HEADER VIRAL PROTEIN 31-AUG-23 8U1D TITLE CRYO-EM STRUCTURE OF VACCINE-ELICITED CD4 BINDING SITE ANTIBODY DH1285 TITLE 2 BOUND TO HIV-1 CH505TFCHIM.6R.SOSIP.664V4.1 ENV LOCAL REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP120; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CH505M5CHIMER.6R.SOSIP.664V4.1; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DH1285 HEAVY CHAIN; COMPND 8 CHAIN: I; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DH1285 LIGHT CHAIN; COMPND 12 CHAIN: J; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 9 ORGANISM_COMMON: RHESUS MONKEY; SOURCE 10 ORGANISM_TAXID: 9544; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 16 ORGANISM_COMMON: RHESUS MONKEY; SOURCE 17 ORGANISM_TAXID: 9544; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS HIV-1 VACCINE INDUCED NEUTRALIZING ANTIBODY, CD4 BINDING SITE KEYWDS 2 ANTIBODY, GP120, DH1285, IGG, RHESUS MACAQUES, KEYWDS 3 CH505M5CHIMER.6R.SOSIP.664V4.1 ENV, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR B.THAKUR,V.D.STALLS,P.ACHARYA REVDAT 2 17-JUL-24 8U1D 1 JRNL REVDAT 1 03-JAN-24 8U1D 0 JRNL AUTH K.O.SAUNDERS,J.COUNTS,B.THAKUR,V.STALLS,R.EDWARDS,K.MANNE, JRNL AUTH 2 X.LU,K.MANSOURI,Y.CHEN,R.PARKS,M.BARR,L.SUTHERLAND,J.BAL, JRNL AUTH 3 N.HAVILL,H.CHEN,E.MACHIELE,N.JAMIESON,B.HORA,M.KOPP, JRNL AUTH 4 K.JANOWSKA,K.ANASTI,C.JIANG,E.VAN ITALLIE,S.VENKATAYOGI, JRNL AUTH 5 A.EATON,R.HENDERSON,C.BARBOSA,S.M.ALAM,S.SANTRA,D.WEISSMAN, JRNL AUTH 6 M.A.MOODY,D.W.CAIN,Y.K.TAM,M.LEWIS,W.B.WILLIAMS,K.WIEHE, JRNL AUTH 7 D.C.MONTEFIORI,P.ACHARYA,B.F.HAYNES JRNL TITL VACCINE INDUCTION OF CD4-MIMICKING HIV-1 BROADLY JRNL TITL 2 NEUTRALIZING ANTIBODY PRECURSORS IN MACAQUES. JRNL REF CELL V. 187 79 2024 JRNL REFN ISSN 1097-4172 JRNL PMID 38181743 JRNL DOI 10.1016/J.CELL.2023.12.002 REMARK 2 REMARK 2 RESOLUTION. 4.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, 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 : 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) : 4.250 REMARK 3 NUMBER OF PARTICLES : 146444 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 8U1D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000277066. 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 : THE COMPLEX OF VACCINE ELICITED REMARK 245 CD4 BINDING SITE NEUTRALIZING REMARK 245 ANTIBODY DH1285 FAB WITH REMARK 245 CH505M5CHIMER.6R.SOSIP.664V4.1 E REMARK 245 NV; ENVELOPE GLYCOPROTEIN GP120; REMARK 245 DH1285 HEAVY CHAIN, DH1285 REMARK 245 LIGHT CHAIN 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 : ONE OF THE GP120 PROTOMER BOUND REMARK 245 TO DH1285 LOCALLY REFINED TO GET PRECISE INFORMATION ABOUT THE REMARK 245 INTERACTING RESIDUES. 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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) : 5910.