HEADER ENDOCYTOSIS 22-NOV-18 6N5Y TITLE CRYSTAL STRUCTURE OF THE SNX5 PX DOMAIN IN COMPLEX WITH THE CI-MPR TITLE 2 (SPACE GROUP P212121 - FORM 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTING NEXIN-5,CATION-INDEPENDENT MANNOSE-6-PHOSPHATE COMPND 3 RECEPTOR; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: M6PR,300 KDA MANNOSE 6-PHOSPHATE RECEPTOR,MPR 300,INSULIN- COMPND 6 LIKE GROWTH FACTOR 2 RECEPTOR,INSULIN-LIKE GROWTH FACTOR II RECEPTOR, COMPND 7 IGF-II RECEPTOR,M6P/IGF2 RECEPTOR,M6P/IGF2R; COMPND 8 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: SNX5, IGF2R, MPRI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SORTING NEXIN, SNX, ENDOSOME, ENDOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR B.COLLINS,B.PAUL,S.WEERATUNGA REVDAT 3 13-MAR-24 6N5Y 1 REMARK REVDAT 2 23-OCT-19 6N5Y 1 JRNL REVDAT 1 18-SEP-19 6N5Y 0 JRNL AUTH B.SIMONETTI,B.PAUL,K.CHAUDHARI,S.WEERATUNGA,F.STEINBERG, JRNL AUTH 2 M.GORLA,K.J.HEESOM,G.J.BASHAW,B.M.COLLINS,P.J.CULLEN JRNL TITL MOLECULAR IDENTIFICATION OF A BAR DOMAIN-CONTAINING COAT JRNL TITL 2 COMPLEX FOR ENDOSOMAL RECYCLING OF TRANSMEMBRANE PROTEINS. JRNL REF NAT.CELL BIOL. V. 21 1219 2019 JRNL REFN ISSN 1465-7392 JRNL PMID 31576058 JRNL DOI 10.1038/S41556-019-0393-3 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10710 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1072 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 49.1446 - 4.5162 1.00 1297 144 0.2062 0.2168 REMARK 3 2 4.5162 - 3.5850 1.00 1226 136 0.1873 0.1843 REMARK 3 3 3.5850 - 3.1319 1.00 1199 134 0.2002 0.2704 REMARK 3 4 3.1319 - 2.8456 1.00 1203 134 0.2145 0.2850 REMARK 3 5 2.8456 - 2.6416 1.00 1189 132 0.2150 0.2372 REMARK 3 6 2.6416 - 2.4859 1.00 1183 131 0.2220 0.2483 REMARK 3 7 2.4859 - 2.3614 1.00 1167 131 0.2440 0.2907 REMARK 3 8 2.3614 - 2.2600 0.99 1174 130 0.2958 0.3554 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1357 REMARK 3 ANGLE : 0.838 1835 REMARK 3 CHIRALITY : 0.045 200 REMARK 3 PLANARITY : 0.006 236 REMARK 3 DIHEDRAL : 18.461 824 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 6N5Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000238032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.97803 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10740 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 REMARK 200 RESOLUTION RANGE LOW (A) : 49.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 75% OF 0.2 M (NH4)SO4, 0.1 M MES PH REMARK 280 6.5, 30% (W/V) PEG5000 MME + 15% GLYCEROL + 30% V/V (+/-)-2- REMARK 280 METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 49.13300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.13300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 16.53150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.29200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 16.53150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.29200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.13300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 16.53150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 67.29200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.13300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 16.53150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 67.29200 REMARK 290 SMTRY3 8 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 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 GLY A 20 REMARK 465 SER A 21 REMARK 465 SER A 22 REMARK 465 VAL A 23 REMARK 465 ASP A 24 REMARK 465 LEU A 25 REMARK 465 ASN A 26 REMARK 465 VAL A 27 REMARK 465 ASP A 28 REMARK 465 ASN A 180A REMARK 465 LYS A 180B REMARK 465 GLU A 180C REMARK 465 GLU A 180D REMARK 465 GLU A 180E REMARK 465 THR A 180F REMARK 465 ASP A 180G REMARK 465 GLU A 180H REMARK 465 ASN A 180I REMARK 465 GLU A 180J REMARK 465 THR A 180K 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 PRO A 29 CB CG CD 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 O THR A 117 N GLU A 119 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 118 CE LYS A 118 NZ -0.190 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 LYS A 118 -22.28 -22.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 6N5Y A 22 170 UNP Q9Y5X3 SNX5_HUMAN 22 170 DBREF 6N5Y A 171 200 UNP P11717 MPRI_HUMAN 2347 2377 SEQADV 6N5Y GLY A 20 UNP Q9Y5X3 EXPRESSION TAG SEQADV 6N5Y SER A 21 UNP Q9Y5X3 EXPRESSION TAG SEQRES 1 A 182 GLY SER SER VAL ASP LEU ASN VAL ASP PRO SER LEU GLN SEQRES 2 A 182 ILE ASP ILE PRO ASP ALA LEU SER GLU ARG ASP LYS VAL SEQRES 3 A 182 LYS PHE THR VAL HIS THR LYS THR THR LEU PRO THR PHE SEQRES 4 A 182 GLN SER PRO GLU PHE SER VAL THR ARG GLN HIS GLU ASP SEQRES 5 A 182 PHE VAL TRP LEU HIS ASP THR LEU ILE GLU THR THR ASP SEQRES 6 A 182 TYR ALA GLY LEU ILE ILE PRO PRO ALA PRO THR LYS PRO SEQRES 7 A 182 ASP PHE ASP GLY PRO ARG GLU LYS MET GLN LYS LEU GLY SEQRES 8 A 182 GLU GLY GLU GLY SER MET THR LYS GLU GLU PHE ALA LYS SEQRES 9 A 182 MET LYS GLN GLU LEU GLU ALA GLU TYR LEU ALA VAL PHE SEQRES 10 A 182 LYS LYS THR VAL SER SER HIS GLU VAL PHE LEU GLN ARG SEQRES 11 A 182 LEU SER SER HIS PRO VAL LEU SER LYS ASP ARG ASN PHE SEQRES 12 A 182 HIS VAL PHE LEU GLU TYR ASP GLN SER ASN VAL SER TYR SEQRES 13 A 182 LYS TYR SER LYS VAL ASN LYS GLU GLU GLU THR ASP GLU SEQRES 14 A 182 ASN GLU THR GLU TRP LEU MET GLU GLU ILE GLN LEU PRO FORMUL 2 HOH *26(H2 O) HELIX 1 AA1 HIS A 69 GLU A 81 1 13 HELIX 2 AA2 THR A 82 ALA A 86 5 5 HELIX 3 AA3 PHE A 99 GLY A 112 1 14 HELIX 4 AA4 GLU A 113 SER A 115 5 3 HELIX 5 AA5 LYS A 118 HIS A 153 1 36 HELIX 6 AA6 VAL A 155 LYS A 158 5 4 HELIX 7 AA7 ASP A 159 TYR A 168 1 10 SHEET 1 AA1 3 LEU A 31 GLU A 41 0 SHEET 2 AA1 3 LYS A 44 THR A 53 -1 O LYS A 44 N GLU A 41 SHEET 3 AA1 3 GLU A 62 GLN A 68 -1 O ARG A 67 N PHE A 47 SHEET 1 AA2 2 VAL A 173 SER A 178 0 SHEET 2 AA2 2 LEU A 193 GLN A 198 -1 O ILE A 197 N SER A 174 CRYST1 33.063 134.584 98.266 90.00 90.00 90.00 C 2 2 21 8 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 0.030245 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007430 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010176 0.00000