HEADER TRANSPORT PROTEIN 19-MAR-24 9B3M TITLE NORA IN INWARD-OPEN CONFORMATION (NORA-BRIL FUSION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NORA-BRIL(3A) FUSION; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NORA DOMAIN (1-380) + 3A LINKER (381-383) + BRIL DOMAIN COMPND 5 (384-490); COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: NORA-BRIL(3A) FUSION DETAILS: M1 TO R380 IS NORA COMPND 8 DOMAIN; A381 TO A383 IS THE 3A LINKER; A384 TO L490 IS BRIL DOMAIN COMPND 9 (MOST RESIDUES FOR BRIL DOMAIN WERE NOT BUILT SINCE A MASK WAS ADDED COMPND 10 ONLY AROUND NORA DOMAIN DURING DATA PROCESSING) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: NORA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MEMBRANE PROTEIN, STAPHYLOCOCCUS AUREUS, ANTIBIOTIC RESISTANCE, KEYWDS 2 EFFLUX PUMP, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR P.XIE,Y.LI,H.KUANG,D.N.WANG,N.J.TRAASETH REVDAT 2 25-JUN-25 9B3M 1 JRNL REVDAT 1 11-DEC-24 9B3M 0 JRNL AUTH P.XIE,Y.LI,G.LAMON,H.KUANG,D.N.WANG,N.J.TRAASETH JRNL TITL A FIDUCIAL-ASSISTED STRATEGY COMPATIBLE WITH RESOLVING SMALL JRNL TITL 2 MFS TRANSPORTER STRUCTURES IN MULTIPLE CONFORMATIONS USING JRNL TITL 3 CRYO-EM. JRNL REF NAT COMMUN V. 16 7 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 39746942 JRNL DOI 10.1038/S41467-024-54986-5 REMARK 2 REMARK 2 RESOLUTION. 3.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, PHENIX, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 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 : RIGID BODY FIT 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) : 3.210 REMARK 3 NUMBER OF PARTICLES : 159621 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 9B3M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1000281861. 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 : NORA-BRIL(3A)-FABBRIL REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : HOLD FOR 10 SEC BEFORE 25SEC REMARK 245 GLOW DISCHARGING REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 5.00 REMARK 245 SAMPLE DETAILS : FABBRIL WAS ADDED BUT NOT BUILT REMARK 245 IN MODEL DUE TO MASKING. HERE IS ITS SEQUENCE: HEAVY CHAIN: REMARK 245 SEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGSTSYADSV REMARK 245 KGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQGTLVTVSSASTKG REMARK 245 PSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVT REMARK 245 REMARK 245 VPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS LIGHT CHAIN: DIQMTQSPSSLSASVGDRVTI 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 K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 5554.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ASP A 179 REMARK 465 PRO A 180 REMARK 465 LYS A 181 REMARK 465 LYS A 182 REMARK 465 SER A 183 REMARK 465 THR A 184 REMARK 465 THR A 185 REMARK 465 SER A 186 REMARK 465 GLY A 187 REMARK 465 PHE A 188 REMARK 465 GLN A 189 REMARK 465 LYS A 190 REMARK 465 LEU A 191 REMARK 465 GLU A 192 REMARK 465 PRO A 193 REMARK 465 GLN A 194 REMARK 465 LEU A 195 REMARK 465 LEU A 196 REMARK 465 THR A 197 REMARK 465 LYS A 198 REMARK 465 GLY A 322 REMARK 465 GLU A 323 REMARK 465 ASN A 389 REMARK 465 TRP A 390 REMARK 465 GLU A 391 REMARK 465 THR A 392 REMARK 465 LEU A 393 REMARK 465 ASN A 394 REMARK 465 ASP A 395 REMARK 465 ASN A 396 REMARK 465 LEU A 397 REMARK 465 LYS A 398 REMARK 465 VAL A 399 REMARK 465 ILE A 400 REMARK 