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, I, J 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 7 REMARK 465 PRO A 8 REMARK 465 MET A 9 REMARK 465 GLY A 10 REMARK 465 SER A 11 REMARK 465 LEU A 12 REMARK 465 GLN A 13 REMARK 465 PRO A 14 REMARK 465 LEU A 15 REMARK 465 ALA A 16 REMARK 465 THR A 17 REMARK 465 LEU A 18 REMARK 465 TYR A 19 REMARK 465 LEU A 20 REMARK 465 LEU A 21 REMARK 465 GLY A 22 REMARK 465 MET A 23 REMARK 465 LEU A 24 REMARK 465 VAL A 25 REMARK 465 ALA A 26 REMARK 465 SER A 27 REMARK 465 VAL A 28 REMARK 465 LEU A 29 REMARK 465 ALA A 30 REMARK 465 ALA A 31 REMARK 465 GLU A 32 REMARK 465 ASN A 33 REMARK 465 LEU A 34 REMARK 465 TRP A 35 REMARK 465 VAL A 36 REMARK 465 THR A 37 REMARK 465 VAL A 38 REMARK 465 TYR A 39 REMARK 465 TYR A 40 REMARK 465 GLY A 41 REMARK 465 VAL A 42 REMARK 465 PRO A 43 REMARK 465 VAL A 44 REMARK 465 TRP A 45 REMARK 465 SER A 399 REMARK 465 THR A 400 REMARK 465 ASP A 401 REMARK 465 MET A 402 REMARK 465 ALA A 403 REMARK 465 ASN A 404 REMARK 465 SER A 405 REMARK 465 THR A 406 REMARK 465 GLU A 407 REMARK 465 THR A 408 REMARK 465 LYS A 488 REMARK 465 ILE A 489 REMARK 465 GLU A 490 REMARK 465 PRO A 491 REMARK 465 LEU A 492 REMARK 465 GLY A 493 REMARK 465 VAL A 494 REMARK 465 ALA A 495 REMARK 465 PRO A 496 REMARK 465 THR A 497 REMARK 465 ARG A 498 REMARK 465 CYS A 499 REMARK 465 LYS A 500 REMARK 465 ARG A 501 REMARK 465 ARG A 502 REMARK 465 VAL A 503 REMARK 465 VAL A 504 REMARK 465 GLY A 505 REMARK 465 ARG A 506 REMARK 465 ARG A 507 REMARK 465 ARG A 508 REMARK 465 ARG A 509 REMARK 465 ARG A 510 REMARK 465 ARG A 511 REMARK 465 ALA A 512 REMARK 465 VAL A 513 REMARK 465 GLY A 514 REMARK 465 ILE A 515 REMARK 465 GLY A 516 REMARK 465 ALA A 517 REMARK 465 VAL A 518 REMARK 465 PHE A 519 REMARK 465 LEU A 520 REMARK 465 GLY A 521 REMARK 465 PHE A 522 REMARK 465 LEU A 523 REMARK 465 GLY A 524 REMARK 465 ALA A 525 REMARK 465 ALA A 526 REMARK 465 GLY A 527 REMARK 465 SER A 528 REMARK 465 THR A 529 REMARK 465 MET A 530 REMARK 465 GLY A 531 REMARK 465 ALA A 532 REMARK 465 ALA A 533 REMARK 465 SER A 534 REMARK 465 MET A 535 REMARK 465 THR A 536 REMARK 465 LEU A 537 REMARK 465 THR A 538 REMARK 465 VAL A 539 REMARK 465 GLN A 540 REMARK 465 ALA A 541 REMARK 465 ARG A 542 REMARK 465 ASN A 543 REMARK 465 LEU A 544 REMARK 465 LEU A 545 REMARK 465 SER A 546 REMARK 465 GLY A 547 REMARK 465 ILE A 548 REMARK 465 VAL A 549 REMARK 465 GLN A 550 REMARK 465 GLN A 551 REMARK 465 GLN A 552 REMARK 465 SER A 553 REMARK 465 ASN A 554 REMARK 465 LEU A 555 REMARK 465 LEU A 556 REMARK 465 ARG A 557 REMARK 465 ALA A 558 REMARK 465 PRO A 559 REMARK 465 GLU A 560 REMARK 465 ALA A 561 REMARK 465 GLN A 562 REMARK 465 GLN A 563 REMARK 465 HIS A 564 REMARK 465 LEU A 565 REMARK 465 LEU A 566 REMARK 465 LYS A 567 REMARK 465 LEU A 568 REMARK 465 THR A 569 REMARK 465 VAL A 570 REMARK 465 TRP A 571 REMARK 465 GLY A 572 REMARK 465 ILE A 573 REMARK 465 LYS A 574 REMARK 465 GLN A 575 REMARK 465 LEU A 576 REMARK 465 GLN A 577 REMARK 465 ALA A 578 REMARK 465 ARG A 579 REMARK 465 VAL A 580 REMARK 465 LEU A 581 REMARK 465 ALA A 582 REMARK 465 VAL A 