HEADER LIPID BINDING PROTEIN 23-MAR-20 6W9N TITLE SOLUTION STRUCTURE OF THE FYVE DOMAIN OF ALFY COMPND MOL_ID: 1; COMPND 2 MOLECULE: WD REPEAT AND FYVE DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FYVE DOMAIN; COMPND 5 SYNONYM: AUTOPHAGY-LINKED FYVE PROTEIN,ALFY; 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: WDFY3, KIAA0993; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FYVE DOMAIN, PHOSPHOINOSITIDE BINDING, ZINC BINDING, LIPID BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.F.REINHART,M.PELLEGRINI,M.J.RAGUSA REVDAT 4 15-MAY-24 6W9N 1 REMARK REVDAT 3 14-JUN-23 6W9N 1 REMARK REVDAT 2 10-MAR-21 6W9N 1 JRNL REVDAT 1 23-DEC-20 6W9N 0 JRNL AUTH E.F.REINHART,N.A.LITT,S.KATZENELL,M.PELLEGRINI,A.YAMAMOTO, JRNL AUTH 2 M.J.RAGUSA JRNL TITL A HIGHLY CONSERVED GLUTAMIC ACID IN ALFY INHIBITS MEMBRANE JRNL TITL 2 BINDING TO AID IN AGGREGATE CLEARANCE. JRNL REF TRAFFIC V. 22 23 2021 JRNL REFN ESSN 1600-0854 JRNL PMID 33225481 JRNL DOI 10.1111/TRA.12771 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6W9N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247555. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298 REMARK 210 PH : 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 150; 150; 150 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 583 UM [U-99% 15N] THE FYVE REMARK 210 DOMAIN OF ALFY, 20 MM SODIUM REMARK 210 PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 0.2 MM TCEP, 99% H2O/1% REMARK 210 D2O; 768 UM [U-99% 13C; U-99% REMARK 210 15N] THE FYVE DOMAIN OF ALFY, 20 REMARK 210 MM SODIUM PHOSPHATE, 150 MM REMARK 210 SODIUM CHLORIDE, 0.2 MM TCEP, 95% REMARK 210 H2O/5% D2O; 589 UM THE FYVE REMARK 210 DOMAIN OF ALFY, 20 MM SODIUM REMARK 210 PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 0.2 MM TCEP, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D CBCA(CO)NH; 3D HN(CO)CA; 3D REMARK 210 HNCA; 3D HNCACB; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HBHA(CBCACO)NH; 3D REMARK 210 (H)C(CCO)NH; 3D H(CCCO)NH; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 2D 1H-13C REMARK 210 HSQC ALIPHATIC; 3D HCCH-COSY; 3D REMARK 210 HCCH-TOCSY; 2D 1H-1H NOESY; 2D REMARK 210 1H-1H COSY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CARA, CANDID REMARK 210 METHOD USED : NA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 1 ARG A 5 142.67 -172.76 REMARK 500 1 SER A 6 -175.25 -176.54 REMARK 500 1 LYS A 13 103.76 -170.95 REMARK 500 1 ASP A 14 25.44 -158.58 REMARK 500 1 ASP A 18 37.46 -159.17 REMARK 500 1 CYS A 23 -29.96 -145.92 REMARK 500 1 ARG A 49 29.08 36.56 REMARK 500 2 ARG A 5 -72.52 179.28 REMARK 500 2 SER A 6 -45.17 -179.47 REMARK 