HEADER SIGNALING PROTEIN 07-NOV-21 7SR1 TITLE CRYSTAL STRUCTURE OF THE HUMAN SNX25 REGULATOR OF G-PROTEIN SIGNALLING TITLE 2 (RGS) DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTING NEXIN-25; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SNX25; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENDOSOME, SORTING NEXIN, SNX, RGS, SNX25, LIPID DROPLET, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.M.COLLINS,B.PAUL,S.WEERATUNGA REVDAT 4 16-OCT-24 7SR1 1 REMARK REVDAT 3 18-OCT-23 7SR1 1 REMARK REVDAT 2 01-JUN-22 7SR1 1 JRNL REVDAT 1 17-NOV-21 7SR1 0 JRNL AUTH B.PAUL,S.WEERATUNGA,V.A.TILLU,H.HARIRI,W.M.HENNE,B.M.COLLINS JRNL TITL STRUCTURAL PREDICTIONS OF THE SNX-RGS PROTEINS SUGGEST THEY JRNL TITL 2 BELONG TO A NEW CLASS OF LIPID TRANSFER PROTEINS. JRNL REF FRONT CELL DEV BIOL V. 10 26688 2022 JRNL REFN ESSN 2296-634X JRNL PMID 35223850 JRNL DOI 10.3389/FCELL.2022.826688 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20RC3_4406 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 13199 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 654 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 45.8400 - 4.1000 1.00 2668 123 0.1868 0.1954 REMARK 3 2 4.1000 - 3.2600 1.00 2585 140 0.2034 0.2210 REMARK 3 3 3.2600 - 2.8500 1.00 2592 133 0.2571 0.3049 REMARK 3 4 2.8500 - 2.5900 0.99 2574 131 0.2510 0.3084 REMARK 3 5 2.5900 - 2.4000 0.83 2126 127 0.2830 0.3212 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) : 0.346 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.028 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.51 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 : 0.003 2124 REMARK 3 ANGLE : 0.521 2852 REMARK 3 CHIRALITY : 0.038 300 REMARK 3 PLANARITY : 0.003 362 REMARK 3 DIHEDRAL : 25.666 812 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 7SR1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000260917. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.006 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13200 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 45.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2BV1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.2 M SODIUM ACETATE, REMARK 280 0.1 M TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.57000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY A 444 REMARK 465 SER A 445 REMARK 465 SER A 446 REMARK 465 GLY B 444 REMARK 465 SER B 445 REMARK 465 SER B 446 REMARK 465 GLN B 447 REMARK 465 GLU B 569 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 OE1 GLU A 485 O HOH A 601 1.86 REMARK 500 O HOH B 615 O HOH B 624 1.91 REMARK 500 OE2 GLU B 482 O HOH B 601 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 SG CYS A 526 CB CYS B 526 1454 1.73 REMARK 500 O HOH A 633 O HOH B 632 2745 2.12 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 