583 REMARK 465 GLU A 584 REMARK 465 ARG A 585 REMARK 465 TYR A 586 REMARK 465 LEU A 587 REMARK 465 ARG A 588 REMARK 465 ASP A 589 REMARK 465 GLN A 590 REMARK 465 GLN A 591 REMARK 465 LEU A 592 REMARK 465 LEU A 593 REMARK 465 GLY A 594 REMARK 465 ILE A 595 REMARK 465 TRP A 596 REMARK 465 GLY A 597 REMARK 465 CYS A 598 REMARK 465 SER A 599 REMARK 465 GLY A 600 REMARK 465 LYS A 601 REMARK 465 LEU A 602 REMARK 465 ILE A 603 REMARK 465 CYS A 604 REMARK 465 CYS A 605 REMARK 465 THR A 606 REMARK 465 ASN A 607 REMARK 465 VAL A 608 REMARK 465 PRO A 609 REMARK 465 TRP A 610 REMARK 465 ASN A 611 REMARK 465 SER A 612 REMARK 465 SER A 613 REMARK 465 TRP A 614 REMARK 465 SER A 615 REMARK 465 ASN A 616 REMARK 465 ARG A 617 REMARK 465 ASN A 618 REMARK 465 LEU A 619 REMARK 465 SER A 620 REMARK 465 GLU A 621 REMARK 465 ILE A 622 REMARK 465 TRP A 623 REMARK 465 ASP A 624 REMARK 465 ASN A 625 REMARK 465 MET A 626 REMARK 465 THR A 627 REMARK 465 TRP A 628 REMARK 465 LEU A 629 REMARK 465 GLN A 630 REMARK 465 TRP A 631 REMARK 465 ASP A 632 REMARK 465 LYS A 633 REMARK 465 GLU A 634 REMARK 465 ILE A 635 REMARK 465 SER A 636 REMARK 465 ASN A 637 REMARK 465 TYR A 638 REMARK 465 THR A 639 REMARK 465 GLN A 640 REMARK 465 ILE A 641 REMARK 465 ILE A 642 REMARK 465 TYR A 643 REMARK 465 GLY A 644 REMARK 465 LEU A 645 REMARK 465 LEU A 646 REMARK 465 GLU A 647 REMARK 465 GLU A 648 REMARK 465 SER A 649 REMARK 465 GLN A 650 REMARK 465 ASN A 651 REMARK 465 GLN A 652 REMARK 465 GLN A 653 REMARK 465 GLU A 654 REMARK 465 LYS A 655 REMARK 465 ASN A 656 REMARK 465 GLU A 657 REMARK 465 GLN A 658 REMARK 465 ASP A 659 REMARK 465 LEU A 660 REMARK 465 LEU A 661 REMARK 465 ALA A 662 REMARK 465 LEU A 663 REMARK 465 ASP A 664 REMARK 465 MET I -18 REMARK 465 GLY I -17 REMARK 465 TRP I -16 REMARK 465 SER I -15 REMARK 465 CYS I -14 REMARK 465 ILE I -13 REMARK 465 ILE I -12 REMARK 465 LEU I -11 REMARK 465 PHE I -10 REMARK 465 LEU I -9 REMARK 465 VAL I -8 REMARK 465 ALA I -7 REMARK 465 THR I -6 REMARK 465 ALA I -5 REMARK 465 THR I -4 REMARK 465 GLY I -3 REMARK 465 VAL I -2 REMARK 465 HIS I -1 REMARK 465 ALA I 0 REMARK 465 ALA I 114 REMARK 465 SER I 115 REMARK 465 THR I 116 REMARK 465 LYS I 117 REMARK 465 GLY I 118 REMARK 465 PRO I 119 REMARK 465 SER I 120 REMARK 465 VAL I 121 REMARK 465 PHE I 122 REMARK 465 PRO I 123 REMARK 465 LEU I 124 REMARK 465 ALA I 125 REMARK 465 PRO I 126 REMARK 465 SER I 127 REMARK 465 SER I 128 REMARK 465 ARG I 129 REMARK 465 SER I 130 REMARK 465 THR I 131 REMARK 465 SER I 132 REMARK 465 GLU I 133 REMARK 465 SER I 134 REMARK 465 THR I 135 REMARK 465 ALA I 136 REMARK 465 ALA I 137 REMARK 465 LEU I 138 REMARK 465 GLY I 139 REMARK 465 CYS I 140 REMARK 465 LEU I 141 REMARK 465 VAL I 142 REMARK 465 LYS I 143 REMARK 465 ASP I 144 REMARK 465 TYR I 145 REMARK 465 PHE I 146 REMARK 465 PRO I 147 REMARK 465 GLU I 148 REMARK 465 PRO I 149 REMARK 465 VAL I 150 REMARK 465 THR I 151 REMARK 465 VAL I 152 REMARK 465 SER I 153 REMARK 