V.PUGLISI REVDAT 3 06-MAR-24 6WAZ 1 REMARK REVDAT 2 05-AUG-20 6WAZ 1 JRNL REVDAT 1 24-JUN-20 6WAZ 0 JRNL AUTH K.P.LARSEN,J.CHOI,L.N.JACKSON,K.KAPPEL,J.ZHANG,B.HA, JRNL AUTH 2 D.H.CHEN,E.V.PUGLISI JRNL TITL DISTINCT CONFORMATIONAL STATES UNDERLIE PAUSING DURING JRNL TITL 2 INITIATION OF HIV-1 REVERSE TRANSCRIPTION. JRNL REF J.MOL.BIOL. V. 432 4499 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 32512005 JRNL DOI 10.1016/J.JMB.2020.06.003 REMARK 2 REMARK 2 RESOLUTION. 4.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, GCTF, RELION, RELION, RELION, REMARK 3 RELION 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 : 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) : 4.100 REMARK 3 NUMBER OF PARTICLES : 394434 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 6WAZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247894. 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 : +1 EXTENDED HIV-1 REVERSE REMARK 245 TRANSCRIPTASE INITIATION REMARK 245 COMPLEX CORE; HIV-1 REVERSE REMARK 245 TRANSCRIPTASE; HIV-1 RNA GENOME REMARK 245 FRAGMENT; TRNA LYSINE 3 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 5.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : 3 MICROLITERS APPLIED, 2S PRE REMARK 245 -BLOT, 1.5S BLOT. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : PERIPHERAL DYNAMIC RNA ELEMENTS REMARK 245 BELONGING TO THE TRNA LYSINE 3 PRIMER AND THE HIV-1 VIRAL RNA REMARK 245 GENOMIC TEMPLATE HAVE BEEN MASKED OUT DURING CRYO-EM DATA REMARK 245 PROCESSING.; THE C-TERMINUS OF P66 CONTAINS AN UNSTRUCTURED REMARK 245 LINKER AND A SIX-HISTIDINE TAG THAT WAS CLEAVED PRIOR TO FULL REMARK 245 COMPLEX FORMATION.; A FRAGMENT OF THE HIV-1 RNA GENOME THAT IS REMARK 245 101 NUCLEOTIDES IN LENGTH.; CHEMICALLY SYNTHESIZED AND EXTENDED REMARK 245 TRNA LYSINE 3. A MODIFIED DG CONTAINING AN N2-CYSTAMINE WAS REMARK 245 PLACED AT POSITION 71. THE TRNA PRIMER WAS ALSO EXTENDED BY A REMARK 245 SINGLE DDC DURING COMPLEX FORMATION, BRINGING ITS TOTAL LENGTH REMARK 245 TO 77 NUCLEOTIDES. 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 K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 6230.00 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: A, B, C, D 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 MET A -1 REMARK 465 VAL A 0 REMARK 465 PRO A 1 REMARK 465 ILE A 2 REMARK 465 SER A 134 REMARK 465 ILE A 135 REMARK 465 ASN A 136 REMARK 465 ASN A 137 REMARK 465 GLU A 138 REMARK 465 THR A 139 REMARK 465 ILE A 559 REMARK 465 LEU A 560 REMARK 465 MET B -1 REMARK 465 VAL B 0 REMARK 465 PRO B 1 REMARK 465 ILE B 2 REMARK 465 SER B 3 REMARK 465 ASP B 218 REMARK 465 LYS B 219 REMARK 465 LYS B 220 REMARK 465 HIS B 221 REMARK 465 GLN B 222 REMARK 465 LYS B 223 REMARK 465 GLU B 224 REMARK 465 PRO B 225 REMARK 465 PRO B 226 REMARK 465 PHE B 227 REMARK 465 LEU B 228 REMARK 465 TRP B 229 REMARK 465 MET B 230 REMARK 465 ARG B 356 REMARK 465 MET B 357 REMARK 465 ARG B 358 REMARK 465 GLY B 359 REMARK 465 ALA B 360 REMARK 465 HIS B 361 REMARK 465 THR B 362 