HEADER LIPID TRANSPORT 16-NOV-20 7AZN TITLE STRUCTURE OF MOUSE ASTERC (GRAMD1C) WITH A NEW CHOLESTEROL-DERIVED TITLE 2 COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ASTER-C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GRAM DOMAIN-CONTAINING PROTEIN 1C; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: GRAMD1C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS NON VESICULAR CHOLESTEROL TRANSPORT, LIPID-BINDING, ENDOPLASMIC KEYWDS 2 RETICULUM, MEMBRANE CONTACT SITES, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR B.ROMARTINEZ-ALONSO,K.SIRVYDIS,Y.KIM,X.XIAO,M.JUNG,P.TONTONOZ, AUTHOR 2 J.SCHWABE REVDAT 2 31-JAN-24 7AZN 1 REMARK REVDAT 1 13-JAN-21 7AZN 0 JRNL AUTH X.XIAO,Y.KIM,B.ROMARTINEZ-ALONSO,K.SIRVYDIS,D.S.ORY, JRNL AUTH 2 J.W.R.SCHWABE,M.E.JUNG,P.TONTONOZ JRNL TITL SELECTIVE ASTER INHIBITORS DISTINGUISH VESICULAR AND JRNL TITL 2 NONVESICULAR STEROL TRANSPORT MECHANISMS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33376205 JRNL DOI 10.1073/PNAS.2024149118 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 11448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 580 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.7700 - 3.3100 0.97 2769 138 0.1870 0.2240 REMARK 3 2 3.3100 - 2.6300 1.00 2763 149 0.2369 0.2538 REMARK 3 3 2.6300 - 2.3000 1.00 2754 150 0.2473 0.3290 REMARK 3 4 2.3000 - 2.0900 0.94 2582 143 0.2943 0.3431 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7AZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1292111964. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 28.900 M REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11465 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 26.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.25200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 6GQF REMARK 200 REMARK 200 REMARK: A SINGLE 100-MICROMETRES RECTANGULAR PRISM. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SPG BUFFER PH 4 25 % PEG 1500, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 32.99750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.69850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.99750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.69850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 TOTAL BURIED SURFACE AREA: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 20.0 KCAL/MOL 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 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 TRP A 463 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 463 CZ3 CH2 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 HIS A 336 45.13 -85.55 REMARK 500 ALA A 412 11.52 56.26 REMARK 500 GLN A 413 -50.48 -125.68 REMARK 500 ALA A 444 -122.76 -125.05 REMARK 500 GLN A 461 76.97 50.12 REMARK 500 SER A 474 -56.67 -136.