465 TRP I 154 REMARK 465 ASN I 155 REMARK 465 SER I 156 REMARK 465 GLY I 157 REMARK 465 SER I 158 REMARK 465 LEU I 159 REMARK 465 THR I 160 REMARK 465 SER I 161 REMARK 465 GLY I 162 REMARK 465 VAL I 163 REMARK 465 HIS I 164 REMARK 465 THR I 165 REMARK 465 PHE I 166 REMARK 465 PRO I 167 REMARK 465 ALA I 168 REMARK 465 VAL I 169 REMARK 465 LEU I 170 REMARK 465 GLN I 171 REMARK 465 SER I 172 REMARK 465 SER I 173 REMARK 465 GLY I 174 REMARK 465 LEU I 175 REMARK 465 TYR I 176 REMARK 465 SER I 177 REMARK 465 LEU I 178 REMARK 465 SER I 179 REMARK 465 SER I 180 REMARK 465 VAL I 181 REMARK 465 VAL I 182 REMARK 465 THR I 183 REMARK 465 VAL I 184 REMARK 465 PRO I 185 REMARK 465 SER I 186 REMARK 465 SER I 187 REMARK 465 SER I 188 REMARK 465 LEU I 189 REMARK 465 GLY I 190 REMARK 465 THR I 191 REMARK 465 GLN I 192 REMARK 465 THR I 193 REMARK 465 TYR I 194 REMARK 465 VAL I 195 REMARK 465 CYS I 196 REMARK 465 ASN I 197 REMARK 465 VAL I 198 REMARK 465 ASN I 199 REMARK 465 HIS I 200 REMARK 465 LYS I 201 REMARK 465 PRO I 202 REMARK 465 SER I 203 REMARK 465 ASN I 204 REMARK 465 THR I 205 REMARK 465 LYS I 206 REMARK 465 VAL I 207 REMARK 465 ASP I 208 REMARK 465 LYS I 209 REMARK 465 ARG I 210 REMARK 465 VAL I 211 REMARK 465 GLU I 212 REMARK 465 ILE I 213 REMARK 465 LYS I 214 REMARK 465 THR I 215 REMARK 465 MET J -18 REMARK 465 GLY J -17 REMARK 465 TRP J -16 REMARK 465 SER J -15 REMARK 465 CYS J -14 REMARK 465 ILE J -13 REMARK 465 ILE J -12 REMARK 465 LEU J -11 REMARK 465 PHE J -10 REMARK 465 LEU J -9 REMARK 465 VAL J -8 REMARK 465 ALA J -7 REMARK 465 THR J -6 REMARK 465 ALA J -5 REMARK 465 THR J -4 REMARK 465 GLY J -3 REMARK 465 VAL J -2 REMARK 465 HIS J -1 REMARK 465 ALA J 0 REMARK 465 ARG J 108 REMARK 465 ALA J 109 REMARK 465 VAL J 110 REMARK 465 ALA J 111 REMARK 465 ALA J 112 REMARK 465 PRO J 113 REMARK 465 SER J 114 REMARK 465 VAL J 115 REMARK 465 PHE J 116 REMARK 465 ILE J 117 REMARK 465 PHE J 118 REMARK 465 PRO J 119 REMARK 465 PRO J 120 REMARK 465 SER J 121 REMARK 465 GLU J 122 REMARK 465 ASP J 123 REMARK 465 GLN J 124 REMARK 465 VAL J 125 REMARK 465 LYS J 126 REMARK 465 SER J 127 REMARK 465 GLY J 128 REMARK 465 THR J 129 REMARK 465 VAL J 130 REMARK 465 SER J 131 REMARK 465 VAL J 132 REMARK 465 VAL J 133 REMARK 465 CYS J 134 REMARK 465 LEU J 135 REMARK 465 LEU J 136 REMARK 465 ASN J 137 REMARK 465 ASN J 138 REMARK 465 PHE J 139 REMARK 465 TYR J 140 REMARK 465 PRO J 141 REMARK 465 ARG J 142 REMARK 465 GLU J 143 REMARK 465 ALA J 144 REMARK 465 SER J 145 REMARK 465 VAL J 146 REMARK 465 LYS J 147 REMARK 465 TRP J 148 REMARK 465 LYS J 149 REMARK 465 VAL J 150 REMARK 465 ASP J 151 REMARK 465 GLY J 152 REMARK 465 VAL J 153 REMARK 465 LEU J 154 REMARK 465 LYS J 155 REMARK 465 THR J 156 REMARK 465 GLY J 157 REMARK 465 ASN J 158 REMARK 465 SER J 159 REMARK 465 GLN J 160 REMARK 465 GLU J 161 REMARK 465 SER J 162 REMARK 465 VAL J 163 REMARK 465 THR J 164 REMARK 465 GLU J 165 REMARK 465 GLN J 166 REMARK 465 