REMARK 465 LEU B 429 REMARK 465 GLU B 430 REMARK 465 LYS B 431 REMARK 465 GLU B 432 REMARK 465 PRO B 433 REMARK 465 ILE B 434 REMARK 465 VAL B 435 REMARK 465 GLY B 436 REMARK 465 ALA B 437 REMARK 465 GLU B 438 REMARK 465 THR B 439 REMARK 465 PHE B 440 REMARK 465 G C 123 REMARK 465 A C 124 REMARK 465 C C 125 REMARK 465 U C 126 REMARK 465 C C 127 REMARK 465 U C 128 REMARK 465 G C 129 REMARK 465 G C 130 REMARK 465 U C 131 REMARK 465 A C 132 REMARK 465 A C 133 REMARK 465 C C 134 REMARK 465 U C 135 REMARK 465 A C 136 REMARK 465 G C 137 REMARK 465 A C 138 REMARK 465 G C 139 REMARK 465 A C 140 REMARK 465 U C 141 REMARK 465 C C 142 REMARK 465 C C 143 REMARK 465 C C 144 REMARK 465 U C 145 REMARK 465 C C 146 REMARK 465 A C 147 REMARK 465 G C 148 REMARK 465 A C 149 REMARK 465 C C 150 REMARK 465 C C 151 REMARK 465 C C 152 REMARK 465 U C 153 REMARK 465 U C 154 REMARK 465 U C 155 REMARK 465 U C 156 REMARK 465 A C 157 REMARK 465 G C 158 REMARK 465 U C 159 REMARK 465 C C 160 REMARK 465 A C 161 REMARK 465 G C 162 REMARK 465 U C 163 REMARK 465 G C 164 REMARK 465 U C 165 REMARK 465 G C 166 REMARK 465 G C 167 REMARK 465 A C 168 REMARK 465 A C 169 REMARK 465 A C 170 REMARK 465 A C 171 REMARK 465 U C 172 REMARK 465 C C 173 REMARK 465 U C 174 REMARK 465 C C 175 REMARK 465 U C 176 REMARK 465 A C 177 REMARK 465 G C 178 REMARK 465 C C 179 REMARK 465 A C 180 REMARK 465 A C 204 REMARK 465 A C 205 REMARK 465 G C 206 REMARK 465 C C 207 REMARK 465 G C 208 REMARK 465 A C 209 REMARK 465 A C 210 REMARK 465 A C 211 REMARK 465 G C 212 REMARK 465 U C 213 REMARK 465 A C 214 REMARK 465 A C 215 REMARK 465 A C 216 REMARK 465 G C 217 REMARK 465 C C 218 REMARK 465 C C 219 REMARK 465 A C 220 REMARK 465 G C 221 REMARK 465 A C 222 REMARK 465 G C 223 REMARK 465 G D 5 REMARK 465 G D 6 REMARK 465 A D 7 REMARK 465 U D 8 REMARK 465 A D 9 REMARK 465 G D 10 REMARK 465 C D 11 REMARK 465 U D 12 REMARK 465 C D 13 REMARK 465 A D 14 REMARK 465 G D 15 REMARK 465 U D 16 REMARK 465 C D 17 REMARK 465 G D 18 REMARK 465 G D 19 REMARK 465 U D 20 REMARK 465 A D 21 REMARK 465 G D 22 REMARK 465 A D 23 REMARK 465 G D 24 REMARK 465 C D 25 REMARK 465 A D 26 REMARK 465 U D 27 REMARK 465 C D 28 REMARK 465 A D 29 REMARK 465 G D 30 REMARK 465 A D 31 REMARK 465 C D 32 REMARK 465 U D 33 REMARK 465 U D 34 REMARK 465 U D 35 REMARK 465 U D 36 REMARK 465 A D 37 REMARK 465 A D 38 REMARK 465 U D 39 REMARK 465 C D 40 REMARK 465 U D 41 REMARK 465 G D 42 REMARK 465 A D 43 REMARK 465 G D 44 REMARK 465 G D 45 REMARK 465 G D 46 REMARK 465 U D 47 REMARK 465 C D 48 REMARK 465 C D 49 REMARK 465 A D 50 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 GLU A 6 CG CD OE1 OE2 REMARK 470 TRP A 24 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 24 CZ3 CH2 REMARK 470 GLU A 29 CG CD OE1 OE2 REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 VAL A 35 CG1 CG2 REMARK 470 GLU A 36 CG CD OE1 OE2 REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 470 MET A 41 CG SD CE REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 SER A 48 OG REMARK 