465 GLU A 401 REMARK 465 LYS A 402 REMARK 465 ALA A 403 REMARK 465 ASP A 404 REMARK 465 ASN A 405 REMARK 465 ALA A 406 REMARK 465 ALA A 407 REMARK 465 GLN A 408 REMARK 465 VAL A 409 REMARK 465 LYS A 410 REMARK 465 ASP A 411 REMARK 465 ALA A 412 REMARK 465 LEU A 413 REMARK 465 THR A 414 REMARK 465 LYS A 415 REMARK 465 MET A 416 REMARK 465 ARG A 417 REMARK 465 ALA A 418 REMARK 465 ALA A 419 REMARK 465 ALA A 420 REMARK 465 LEU A 421 REMARK 465 ASP A 422 REMARK 465 ALA A 423 REMARK 465 GLN A 424 REMARK 465 LYS A 425 REMARK 465 ALA A 426 REMARK 465 THR A 427 REMARK 465 PRO A 428 REMARK 465 PRO A 429 REMARK 465 LYS A 430 REMARK 465 LEU A 431 REMARK 465 GLU A 432 REMARK 465 ASP A 433 REMARK 465 LYS A 434 REMARK 465 SER A 435 REMARK 465 PRO A 436 REMARK 465 ASP A 437 REMARK 465 SER A 438 REMARK 465 PRO A 439 REMARK 465 GLU A 440 REMARK 465 MET A 441 REMARK 465 LYS A 442 REMARK 465 ASP A 443 REMARK 465 PHE A 444 REMARK 465 ARG A 445 REMARK 465 HIS A 446 REMARK 465 GLY A 447 REMARK 465 PHE A 448 REMARK 465 ASP A 449 REMARK 465 ILE A 450 REMARK 465 LEU A 451 REMARK 465 VAL A 452 REMARK 465 GLY A 453 REMARK 465 GLN A 454 REMARK 465 ILE A 455 REMARK 465 ASP A 456 REMARK 465 ASP A 457 REMARK 465 ALA A 458 REMARK 465 LEU A 459 REMARK 465 LYS A 460 REMARK 465 LEU A 461 REMARK 465 ALA A 462 REMARK 465 ASN A 463 REMARK 465 GLU A 464 REMARK 465 GLY A 465 REMARK 465 LYS A 466 REMARK 465 VAL A 467 REMARK 465 LYS A 468 REMARK 465 GLU A 469 REMARK 465 ALA A 470 REMARK 465 GLN A 471 REMARK 465 ALA A 472 REMARK 465 ALA A 473 REMARK 465 ALA A 474 REMARK 465 GLU A 475 REMARK 465 GLN A 476 REMARK 465 LEU A 477 REMARK 465 LYS A 478 REMARK 465 THR A 479 REMARK 465 THR A 480 REMARK 465 ARG A 481 REMARK 465 ASN A 482 REMARK 465 ALA A 483 REMARK 465 TYR A 484 REMARK 465 ILE A 485 REMARK 465 GLN A 486 REMARK 465 LYS A 487 REMARK 465 TYR A 488 REMARK 465 LEU A 489 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 ASN A 2 CG OD1 ND2 REMARK 470 GLN A 4 CG CD OE1 NE2 REMARK 470 ILE A 5 CG1 CG2 CD1 REMARK 470 PHE A 6 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE A 12 CG1 CG2 CD1 REMARK 470 LEU A 30 CG CD1 CD2 REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 ASP A 32 CG OD1 OD2 REMARK 470 ASP A 39 CG OD1 OD2 REMARK 470 LEU A 61 CG CD1 CD2 REMARK 470 ASP A 63 CG OD1 OD2 REMARK 470 LEU A 65 CG CD1 CD2 REMARK 470 SER A 104 OG REMARK 470 MET A 109 CG SD CE REMARK 470 LEU A 115 CG CD1 CD2 REMARK 470 ILE A 116 CG1 CG2 CD1 REMARK 470 ASP A 118 CG OD1 OD2 REMARK 470 SER A 120 OG REMARK 470 SER A 122 OG REMARK 470 HIS A 123 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 128 CG OD1 ND2 REMARK 470 MET A 132 CG SD CE REMARK 470 GLU A 152 CG CD OE1 OE2 REMARK 470 LEU A 168 CG CD1 CD2 REMARK 470 ILE A 171 CG1 CG2 CD1 REMARK 470 VAL A 175 CG1 CG2 REMARK 470 LEU A 176 CG CD1 CD2 REMARK 470 HIS A 178 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 ASP A 231 CG OD1 OD2 REMARK 470 ASN A 234 CG OD1 ND2 REMARK 470 SER A 236 OG REMARK 470 LYS A 264 CG CD CE NZ REMARK 470 GLU A 268 CG CD OE1 OE2 REMARK 470 ASN A 319 CG OD1 ND2 REMARK 470 ARG A 324 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 385 CG OD1 OD2 REMARK 470 LEU A 386 CG CD1 CD2 REMARK 470 GLU A 387 CG CD OE1 OE2 REMARK 470 ASP A 388 CG OD1 OD2 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 MET A 132 -70.14 -62.70 REMARK 500 PHE A 258 15.28 -141.