ASP J 167 REMARK 465 SER J 168 REMARK 465 LYS J 169 REMARK 465 ASP J 170 REMARK 465 ASN J 171 REMARK 465 THR J 172 REMARK 465 TYR J 173 REMARK 465 SER J 174 REMARK 465 LEU J 175 REMARK 465 SER J 176 REMARK 465 SER J 177 REMARK 465 THR J 178 REMARK 465 LEU J 179 REMARK 465 THR J 180 REMARK 465 LEU J 181 REMARK 465 SER J 182 REMARK 465 SER J 183 REMARK 465 THR J 184 REMARK 465 ASP J 185 REMARK 465 TYR J 186 REMARK 465 GLN J 187 REMARK 465 SER J 188 REMARK 465 HIS J 189 REMARK 465 ASN J 190 REMARK 465 VAL J 191 REMARK 465 TYR J 192 REMARK 465 ALA J 193 REMARK 465 CYS J 194 REMARK 465 GLU J 195 REMARK 465 VAL J 196 REMARK 465 THR J 197 REMARK 465 HIS J 198 REMARK 465 GLN J 199 REMARK 465 GLY J 200 REMARK 465 LEU J 201 REMARK 465 SER J 202 REMARK 465 SER J 203 REMARK 465 PRO J 204 REMARK 465 VAL J 205 REMARK 465 THR J 206 REMARK 465 LYS J 207 REMARK 465 SER J 208 REMARK 465 PHE J 209 REMARK 465 ASN J 210 REMARK 465 ARG J 211 REMARK 465 GLY J 212 REMARK 465 GLU J 213 REMARK 465 CYS J 214 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 ASP A 78 56.27 36.73 REMARK 500 ASN A 92 98.69 -69.77 REMARK 500 ASN A 240 -158.41 -135.87 REMARK 500 SER A 274 -155.58 174.11 REMARK 500 LYS A 282 -59.44 -125.46 REMARK 500 PRO A 354 47.20 -84.58 REMARK 500 HIS A 355 -35.12 -130.95 REMARK 500 THR A 387 18.57 59.78 REMARK 500 MET A 426 -130.18 59.90 REMARK 500 ARG I 42 -6.83 73.97 REMARK 500 MET I 48 -60.05 -95.23 REMARK 500 ASP J 17 -167.29 -118.15 REMARK 500 GLN J 27 -168.96 -127.33 REMARK 500 ASN J 30 -133.16 43.81 REMARK 500 ALA J 51 -4.30 66.52 REMARK 500 SER J 52 -38.36 -131.19 REMARK 500 SER J 94 -179.83 67.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-41810 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF VACCINE ELICITED ANTIBODY DH1285 FAB BOUND TO REMARK 900 THE ONE OF THE GP120 PROMOTER OF CH505M5CHIMER.6R.SOSIP.664V4.1 ENV DBREF 8U1D A 7 664 PDB 8U1D 8U1D 7 664 DBREF 8U1D I -18 215 PDB 8U1D 8U1D -18 215 DBREF 8U1D J -18 214 PDB 8U1D 8U1D -18 214 SEQRES 1 A 647 MET PRO MET GLY SER LEU GLN PRO LEU ALA THR LEU TYR SEQRES 2 A 647 LEU LEU GLY MET LEU VAL ALA SER VAL LEU ALA ALA GLU SEQRES 3 A 647 ASN LEU TRP VAL THR VAL TYR TYR GLY VAL PRO VAL TRP SEQRES 4 A 647 LYS GLU ALA LYS THR THR LEU PHE CYS ALA SER ASP ALA SEQRES 5 A 647 LYS ALA TYR GLU LYS LYS VAL HIS ASN VAL TRP ALA THR SEQRES 6 A 647 HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN GLU MET SEQRES 7 A 647 VAL LEU LYS ASN VAL THR GLU ASN PHE ASN MET TRP LYS SEQRES 8 A 647 ASN ASP MET VAL ASP GLN MET HIS GLU ASP VAL ILE SER SEQRES 9 A 647 LEU TRP ASP GLN SER LEU LYS PRO CYS VAL LYS LEU THR SEQRES 10 A 647 PRO LEU CYS VAL THR LEU ASN CYS THR ASN ALA THR ALA SEQRES 11 A 647 SER ASN SER SER ILE ILE GLU GLY MET LYS ASN CYS SER SEQRES 12 A 647 PHE ASN ILE THR THR GLU LEU ARG ASP LYS ARG GLU LYS SEQRES 13 A 647 LYS ASN ALA LEU PHE TYR LYS LEU ASP ILE VAL GLN LEU SEQRES 14 A 647 ASP GLY ASN SER SER GLN TYR ARG LEU ILE ASN CYS