470 ILE A 50 CG1 CG2 CD1 REMARK 470 GLU A 53 CG CD OE1 OE2 REMARK 470 ASN A 57 CG OD1 ND2 REMARK 470 PHE A 61 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LYS A 65 CG CD CE NZ REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 ASP A 67 CG OD1 OD2 REMARK 470 SER A 68 OG REMARK 470 THR A 69 OG1 CG2 REMARK 470 TRP A 71 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 71 CZ3 CH2 REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 THR A 84 OG1 CG2 REMARK 470 VAL A 90 CG1 CG2 REMARK 470 LYS A 103 CG CD CE NZ REMARK 470 ASP A 110 CG OD1 OD2 REMARK 470 ASP A 113 CG OD1 OD2 REMARK 470 GLU A 122 CG CD OE1 OE2 REMARK 470 ASP A 123 CG OD1 OD2 REMARK 470 LEU A 149 CG CD1 CD2 REMARK 470 GLU A 169 CG CD OE1 OE2 REMARK 470 LYS A 173 CG CD CE NZ REMARK 470 ASP A 192 CG OD1 OD2 REMARK 470 GLN A 197 CG CD OE1 NE2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 GLU A 204 CG CD OE1 OE2 REMARK 470 GLN A 222 CG CD OE1 NE2 REMARK 470 LYS A 223 CG CD CE NZ REMARK 470 GLU A 224 CG CD OE1 OE2 REMARK 470 GLU A 233 CG CD OE1 OE2 REMARK 470 ASP A 237 CG OD1 OD2 REMARK 470 GLU A 248 CG CD OE1 OE2 REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 ASP A 250 CG OD1 OD2 REMARK 470 THR A 286 OG1 CG2 REMARK 470 LEU A 295 CG CD1 CD2 REMARK 470 GLU A 302 CG CD OE1 OE2 REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 GLU A 312 CG CD OE1 OE2 REMARK 470 ASP A 324 CG OD1 OD2 REMARK 470 PHE A 346 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 356 CG CD NE CZ NH1 NH2 REMARK 470 MET A 357 CG SD CE REMARK 470 GLU A 404 CG CD OE1 OE2 REMARK 470 GLU A 413 CG CD OE1 OE2 REMARK 470 GLU A 432 CG CD OE1 OE2 REMARK 470 LYS A 454 CG CD CE NZ REMARK 470 ARG A 463 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 484 CG CD1 CD2 REMARK 470 ASP A 488 CG OD1 OD2 REMARK 470 ASP A 498 CG OD1 OD2 REMARK 470 GLU A 516 CG CD OE1 OE2 REMARK 470 LYS A 528 CG CD CE NZ REMARK 470 ARG A 557 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 13 CG CD CE NZ REMARK 470 MET B 16 CG SD CE REMARK 470 MET B 41 CG SD CE REMARK 470 GLU B 44 CG CD OE1 OE2 REMARK 470 LYS B 46 CG CD CE NZ REMARK 470 GLU B 53 CG CD OE1 OE2 REMARK 470 ASP B 76 CG OD1 OD2 REMARK 470 GLN B 91 CG CD OE1 NE2 REMARK 470 LEU B 92 CG CD1 CD2 REMARK 470 LYS B 102 CG CD CE NZ REMARK 470 LYS B 103 CG CD CE NZ REMARK 470 LYS B 104 CG CD CE NZ REMARK 470 GLU B 122 CG CD OE1 OE2 REMARK 470 MET B 164 CG SD CE REMARK 470 LYS B 166 CG CD CE NZ REMARK 470 GLU B 169 CG CD OE1 OE2 REMARK 470 LYS B 173 CG CD CE NZ REMARK 470 VAL B 179 CG1 CG2 REMARK 470 ASP B 185 CG OD1 OD2 REMARK 470 ASP B 186 CG OD1 OD2 REMARK 470 SER B 191 OG REMARK 470 LEU B 193 CG CD1 CD2 REMARK 470 GLU B 203 CG CD OE1 OE2 REMARK 470 GLU B 204 CG CD OE1 OE2 REMARK 470 ARG B 211 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 237 CG OD1 OD2 REMARK 470 GLU B 248 CG CD OE1 OE2 REMARK 470 LYS B 249 CG CD CE NZ REMARK 470 ASP B 250 CG OD1 OD2 REMARK 470 LYS B 281 CG CD CE NZ REMARK 470 ARG B 284 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 287 CG