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YK8 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 608 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GQF RELATED DB: PDB REMARK 900 6GQF CORRESPONDS TO THE STRUCTURE OF ASTERA WITH 25ALPHA-OH- REMARK 900 CHOLESTEROL, WHICH IS AN ISOFORM OF ASTERC. DBREF 7AZN A 327 503 UNP Q8CI52 ASTRC_MOUSE 327 503 SEQRES 1 A 177 GLY ARG LEU TYR ILE ASN ARG VAL PHE HIS ILE SER ALA SEQRES 2 A 177 GLU ARG MET PHE GLU LEU LEU PHE THR SER SER HIS PHE SEQRES 3 A 177 MET GLN ARG PHE ALA ASN SER ARG ASN ILE ILE ASP VAL SEQRES 4 A 177 VAL SER THR PRO TRP THR VAL GLU SER GLY GLY ASN GLN SEQRES 5 A 177 LEU ARG THR MET THR TYR THR ILE VAL LEU SER ASN PRO SEQRES 6 A 177 LEU THR GLY LYS TYR THR ALA ALA THR GLU LYS GLN THR SEQRES 7 A 177 LEU TYR LYS GLU SER ARG GLU ALA GLN PHE TYR LEU VAL SEQRES 8 A 177 ASP SER GLU VAL LEU THR HIS ASP VAL PRO TYR HIS ASP SEQRES 9 A 177 TYR PHE TYR THR LEU ASN ARG TYR CYS ILE VAL ARG SER SEQRES 10 A 177 ALA LYS GLN ARG CYS ARG LEU ARG VAL SER THR ASP LEU SEQRES 11 A 177 LYS TYR ARG LYS GLN PRO TRP GLY LEU ILE LYS SER LEU SEQRES 12 A 177 ILE GLU LYS ASN SER TRP SER SER LEU GLU SER TYR PHE SEQRES 13 A 177 LYS LYS LEU GLU SER ASP LEU LEU MET GLU GLU SER VAL SEQRES 14 A 177 LEU SER GLN SER ILE GLU ASP ALA HET YK8 A 601 30 HET EOH A 602 3 HET EOH A 603 3 HET EOH A 604 3 HET EOH A 605 3 HET EOH A 606 3 HET EOH A 607 3 HET GOL A 608 6 HETNAM YK8 20ALPHA-HYDROXY-20-(5-METHYLHEXYL)CHOLESTEROL HETNAM EOH ETHANOL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 YK8 C28 H48 O2 FORMUL 3 EOH 6(C2 H6 O) FORMUL 9 GOL C3 H8 O3 FORMUL 10 HOH *50(H2 O) HELIX 1 AA1 SER A 338 THR A 348 1 11 HELIX 2 AA2 SER A 350 ARG A 360 1 11 HELIX 3 AA3 TYR A 428 ASP A 430 5 3 HELIX 4 AA4 GLY A 464 ASN A 473 1 10 HELIX 5 AA5 SER A 474 ALA A 503 1 30 SHEET 1 AA1 7 ARG A 328 PHE A 335 0 SHEET 2 AA1 7 CYS A 448 TYR A 458 -1 O CYS A 448 N PHE A 335 SHEET 3 AA1 7 PHE A 432 ARG A 442 -1 N TYR A 433 O LYS A 457 SHEET 4 AA1 7 PHE A 414 THR A 423 -1 N SER A 419 O ASN A 436 SHEET 5 AA1 7 TYR A 396 LEU A 405 -1 N THR A 400 O LEU A 422 SHEET 6 AA1 7 GLN A 378 VAL A 387 -1 N ARG A 380 O GLN A 403 SHEET 7 AA1 7 ILE A 362 SER A 367 -1 N VAL A 366 O THR A 383 SHEET 1 AA2 7 ARG A 328 PHE A 335 0 SHEET 2 AA2 7 CYS A 448 TYR A 458 -1 O CYS A 448 N PHE A 335 SHEET 3 AA2 7 PHE A 432 ARG A 442 -1 N TYR A 433 O LYS A 457 SHEET 4 AA2 7 PHE A 414 THR A 423 -1 N SER A 419 O ASN A 436 SHEET 5 AA2 7 TYR A 396 LEU A 405 -1 N THR A 400 O LEU A 422 SHEET 6 AA2 7 GLN A 378 VAL A 387 -1 N ARG A 380 O GLN A 403 SHEET 7 AA2 7 THR A 371 VAL A 372 -1 N THR A 371 O LEU A 379 SITE 1 AC1 12 TYR A 384 ILE A 386 GLU A 401 PRO A 427 SITE 2 AC1 12 THR A 434 ASN A 436 ASN A 473 SER A 477 SITE 3 AC1 12 LEU A 478 TYR A 481 GOL A 608 HOH A 708 SITE 1 AC2 7 ASP A 364 THR A 383 TYR A 384 THR A 385 SITE 2 AC2 7 ALA A 398 ALA A 399 HOH A 701 SITE 1 AC3 4 SER A 349 SER A 367 THR A 368 ARG A 380 SITE 1 AC4 5 GLU A 373 ASP A 425 VAL A 426 PRO A 427 SITE 2 AC4 5 HIS A 429 SITE 1 AC5 1 ARG A 360 SITE 1 AC6 5 GLU A 401 GLN A 403 TYR A 438 TYR A 481 SITE 2 AC6 5 GOL A 608 SITE 1 AC7 3 ASN A 332 ARG A 333 GLU A 486 SITE 1 AC8 9 MET A 353 ALA A 357 MET A 382 TYR A 384 SITE 2 AC8 9 GLU A 401 TYR A 481 YK8 A 601 EOH A 606 SITE 3 AC8 9 HOH A 710 CRYST1 65.995 49.397 61.691 90.00 100.07 90.00 C 1 2 1 4 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 0.015153 0.000000 0.002690 0.00000 SCALE2 0.000000 0.020244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016463 0.00000