ASN SEQRES 15 A 647 THR SER VAL ILE THR GLN ALA CYS PRO LYS VAL SER PHE SEQRES 16 A 647 ASP PRO ILE PRO ILE HIS TYR CYS ALA PRO ALA GLY TYR SEQRES 17 A 647 ALA ILE LEU LYS CYS ASN ASN LYS THR PHE THR GLY THR SEQRES 18 A 647 GLY PRO CYS ASN ASN VAL SER THR VAL GLN CYS THR HIS SEQRES 19 A 647 GLY ILE LYS PRO VAL VAL SER THR GLN LEU LEU LEU ASN SEQRES 20 A 647 GLY SER LEU ALA GLU GLY GLU ILE ILE ILE ARG SER GLU SEQRES 21 A 647 ASN ILE THR ASN ASN VAL LYS THR ILE ILE VAL HIS LEU SEQRES 22 A 647 ASN GLU SER VAL LYS ILE GLU CYS THR ARG PRO ASN ASN SEQRES 23 A 647 LYS THR ARG THR SER ILE ARG ILE GLY PRO GLY GLN TRP SEQRES 24 A 647 PHE TYR ALA THR GLY GLN VAL ILE GLY ASP ILE ARG GLU SEQRES 25 A 647 ALA TYR CYS ASN ILE ASN GLU SER LYS TRP ASN GLU THR SEQRES 26 A 647 LEU GLN ARG VAL SER LYS LYS LEU LYS GLU TYR PHE PRO SEQRES 27 A 647 HIS LYS ASN ILE THR PHE GLN PRO SER SER GLY GLY ASP SEQRES 28 A 647 LEU GLU ILE THR THR HIS SER PHE ASN CYS GLY GLY GLU SEQRES 29 A 647 PHE PHE TYR CYS ASN THR SER SER LEU PHE ASN ARG THR SEQRES 30 A 647 TYR MET ALA ASN SER THR ASP MET ALA ASN SER THR GLU SEQRES 31 A 647 THR ASN SER THR ARG THR ILE THR ILE HIS CYS ARG ILE SEQRES 32 A 647 LYS GLN ILE ILE ASN MET TRP GLN GLU VAL GLY ARG ALA SEQRES 33 A 647 MET TYR ALA PRO PRO ILE ALA GLY ASN ILE THR CYS ILE SEQRES 34 A 647 SER ASN ILE THR GLY LEU LEU LEU THR ARG ASP GLY GLY SEQRES 35 A 647 LYS ASN ASN THR GLU THR PHE ARG PRO GLY GLY GLY ASN SEQRES 36 A 647 MET LYS ASP ASN TRP ARG SER GLU LEU TYR LYS TYR LYS SEQRES 37 A 647 VAL VAL LYS ILE GLU PRO LEU GLY VAL ALA PRO THR ARG SEQRES 38 A 647 CYS LYS ARG ARG VAL VAL GLY ARG ARG ARG ARG ARG ARG SEQRES 39 A 647 ALA VAL GLY ILE GLY ALA VAL PHE LEU GLY PHE LEU GLY SEQRES 40 A 647 ALA ALA GLY SER THR MET GLY ALA ALA SER MET THR LEU SEQRES 41 A 647 THR VAL GLN ALA ARG ASN LEU LEU SER GLY ILE VAL GLN SEQRES 42 A 647 GLN GLN SER ASN LEU LEU ARG ALA PRO GLU ALA GLN GLN SEQRES 43 A 647 HIS LEU LEU LYS LEU THR VAL TRP GLY ILE LYS GLN LEU SEQRES 44 A 647 GLN ALA ARG VAL LEU ALA VAL GLU ARG TYR LEU ARG ASP SEQRES 45 A 647 GLN GLN LEU LEU GLY ILE TRP GLY CYS SER GLY LYS LEU SEQRES 46 A 647 ILE CYS CYS THR ASN VAL PRO TRP ASN SER SER TRP SER SEQRES 47 A 647 ASN ARG ASN LEU SER GLU ILE TRP ASP ASN MET THR TRP SEQRES 48 A 647 LEU GLN TRP ASP LYS GLU ILE SER ASN TYR THR GLN ILE SEQRES 49 A 647 ILE TYR GLY LEU LEU GLU GLU SER GLN ASN GLN GLN GLU SEQRES 50 A 647 LYS ASN GLU GLN ASP LEU LEU ALA LEU ASP SEQRES 1 I 243 MET GLY TRP SER CYS ILE ILE LEU PHE LEU VAL ALA THR SEQRES 2 I 243 ALA THR GLY VAL HIS ALA GLN VAL HIS LEU GLU GLN SER SEQRES 3 I 243 GLY ALA GLU VAL LYS GLU PRO GLY SER SER VAL ARG LEU SEQRES 4 I 243 SER CYS GLU ALA SER GLY TYR THR PHE THR ASP TYR TYR SEQRES 5 I 243 ILE HIS TRP VAL ARG GLN SER PRO ARG GLN GLY LEU GLU SEQRES 6 I 243 TRP MET GLY TRP ILE ASN PRO TYR TYR GLY ASN THR HIS SEQRES 7 I 243 TYR ALA GLU LYS PHE GLN GLY ARG VAL ALA MET THR ARG SEQRES 8 I 243 ASP ARG SER