CD CE NZ REMARK 470 GLU B 291 CG CD OE1 OE2 REMARK 470 GLU B 297 CG CD OE1 OE2 REMARK 470 GLU B 302 CG CD OE1 OE2 REMARK 470 GLU B 305 CG CD OE1 OE2 REMARK 470 GLU B 308 CG CD OE1 OE2 REMARK 470 LYS B 311 CG CD CE NZ REMARK 470 HIS B 315 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 323 CG CD CE NZ REMARK 470 GLU B 344 CG CD OE1 OE2 REMARK 470 LYS B 347 CG CD CE NZ REMARK 470 GLU B 396 CG CD OE1 OE2 REMARK 470 GLN B 428 CG CD OE1 NE2 REMARK 470 G C 181 P OP1 OP2 O5' REMARK 470 G D 1 O5' REMARK 470 G D 51 P OP1 OP2 O5' REMARK 470 DC D 77 O3' 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 LEU A 26 -169.79 -129.08 REMARK 500 LYS A 65 -167.79 -78.29 REMARK 500 SER A 68 154.48 -48.32 REMARK 500 THR A 69 -4.37 77.39 REMARK 500 THR A 107 -168.79 -162.63 REMARK 500 TYR A 183 -159.21 -150.25 REMARK 500 ASP A 185 18.45 -141.65 REMARK 500 THR A 216 143.78 -170.20 REMARK 500 LYS A 219 30.63 -91.52 REMARK 500 LYS A 220 -166.98 -77.63 REMARK 500 PRO A 225 170.53 -51.69 REMARK 500 GLU A 248 32.47 -96.99 REMARK 500 PRO A 294 -179.59 -63.63 REMARK 500 LEU A 295 50.09 -115.75 REMARK 500 PHE A 346 -0.11 74.50 REMARK 500 ALA A 355 27.31 -140.39 REMARK 500 ILE A 382 -60.07 -92.74 REMARK 500 ASN A 418 58.46 -97.30 REMARK 500 LYS A 465 148.50 -172.88 REMARK 500 LEU A 491 -61.07 -99.68 REMARK 500 GLU A 514 -61.77 -90.01 REMARK 500 ILE A 556 -63.31 -121.86 REMARK 500 PHE B 77 32.68 -93.90 REMARK 500 ALA B 98 27.32 -140.47 REMARK 500 LYS B 154 35.31 -98.15 REMARK 500 ASN B 175 79.83 -112.10 REMARK 500 ASP B 177 6.19 -64.34 REMARK 500 MET B 184 -159.04 -147.55 REMARK 500 THR B 351 -168.61 -126.81 REMARK 500 PRO B 421 44.60 -85.05 REMARK 500 LEU B 422 -32.12 -130.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6B19 RELATED DB: PDB REMARK 900 RELATED ID: EMD-21582 RELATED DB: EMDB REMARK 900 +1 EXTENDED HIV-1 REVERSE TRANSCRIPTASE INITIATION COMPLEX CORE REMARK 900 (PRE-TRANSLOCATION STATE) DBREF 6WAZ A 1 560 UNP P03366 POL_HV1B1 600 1159 DBREF 6WAZ B 1 440 UNP P03366 POL_HV1B1 600 1039 DBREF 6WAZ C 123 223 GB 60651827 AY835748.1 577 677 DBREF 6WAZ D 1 77 PDB 6WAZ 6WAZ 1 77 SEQADV 6WAZ MET A -1 UNP P03366 EXPRESSION TAG SEQADV 6WAZ VAL A 0 UNP P03366 EXPRESSION TAG SEQADV 6WAZ CYS A 258 UNP P03366 GLN 857 ENGINEERED MUTATION SEQADV 6WAZ SER A 280 UNP P03366 CYS 879 CONFLICT SEQADV 6WAZ GLN A 478 UNP P03366 GLU 1077 ENGINEERED MUTATION SEQADV 6WAZ MET B -1 UNP P03366 EXPRESSION TAG SEQADV 6WAZ VAL B 0 UNP P03366 EXPRESSION TAG SEQADV 6WAZ SER B 280 UNP P03366 CYS 879 ENGINEERED MUTATION SEQRES 1 A 562 MET VAL PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS SEQRES 2 A 562 LEU LYS PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP SEQRES 3 A 562 PRO LEU THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE SEQRES 4 A 562 CYS THR GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE SEQRES 5 A 562 GLY PRO GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE SEQRES 6 A 562 LYS LYS LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP SEQRES 7 A 562 PHE