SER B 510 -132.61 45.00 REMARK 500 GLU B 512 -129.19 58.25 REMARK 500 VAL B 515 -56.54 67.57 REMARK 500 ASN B 530 -123.94 61.89 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7SR1 A 446 569 UNP A0A494C0S0_HUMAN DBREF2 7SR1 A A0A494C0S0 446 569 DBREF1 7SR1 B 446 569 UNP A0A494C0S0_HUMAN DBREF2 7SR1 B A0A494C0S0 446 569 SEQADV 7SR1 GLY A 444 UNP A0A494C0S EXPRESSION TAG SEQADV 7SR1 SER A 445 UNP A0A494C0S EXPRESSION TAG SEQADV 7SR1 GLY B 444 UNP A0A494C0S EXPRESSION TAG SEQADV 7SR1 SER B 445 UNP A0A494C0S EXPRESSION TAG SEQRES 1 A 126 GLY SER SER GLN LYS ILE LEU GLN PHE GLU ASP ILE LEU SEQRES 2 A 126 ALA ASN THR PHE TYR ARG GLU HIS PHE GLY MET TYR MET SEQRES 3 A 126 GLU ARG MET ASP LYS ARG ALA LEU ILE SER PHE TRP GLU SEQRES 4 A 126 SER VAL GLU HIS LEU LYS ASN ALA ASN LYS ASN GLU ILE SEQRES 5 A 126 PRO GLN LEU VAL GLY GLU ILE TYR GLN ASN PHE PHE VAL SEQRES 6 A 126 GLU SER LYS GLU ILE SER VAL GLU LYS SER LEU TYR LYS SEQRES 7 A 126 GLU ILE GLN GLN CYS LEU VAL GLY ASN LYS GLY ILE GLU SEQRES 8 A 126 VAL PHE TYR LYS ILE GLN GLU ASP VAL TYR GLU THR LEU SEQRES 9 A 126 LYS ASP ARG TYR TYR PRO SER PHE ILE VAL SER ASP LEU SEQRES 10 A 126 TYR GLU LYS LEU LEU ILE LYS GLU GLU SEQRES 1 B 126 GLY SER SER GLN LYS ILE LEU GLN PHE GLU ASP ILE LEU SEQRES 2 B 126 ALA ASN THR PHE TYR ARG GLU HIS PHE GLY MET TYR MET SEQRES 3 B 126 GLU ARG MET ASP LYS ARG ALA LEU ILE SER PHE TRP GLU SEQRES 4 B 126 SER VAL GLU HIS LEU LYS ASN ALA ASN LYS ASN GLU ILE SEQRES 5 B 126 PRO GLN LEU VAL GLY GLU ILE TYR GLN ASN PHE PHE VAL SEQRES 6 B 126 GLU SER LYS GLU ILE SER VAL GLU LYS SER LEU TYR LYS SEQRES 7 B 126 GLU ILE GLN GLN CYS LEU VAL GLY ASN LYS GLY ILE GLU SEQRES 8 B 126 VAL PHE TYR LYS ILE GLN GLU ASP VAL TYR GLU THR LEU SEQRES 9 B 126 LYS ASP ARG TYR TYR PRO SER PHE ILE VAL SER ASP LEU SEQRES 10 B 126 TYR GLU LYS LEU LEU ILE LYS GLU GLU FORMUL 3 HOH *77(H2 O) HELIX 1 AA1 GLN A 451 ASN A 458 1 8 HELIX 2 AA2 ASN A 458 MET A 472 1 15 HELIX 3 AA3 LYS A 474 ASN A 489 1 16 HELIX 4 AA4 GLU A 494 PHE A 507 1 14 HELIX 5 AA5 SER A 514 LEU A 519 1 6 HELIX 6 AA6 LEU A 519 CYS A 526 1 8 HELIX 7 AA7 GLY A 529 TYR A 551 1 23 HELIX 8 AA8 TYR A 551 VAL A 557 1 7 HELIX 9 AA9 LEU A 560 LEU A 565 5 6 HELIX 10 AB1 GLN B 451 ASN B 458 1 8 HELIX 11 AB2 ASN B 458 MET B 472 1 15 HELIX 12 AB3 LYS B 474 ASN B 489 1 16 HELIX 13 AB4 GLU B 494 VAL B 508 1 15 HELIX 14 AB5 VAL B 515 ILE B 523 1 9 HELIX 15 AB6 ILE B 523 GLY B 529 1 7 HELIX 16 AB7 LYS B 531 TYR B 551 1 21 HELIX 17 AB8 TYR B 551 VAL B 557 1 7 HELIX 18 AB9 LEU B 560 LEU B 565 5 6 SSBOND 1 CYS A 526 CYS B 526 1555 1454 2.03 CRYST1 48.620 57.140 66.980 90.00 109.48 90.00 P 1 21 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 0.020568 0.000000 0.007275 0.00000 SCALE2 0.000000 0.017501 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015836 0.00000