THR THR THR ALA TYR MET ASP LEU SER SER SEQRES 9 I 243 LEU THR SER GLU ASP THR ALA VAL TYR TYR CYS ALA ARG SEQRES 10 I 243 ASP GLU GLY GLY SER GLY SER TYR SER TYR PHE ASP SER SEQRES 11 I 243 TRP GLY GLN GLY VAL LEU VAL THR VAL SER SER ALA SER SEQRES 12 I 243 THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER SEQRES 13 I 243 ARG SER THR SER GLU SER THR ALA ALA LEU GLY CYS LEU SEQRES 14 I 243 VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP SEQRES 15 I 243 ASN SER GLY SER LEU THR SER GLY VAL HIS THR PHE PRO SEQRES 16 I 243 ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SER SEQRES 17 I 243 VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN THR SEQRES 18 I 243 TYR VAL CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS SEQRES 19 I 243 VAL ASP LYS ARG VAL GLU ILE LYS THR SEQRES 1 J 233 MET GLY TRP SER CYS ILE ILE LEU PHE LEU VAL ALA THR SEQRES 2 J 233 ALA THR GLY VAL HIS ALA ASP ILE GLN MET THR GLN SER SEQRES 3 J 233 PRO SER SER LEU SER ALA SER VAL GLY ASP THR VAL THR SEQRES 4 J 233 ILE THR CYS ARG ALA SER GLN ASP ILE ASN ASN HIS LEU SEQRES 5 J 233 SER TRP TYR GLN GLN LYS PRO GLY ARG ALA PRO LYS ALA SEQRES 6 J 233 LEU ILE TYR SER ALA SER SER LEU GLU THR GLY VAL PRO SEQRES 7 J 233 SER ARG PHE SER GLY SER GLY SER GLY THR ASP TYR THR SEQRES 8 J 233 LEU THR ILE SER SER LEU GLN PRO GLU ASP PHE ALA THR SEQRES 9 J 233 TYR TYR CYS GLN HIS TYR SER THR SER PRO TYR THR PHE SEQRES 10 J 233 GLY ARG GLY THR LYS VAL ASP ILE LYS ARG ALA VAL ALA SEQRES 11 J 233 ALA PRO SER VAL PHE ILE PHE PRO PRO SER GLU ASP GLN SEQRES 12 J 233 VAL LYS SER GLY THR VAL SER VAL VAL CYS LEU LEU ASN SEQRES 13 J 233 ASN PHE TYR PRO ARG GLU ALA SER VAL LYS TRP LYS VAL SEQRES 14 J 233 ASP GLY VAL LEU LYS THR GLY ASN SER GLN GLU SER VAL SEQRES 15 J 233 THR GLU GLN ASP SER LYS ASP ASN THR TYR SER LEU SER SEQRES 16 J 233 SER THR LEU THR LEU SER SER THR ASP TYR GLN SER HIS SEQRES 17 J 233 ASN VAL TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SEQRES 18 J 233 SER PRO VAL THR LYS SER PHE ASN ARG GLY GLU CYS HET NAG A 701 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG C8 H15 N O6 HELIX 1 AA1 VAL A 65 ALA A 70 1 6 HELIX 2 AA2 THR A 71 ALA A 73 5 3 HELIX 3 AA3 ASP A 99 SER A 115 1 17 HELIX 4 AA4 LEU A 122 CYS A 126 5 5 HELIX 5 AA5 ASN A 138 ILE A 142 5 5 HELIX 6 AA6 CYS A 205 SER A 209 5 5 HELIX 7 AA7 ASN A 334 LYS A 350 1 17 HELIX 8 AA8 ASP A 368 THR A 373 1 6 HELIX 9 AA9 SER A 388 ASN A 392 5 5 HELIX 10 AB1 MET A 473 ARG A 478 1 6 HELIX 11 AB2 THR I 28 TYR I 32 5 5 HELIX 12 AB3 THR I 83 THR I 87 5 5 HELIX 13 AB4 GLN J 79 PHE J 83 5 5 SHEET 1 AA1 4 GLU A 83 LEU A 86 0 SHEET 2 AA1 4 VAL A 242 VAL A 245 -1 O THR A 244 N MET A 84 SHEET 3 AA1 4 ALA A 224 CYS A 228 -1 N LYS A 227 O SER A 243 SHEET 4 AA1 4 VAL A 486 VAL A 487 -1 O VAL A 487 N ALA A 224 SHEET 1 AA2 2 ASN A 92 ASN A 94 0 SHEET 2 AA2 2 THR A 236 PRO A 238 -1 O GLY A 237 N PHE A 93 SHEET 1 AA3 5 GLU A 170 ALA A 174 0 SHEET 2 AA3 5 CYS A 