ARG GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU SEQRES 8 A 562 VAL GLN LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS SEQRES 9 A 562 LYS LYS SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR SEQRES 10 A 562 PHE SER VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR SEQRES 11 A 562 ALA PHE THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY SEQRES 12 A 562 ILE ARG TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS SEQRES 13 A 562 GLY SER PRO ALA ILE PHE GLN SER SER MET THR LYS ILE SEQRES 14 A 562 LEU GLU PRO PHE LYS LYS GLN ASN PRO ASP ILE VAL ILE SEQRES 15 A 562 TYR GLN TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU SEQRES 16 A 562 GLU ILE GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG SEQRES 17 A 562 GLN HIS LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS SEQRES 18 A 562 LYS HIS GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR SEQRES 19 A 562 GLU LEU HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL SEQRES 20 A 562 LEU PRO GLU LYS ASP SER TRP THR VAL ASN ASP ILE CYS SEQRES 21 A 562 LYS LEU VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR SEQRES 22 A 562 PRO GLY ILE LYS VAL ARG GLN LEU SER LYS LEU LEU ARG SEQRES 23 A 562 GLY THR LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU SEQRES 24 A 562 GLU ALA GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU SEQRES 25 A 562 LYS GLU PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS SEQRES 26 A 562 ASP LEU ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN SEQRES 27 A 562 TRP THR TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU SEQRES 28 A 562 LYS THR GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR SEQRES 29 A 562 ASN ASP VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE SEQRES 30 A 562 THR THR GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS SEQRES 31 A 562 PHE LYS LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP SEQRES 32 A 562 TRP THR GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP SEQRES 33 A 562 GLU PHE VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR SEQRES 34 A 562 GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE SEQRES 35 A 562 TYR VAL ASP GLY ALA ALA ASN ARG GLU THR LYS LEU GLY SEQRES 36 A 562 LYS ALA GLY TYR VAL THR ASN LYS GLY ARG GLN LYS VAL SEQRES 37 A 562 VAL PRO LEU THR ASN THR THR ASN GLN LYS THR GLN LEU SEQRES 38 A 562 GLN ALA ILE TYR LEU ALA LEU GLN ASP SER GLY LEU GLU SEQRES 39 A 562 VAL ASN ILE VAL THR ASP SER GLN TYR ALA LEU GLY ILE SEQRES 40 A 562 ILE GLN ALA GLN PRO ASP LYS SER GLU SER GLU LEU VAL SEQRES 41 A 562 ASN GLN ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS VAL SEQRES 42 A 562 TYR LEU ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY GLY SEQRES 43 A 562 ASN GLU GLN VAL ASP LYS LEU VAL SER ALA GLY ILE ARG SEQRES 44 A 562 LYS ILE LEU SEQRES 1 B 442 MET VAL PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS SEQRES 2 B 442 LEU LYS PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP SEQRES 3 B 442 PRO LEU THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE SEQRES 4 B 442 CYS THR GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE SEQRES 5 B 442 GLY PRO GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE SEQRES 6 B 442 LYS LYS LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP SEQRES 7 B 442 PHE ARG GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU SEQRES 8 B 442 VAL GLN LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS SEQRES 9 B 442 LYS LYS SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR SEQRES 10 B 442 PHE SER VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR SEQRES 11 B 442 ALA PHE THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY SEQRES 12 B 442 ILE ARG TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS SEQRES 13 B 442 GLY SER PRO ALA ILE PHE GLN SER SER MET THR LYS ILE SEQRES 14 B 442 LEU GLU PRO PHE LYS LYS GLN ASN PRO ASP ILE VAL ILE SEQRES 15 B 442 TYR GLN TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU SEQRES 16 B 442 GLU ILE GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG SEQRES 17 B 442 GLN HIS LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS SEQRES 18 B 442 LYS HIS GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR SEQRES 19 B 442 GLU LEU HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL SEQRES 20 B 442 LEU PRO GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN SEQRES 21 B 442 LYS LEU VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR SEQRES 22 B 442 PRO GLY ILE LYS VAL ARG GLN LEU SER LYS LEU LEU ARG SEQRES 23 B 442 GLY THR LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU SEQRES 24 B 442 GLU ALA GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU SEQRES 25 B 442 LYS GLU PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS SEQRES 26 B 442 ASP LEU ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN SEQRES 27 B 442 TRP THR TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU SEQRES 28 B 442 LYS THR GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR SEQRES 29 B 442 ASN ASP VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE SEQRES 30 B 442 THR THR GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS SEQRES 31 B 442 PHE LYS LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP SEQRES 32 B 442 TRP THR GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP SEQRES 33 B 442 GLU PHE VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR SEQRES 34 B 442 GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE SEQRES 1 C 101 G A C U C U G G U A A C U SEQRES 2 C 101 A G A G A U C C C U C A G SEQRES 3 C 101 A C C C U U U U A G U C A SEQRES 4 C 101 G U G U G G A A A A U C U SEQRES 5 C 101 C U A G C A G U G G C G C SEQRES 6 C 101 C C G A A C A G G G A C U SEQRES 7 C 101 U G A A A G C G A A A G U SEQRES 8 C 101 A A A G C C A G A G SEQRES 1 D 77 G C C C G G A U A G C U C SEQRES 2 D 77 A G U C G G U A G A G C A SEQRES 3 D 77 U C A G A C U U U U A A U SEQRES 4 D 77 C U G A G G G U C C A G G SEQRES 5 D 77 G U U C A A G U C C C U G SEQRES 6 