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-44145 RELATED DB: EMDB REMARK 900 NORA IN INWARD-OPEN CONFORMATION (NORA-BRIL FUSION) DBREF 9B3M A 1 381 UNP Q53459 Q53459_STAAU 1 381 DBREF 9B3M A 382 489 PDB 9B3M 9B3M 382 489 SEQRES 1 A 489 MET ASN LYS GLN ILE PHE VAL LEU TYR PHE ASN ILE PHE SEQRES 2 A 489 LEU ILE PHE LEU GLY ILE GLY LEU VAL ILE PRO VAL LEU SEQRES 3 A 489 PRO VAL TYR LEU LYS ASP LEU GLY LEU THR GLY SER ASP SEQRES 4 A 489 LEU GLY LEU LEU VAL ALA ALA PHE ALA LEU SER GLN MET SEQRES 5 A 489 ILE ILE SER PRO PHE GLY GLY THR LEU ALA ASP LYS LEU SEQRES 6 A 489 GLY LYS LYS LEU ILE ILE CYS ILE GLY LEU ILE LEU PHE SEQRES 7 A 489 SER VAL SER GLU PHE MET PHE ALA VAL GLY HIS ASN PHE SEQRES 8 A 489 SER VAL LEU MET LEU SER ARG VAL ILE GLY GLY MET SER SEQRES 9 A 489 ALA GLY MET VAL MET PRO GLY VAL THR GLY LEU ILE ALA SEQRES 10 A 489 ASP ILE SER PRO SER HIS GLN LYS ALA LYS ASN PHE GLY SEQRES 11 A 489 TYR MET SER ALA ILE ILE ASN SER GLY PHE ILE LEU GLY SEQRES 12 A 489 PRO GLY ILE GLY GLY PHE MET ALA GLU VAL SER HIS ARG SEQRES 13 A 489 MET PRO PHE TYR PHE ALA GLY ALA LEU GLY ILE LEU ALA SEQRES 14 A 489 PHE ILE MET SER ILE VAL LEU ILE HIS ASP PRO LYS LYS SEQRES 15 A 489 SER THR THR SER GLY PHE GLN LYS LEU GLU PRO GLN LEU SEQRES 16 A 489 LEU THR LYS ILE ASN TRP LYS VAL PHE ILE THR PRO VAL SEQRES 17 A 489 ILE LEU THR LEU VAL LEU SER PHE GLY LEU SER ALA PHE SEQRES 18 A 489 GLU THR LEU TYR SER LEU TYR THR ALA ASP LYS VAL ASN SEQRES 19 A 489 TYR SER PRO LYS ASP ILE SER ILE ALA ILE THR GLY GLY SEQRES 20 A 489 GLY ILE PHE GLY ALA LEU PHE GLN ILE TYR PHE PHE ASP SEQRES 21 A 489 LYS PHE MET LYS TYR PHE SER GLU LEU THR PHE ILE ALA SEQRES 22 A 489 TRP SER LEU LEU TYR SER VAL VAL VAL LEU ILE LEU LEU SEQRES 23 A 489 VAL PHE ALA ASN ASP TYR TRP SER ILE MET LEU ILE SER SEQRES 24 A 489 PHE VAL VAL PHE ILE GLY PHE ASP MET ILE ARG PRO ALA SEQRES 25 A 489 ILE THR ASN TYR PHE SER ASN ILE ALA GLY GLU ARG GLN SEQRES 26 A 489 GLY PHE ALA GLY GLY LEU ASN SER THR PHE THR SER MET SEQRES 27 A 489 GLY ASN PHE ILE GLY PRO LEU ILE ALA GLY ALA LEU PHE SEQRES 28 A 489 ASP VAL HIS ILE GLU ALA PRO ILE TYR MET ALA ILE GLY SEQRES 29 A 489 VAL SER LEU ALA GLY VAL VAL ILE VAL LEU ILE GLU LYS SEQRES 30 A 489 GLN HIS ARG ALA ALA ALA ALA ASP LEU GLU ASP ASN TRP SEQRES 31 A 489 GLU THR LEU ASN ASP ASN LEU LYS VAL ILE GLU LYS ALA SEQRES 32 A 489 ASP ASN ALA ALA GLN VAL LYS ASP ALA LEU THR LYS MET SEQRES 33 A 489 ARG ALA ALA ALA LEU ASP ALA GLN LYS ALA THR PRO PRO SEQRES 34 A 489 LYS LEU GLU ASP LYS SER PRO ASP SER PRO GLU MET LYS SEQRES 35 A 489 ASP PHE ARG HIS GLY PHE ASP ILE LEU VAL GLY GLN ILE SEQRES 36 A 489 ASP ASP ALA LEU LYS LEU ALA ASN GLU GLY LYS VAL LYS SEQRES 37 A 489 GLU ALA GLN ALA ALA ALA GLU GLN LEU LYS THR THR ARG SEQRES 38 A 489 ASN ALA TYR ILE GLN LYS TYR LEU HELIX 1 AA1 LYS A 3 GLY A 18 1 16 HELIX 2 AA2 LEU A 21 LEU A 33 1 13 HELIX 3 AA3 THR A 36 LEU A 65 1 30 HELIX 4 AA4 LYS A 67 GLY A 88 1 22 HELIX 5 AA5 ASN A 90 SER A 120 1 31 HELIX 6 AA6 GLN A 124 SER A 154 1 31 HELIX 7 AA7 ARG A 156 ILE A 177 1 22 HELIX 8 AA8 ASN A 200 ASN A 234 1 35 HELIX 9 AA9 SER A 236 PHE A 266 1 31 HELIX 10 AB1 SER A 267 PHE A 288 1 22 HELIX 11 AB2 ASP A 291 ALA A 321 1 31 HELIX 12 AB3 GLN A 325 HIS A 354 1 30 HELIX 13 AB4 GLU A 356 ASP A 388 1 33 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 2670 ASP A 388 MASTER 305 0 0 13 0 0 0 6 2669 1 0 38 END