HEADER RNA BINDING PROTEIN 08-JUN-22 8A3P TITLE STRUCTURE OF HUMAN FY-5. COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINE AMIDOTRANSFERASE-LIKE CLASS 1 DOMAIN-CONTAINING COMPND 3 PROTEIN 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PARKINSON DISEASE 7 DOMAIN-CONTAINING PROTEIN 1; COMPND 6 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: GATD1, PDDC1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS FERRY COMPLEX, RNA BINDING, RNA TRANSPORT, EARLY ENDOSOME, RNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.S.SCHUHMACHER,M.ZERIAL REVDAT 4 07-FEB-24 8A3P 1 REMARK REVDAT 3 14-JUN-23 8A3P 1 JRNL REVDAT 2 20-JUL-22 8A3P 1 TITLE REVDAT 1 29-JUN-22 8A3P 0 JRNL AUTH D.QUENTIN,J.S.SCHUHMACHER,B.U.KLINK,J.LAUER,T.R.SHAIKH, JRNL AUTH 2 P.J.HUIS IN 'T VELD,L.M.WELP,H.URLAUB,M.ZERIAL,S.RAUNSER JRNL TITL STRUCTURAL BASIS OF MRNA BINDING BY THE HUMAN FERRY RAB5 JRNL TITL 2 EFFECTOR COMPLEX. JRNL REF MOL.CELL V. 83 1856 2023 JRNL REFN ISSN 1097-2765 JRNL PMID 37267906 JRNL DOI 10.1016/J.MOLCEL.2023.05.009 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 8293 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.090 REMARK 3 FREE R VALUE TEST SET COUNT : 837 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 47.3090 - 4.9052 1.00 1317 151 0.2180 0.2700 REMARK 3 2 4.9052 - 3.8940 0.97 1230 135 0.1800 0.2154 REMARK 3 3 3.8940 - 3.4019 1.00 1239 147 0.2278 0.2888 REMARK 3 4 3.4019 - 3.0909 1.00 1233 130 0.2399 0.2773 REMARK 3 5 3.0909 - 2.8694 0.99 1214 141 0.2756 0.3202 REMARK 3 6 2.8694 - 2.7003 0.99 1223 133 0.2949 0.3455 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.70 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 : 0.006 1455 REMARK 3 ANGLE : 0.894 1980 REMARK 3 CHIRALITY : 0.047 233 REMARK 3 PLANARITY : 0.006 256 REMARK 3 DIHEDRAL : 17.958 863 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 8A3P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1292122997. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.968 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8339 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 47.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.60300 REMARK 200 R SYM FOR SHELL (I) : 0.60300 REMARK 200 FOR SHELL : 1.200 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: 1U9C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 5.0, 0.8 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, 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 31.07900 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 31.07900 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 47.30950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.78650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.30950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.78650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.07900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.30950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.78650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 31.07900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.30950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.78650 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 