D 77 U U C G G DG C G C C A DC HELIX 1 AA1 GLU A 28 GLU A 44 1 17 HELIX 2 AA2 HIS A 96 LEU A 100 5 5 HELIX 3 AA3 ALA A 114 VAL A 118 5 5 HELIX 4 AA4 PHE A 124 THR A 128 5 5 HELIX 5 AA5 GLY A 155 ASN A 175 1 21 HELIX 6 AA6 GLU A 194 ARG A 211 1 18 HELIX 7 AA7 THR A 253 GLN A 269 1 17 HELIX 8 AA8 SER A 280 ARG A 284 5 5 HELIX 9 AA9 THR A 296 GLU A 312 1 17 HELIX 10 AB1 ASN A 363 TRP A 383 1 21 HELIX 11 AB2 GLN A 394 GLU A 404 1 11 HELIX 12 AB3 THR A 473 SER A 489 1 17 HELIX 13 AB4 SER A 499 GLN A 507 1 9 HELIX 14 AB5 SER A 515 ILE A 526 1 12 HELIX 15 AB6 GLY A 543 ALA A 554 1 12 HELIX 16 AB7 THR B 27 GLU B 44 1 18 HELIX 17 AB8 PHE B 77 VAL B 90 1 14 HELIX 18 AB9 GLY B 99 LYS B 103 5 5 HELIX 19 AC1 ASP B 113 VAL B 118 5 6 HELIX 20 AC2 PHE B 124 TYR B 127 5 4 HELIX 21 AC3 SER B 134 GLU B 138 5 5 HELIX 22 AC4 GLY B 155 ASN B 175 1 21 HELIX 23 AC5 GLU B 194 ARG B 211 1 18 HELIX 24 AC6 THR B 253 SER B 268 1 16 HELIX 25 AC7 VAL B 276 LEU B 282 1 7 HELIX 26 AC8 THR B 296 LYS B 311 1 16 HELIX 27 AC9 ASP B 364 GLY B 384 1 21 HELIX 28 AD1 GLN B 394 TRP B 406 1 13 HELIX 29 AD2 LEU B 422 TYR B 427 5 6 SHEET 1 AA1 3 ILE A 47 SER A 48 0 SHEET 2 AA1 3 ILE A 142 TYR A 146 -1 O GLN A 145 N SER A 48 SHEET 3 AA1 3 PHE A 130 ILE A 132 -1 N PHE A 130 O TYR A 144 SHEET 1 AA2 3 VAL A 106 VAL A 108 0 SHEET 2 AA2 3 LEU A 187 GLY A 190 -1 O VAL A 189 N THR A 107 SHEET 3 AA2 3 VAL A 179 GLN A 182 -1 N TYR A 181 O TYR A 188 SHEET 1 AA3 2 TYR A 232 LEU A 234 0 SHEET 2 AA3 2 TRP A 239 VAL A 241 -1 O THR A 240 N GLU A 233 SHEET 1 AA4 3 ILE A 326 GLU A 328 0 SHEET 2 AA4 3 GLN A 340 GLU A 344 -1 O TYR A 342 N ILE A 326 SHEET 3 AA4 3 LYS A 347 THR A 351 -1 O LEU A 349 N ILE A 341 SHEET 1 AA5 5 LYS A 465 PRO A 468 0 SHEET 2 AA5 5 LYS A 454 VAL A 458 -1 N ALA A 455 O VAL A 467 SHEET 3 AA5 5 THR A 439 ALA A 445 -1 N ALA A 445 O LYS A 454 SHEET 4 AA5 5 VAL A 493 VAL A 496 1 O VAL A 496 N PHE A 440 SHEET 5 AA5 5 VAL A 531 TYR A 532 1 O TYR A 532 N VAL A 493 SHEET 1 AA6 3 ILE B 47 SER B 48 0 SHEET 2 AA6 3 ILE B 142 TYR B 146 -1 O GLN B 145 N SER B 48 SHEET 3 AA6 3 ALA B 129 ILE B 132 -1 N ILE B 132 O ILE B 142 SHEET 1 AA7 2 VAL B 60 ALA B 62 0 SHEET 2 AA7 2 LYS B 73 VAL B 75 -1 O LEU B 74 N PHE B 61 SHEET 1 AA8 3 LEU B 109 ASP B 110 0 SHEET 2 AA8 3 ASP B 186 SER B 191 -1 O LEU B 187 N LEU B 109 SHEET 3 AA8 3 ILE B 180 TYR B 181 -1 N TYR B 181 O TYR B 188 SHEET 1 AA9 4 LEU B 109 ASP B 110 0 SHEET 2 AA9 4 ASP B 186 SER B 191 -1 O LEU B 187 N LEU B 109 SHEET 3 AA9 4 SER B 105 THR B 107 -1 N SER B 105 O SER B 191 SHEET 4 AA9 4 GLU B 233 LEU B 234 -1 O LEU B 234 N VAL B 106 SHEET 1 AB1 4 ASN B 348 THR B 351 0 SHEET 2 AB1 4 GLN B 340 TYR B 342 -1 N ILE B 341 O LEU B 349 SHEET 3 AB1 4 ILE B 326 GLU B 328 -1 N GLU B 328 O GLN B 340 SHEET 4 AB1 4 LYS B 388 LYS B 390 1 O LYS B 388 N ALA B 327 SHEET 1 AB2 2 LYS B 331 GLY B 333 0 SHEET 2 AB2 2 GLN B 336 TRP B 337 -1 O GLN B 336 N GLY B 333 CISPEP 1 PRO A 225 PRO A 226 0 14.01 CISPEP 2 PRO A 420 PRO A 421 0 3.57 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