157 ILE A 161 -1 N ILE A 161 O GLU A 170 SHEET 3 AA3 5 LEU A 129 CYS A 131 -1 N ASN A 130 O SER A 158 SHEET 4 AA3 5 GLN A 190 LEU A 193 -1 O TYR A 191 N LEU A 129 SHEET 5 AA3 5 ILE A 181 GLN A 183 -1 N VAL A 182 O ARG A 192 SHEET 1 AA4 3 VAL A 200 GLN A 203 0 SHEET 2 AA4 3 ARG A 432 TYR A 435 1 O TYR A 435 N THR A 202 SHEET 3 AA4 3 ILE A 423 ILE A 424 -1 N ILE A 424 O MET A 434 SHEET 1 AA5 4 LEU A 259 LEU A 261 0 SHEET 2 AA5 4 ILE A 443 LEU A 452 -1 O THR A 450 N LEU A 260 SHEET 3 AA5 4 ILE A 285 ARG A 298 -1 N ILE A 294 O SER A 447 SHEET 4 AA5 4 ILE A 271 ARG A 273 -1 N ARG A 273 O ILE A 285 SHEET 1 AA6 7 LEU A 259 LEU A 261 0 SHEET 2 AA6 7 ILE A 443 LEU A 452 -1 O THR A 450 N LEU A 260 SHEET 3 AA6 7 ILE A 285 ARG A 298 -1 N ILE A 294 O SER A 447 SHEET 4 AA6 7 ALA A 329 ILE A 333 -1 O TYR A 330 N THR A 297 SHEET 5 AA6 7 ILE A 414 LYS A 421 -1 O ILE A 414 N ILE A 333 SHEET 6 AA6 7 GLU A 381 CYS A 385 -1 N TYR A 384 O ARG A 419 SHEET 7 AA6 7 HIS A 374 CYS A 378 -1 N PHE A 376 O PHE A 383 SHEET 1 AA7 2 ASN A 301 ILE A 307 0 SHEET 2 AA7 2 PHE A 317 ILE A 323 -1 O GLY A 321 N THR A 303 SHEET 1 AA8 3 ASN A 357 PHE A 361 0 SHEET 2 AA8 3 THR A 463 PRO A 468 1 O GLU A 464 N ASN A 357 SHEET 3 AA8 3 LEU A 454 GLY A 458 -1 N ASP A 457 O THR A 465 SHEET 1 AA9 4 HIS I 3 GLN I 6 0 SHEET 2 AA9 4 SER I 17 SER I 25 -1 O GLU I 23 N GLU I 5 SHEET 3 AA9 4 THR I 77 SER I 82A-1 O MET I 80 N LEU I 20 SHEET 4 AA9 4 VAL I 67 ASP I 72 -1 N THR I 70 O TYR I 79 SHEET 1 AB1 5 THR I 57 HIS I 58 0 SHEET 2 AB1 5 LEU I 45 ILE I 51 -1 N TRP I 50 O HIS I 58 SHEET 3 AB1 5 ILE I 34 GLN I 39 -1 N ILE I 34 O ILE I 51 SHEET 4 AB1 5 ALA I 88 ARG I 94 -1 O TYR I 91 N VAL I 37 SHEET 5 AB1 5 SER I 102 TRP I 103 -1 O SER I 102 N ARG I 94 SHEET 1 AB2 5 THR I 57 HIS I 58 0 SHEET 2 AB2 5 LEU I 45 ILE I 51 -1 N TRP I 50 O HIS I 58 SHEET 3 AB2 5 ILE I 34 GLN I 39 -1 N ILE I 34 O ILE I 51 SHEET 4 AB2 5 ALA I 88 ARG I 94 -1 O TYR I 91 N VAL I 37 SHEET 5 AB2 5 VAL I 107 VAL I 109 -1 O VAL I 107 N TYR I 90 SHEET 1 AB3 4 THR J 5 GLN J 6 0 SHEET 2 AB3 4 THR J 18 ARG J 24 -1 O ARG J 24 N THR J 5 SHEET 3 AB3 4 ASP J 70 SER J 76 -1 O LEU J 73 N ILE J 21 SHEET 4 AB3 4 PHE J 62 SER J 67 -1 N SER J 63 O THR J 74 SHEET 1 AB4 2 SER J 10 ALA J 13 0 SHEET 2 AB4 2 LYS J 103 ILE J 106 1 O ASP J 105 N LEU J 11 SHEET 1 AB5 4 SER J 53 LEU J 54 0 SHEET 2 AB5 4 LYS J 45 TYR J 49 -1 N TYR J 49 O SER J 53 SHEET 3 AB5 4 LEU J 33 GLN J 38 -1 N TRP J 35 O ILE J 48 SHEET 4 AB5 4 THR J 85 HIS J 90 -1 O GLN J 89 N SER J 34 SSBOND 1 CYS A 119 CYS A 205 1555 1555 2.03 SSBOND 2 CYS A 126 CYS A 196 1555 1555 2.04 SSBOND 3 CYS A 131 CYS A 157 1555 1555 2.04 SSBOND 4 CYS A 228 CYS A 239 1555 1555 2.02 SSBOND 5 CYS A 296 CYS A 331 1555 1555 2.03 SSBOND 6 CYS A 378 CYS A 445 1555 1555 2.03 SSBOND 7 CYS A 385 CYS A 418 1555 1555 2.04 SSBOND 8 CYS J 23 CYS J 88 1555 1555 2.04 LINK ND2 ASN A 386 C1 NAG A 701 1555 1555 1.42 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