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 ALA A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 ARG A 5 REMARK 465 LEU A 6 REMARK 465 PRO A 7 REMARK 465 ASN A 8 REMARK 465 GLU A 155 REMARK 465 LEU A 156 REMARK 465 VAL A 157 REMARK 465 ARG A 158 REMARK 465 ALA A 159 REMARK 465 PRO A 160 REMARK 465 GLY A 161 REMARK 465 PHE A 162 REMARK 465 ALA A 163 REMARK 465 ARG A 164 REMARK 465 LEU A 165 REMARK 465 PRO A 166 REMARK 465 GLY A 177 REMARK 465 ALA A 178 REMARK 465 CYS A 179 REMARK 465 PHE A 180 REMARK 465 SER A 218 REMARK 465 ARG A 219 REMARK 465 LYS A 220 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 GLU A 21 66.68 -116.99 REMARK 500 PHE A 143 55.12 -91.51 REMARK 500 SER A 183 -87.69 -117.49 REMARK 500 ARG A 194 -99.62 50.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7ND2 RELATED DB: PDB REMARK 900 CORE PARTICLE OF THE FERRY COMPLEX DBREF 8A3P A 1 220 UNP Q8NB37 GALD1_HUMAN 1 220 SEQRES 1 A 220 MET ALA SER GLU ARG LEU PRO ASN ARG PRO ALA CYS LEU SEQRES 2 A 220 LEU VAL ALA SER GLY ALA ALA GLU GLY VAL SER ALA GLN SEQRES 3 A 220 SER PHE LEU HIS CYS PHE THR MET ALA SER THR ALA PHE SEQRES 4 A 220 ASN LEU GLN VAL ALA THR PRO GLY GLY LYS ALA MET GLU SEQRES 5 A 220 PHE VAL ASP VAL THR GLU SER ASN ALA ARG TRP VAL GLN SEQRES 6 A 220 ASP PHE ARG LEU LYS ALA TYR ALA SER PRO ALA LYS LEU SEQRES 7 A 220 GLU SER ILE ASP GLY ALA ARG TYR HIS ALA LEU LEU ILE SEQRES 8 A 220 PRO SER CYS PRO GLY ALA LEU THR ASP LEU ALA SER SER SEQRES 9 A 220 GLY SER LEU ALA ARG ILE LEU GLN HIS PHE HIS SER GLU SEQRES 10 A 220 SER LYS PRO ILE CYS ALA VAL GLY HIS GLY VAL ALA ALA SEQRES 11 A 220 LEU CYS CYS ALA THR ASN GLU ASP ARG SER TRP VAL PHE SEQRES 12 A 220 ASP SER TYR SER LEU THR GLY PRO SER VAL CYS GLU LEU SEQRES 13 A 220 VAL ARG ALA PRO GLY PHE ALA ARG LEU PRO LEU VAL VAL SEQRES 14 A 220 GLU ASP PHE VAL LYS ASP SER GLY ALA CYS PHE SER ALA SEQRES 15 A 220 SER GLU PRO ASP ALA VAL HIS VAL VAL LEU ASP ARG HIS SEQRES 16 A 220 LEU VAL THR GLY GLN ASN ALA SER SER THR VAL PRO ALA SEQRES 17 A 220 VAL GLN ASN LEU LEU PHE LEU CYS GLY SER ARG LYS HELIX 1 AA1 ALA A 25 THR A 37 1 13 HELIX 2 AA2 PRO A 46 LYS A 49 5 4 HELIX 3 AA3 ASN A 60 ARG A 68 1 9 HELIX 4 AA4 LEU A 69 SER A 74 5 6 HELIX 5 AA5 GLU A 79 ILE A 81 5 3 HELIX 6 AA6 ASP A 82 TYR A 86 5 5 HELIX 7 AA7 GLY A 96 LEU A 101 1 6 HELIX 8 AA8 SER A 104 GLU A 117 1 14 HELIX 9 AA9 HIS A 126 ALA A 134 5 9 HELIX 10 AB1 ASP A 171 SER A 176 1 6 HELIX 11 AB2 ASN A 201 SER A 203 5 3 HELIX 12 AB3 SER A 204 CYS A 216 1 13 SHEET 1 AA1 7 ALA A 76 LYS A 77 0 SHEET 2 AA1 7 ASN A 40 THR A 45 1 N VAL A 43 O ALA A 76 SHEET 3 AA1 7 ALA A 11 VAL A 15 1 N LEU A 14 O GLN A 42 SHEET 4 AA1 7 ALA A 88 ILE A 91 1 O ALA A 88 N LEU A 13 SHEET 5 AA1 7 ILE A 121 VAL A 124 1 O CYS A 122 N ILE A 91 SHEET 6 AA1 7 LEU A 196 GLY A 199 1 O VAL A 197 N ILE A 121 SHEET 7 AA1 7 VAL A 190 ASP A 193 -1 N ASP A 193 O LEU A 196 SHEET 1 AA2 2 VAL A 23 SER A 24 0 SHEET 2 AA2 2 PHE A 53 VAL A 54 1 O VAL A 54 N VAL A 23 CRYST1 94.619 99.573 62.158 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 0.010569 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010043 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016088 0.00000