500 2 ASP A 9 -58.26 -175.66 REMARK 500 2 ASP A 14 33.80 -179.65 REMARK 500 2 GLU A 15 -82.25 63.66 REMARK 500 2 ASP A 18 49.94 -85.61 REMARK 500 2 ARG A 49 27.82 36.73 REMARK 500 3 ALA A 3 -72.45 -151.41 REMARK 500 3 ARG A 5 144.08 -171.29 REMARK 500 3 SER A 6 174.48 60.92 REMARK 500 3 ASP A 9 118.97 -168.65 REMARK 500 3 HIS A 10 81.31 -170.96 REMARK 500 3 GLU A 15 91.62 -65.08 REMARK 500 3 ASP A 18 39.38 -157.21 REMARK 500 3 ARG A 49 29.69 36.14 REMARK 500 4 ALA A 3 -170.01 62.05 REMARK 500 4 ARG A 5 151.97 63.43 REMARK 500 4 SER A 6 125.55 179.36 REMARK 500 4 ASP A 9 -41.45 -157.19 REMARK 500 4 LYS A 13 29.96 -168.99 REMARK 500 4 CYS A 23 -30.03 -137.96 REMARK 500 4 ARG A 49 27.51 37.40 REMARK 500 5 ASN A 2 -175.06 60.30 REMARK 500 5 ALA A 3 -175.32 -178.09 REMARK 500 5 HIS A 10 67.87 -169.11 REMARK 500 5 ASP A 14 25.40 -144.22 REMARK 500 5 GLU A 15 -37.82 77.14 REMARK 500 5 ARG A 49 28.04 37.06 REMARK 500 6 ALA A 3 -58.95 -142.85 REMARK 500 6 ARG A 5 -170.07 -179.31 REMARK 500 6 SER A 6 -170.47 -60.88 REMARK 500 6 ASP A 9 -72.26 -103.07 REMARK 500 6 LYS A 13 88.29 -171.14 REMARK 500 6 GLU A 15 100.18 -53.42 REMARK 500 6 ASP A 18 55.18 -160.12 REMARK 500 6 ARG A 49 21.53 39.68 REMARK 500 7 ALA A 3 -169.82 -173.33 REMARK 500 7 ALA A 7 -86.71 63.82 REMARK 500 7 ALA A 8 -7.47 72.37 REMARK 500 7 ASP A 9 33.98 174.08 REMARK 500 7 ASP A 14 23.68 -158.19 REMARK 500 7 GLU A 15 -75.80 70.48 REMARK 500 7 ASP A 18 45.07 -89.36 REMARK 500 REMARK 500 THIS ENTRY HAS 151 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 20 SG REMARK 620 2 CYS A 23 SG 123.0 REMARK 620 3 CYS A 44 SG 106.9 122.1 REMARK 620 4 CYS A 47 SG 93.6 99.3 105.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 CYS A 39 SG 114.1 REMARK 620 3 CYS A 66 SG 110.9 115.9 REMARK 620 4 CYS A 69 SG 119.7 97.3 97.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30736 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE FYVE DOMAIN OF ALFY DBREF 6W9N A 4 78 UNP Q8IZQ1 WDFY3_HUMAN 3444 3518 SEQADV 6W9N SER A 1 UNP Q8IZQ1 EXPRESSION TAG SEQADV 6W9N ASN A 2 UNP Q8IZQ1 EXPRESSION TAG SEQADV 6W9N ALA A 3 UNP Q8IZQ1 EXPRESSION TAG SEQRES 1 A 78 SER ASN ALA GLY ARG SER ALA ALA ASP HIS TRP VAL LYS SEQRES 2 A 78 ASP GLU GLY GLY ASP SER CYS SER GLY CYS SER VAL ARG SEQRES 3 A 78 PHE SER LEU THR GLU ARG ARG HIS HIS CYS ARG ASN CYS SEQRES 4 A 78 GLY GLN LEU PHE CYS GLN LYS CYS SER ARG PHE GLN SER SEQRES 5 A 78 GLU ILE LYS ARG LEU LYS ILE SER SER PRO VAL ARG VAL SEQRES 6 A 78 CYS GLN ASN CYS TYR TYR ASN LEU GLN HIS GLU ARG GLY HET ZN A 101 1 HET ZN A 102 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 LYS A 55 LYS A 58 5 4 HELIX 2 AA2 CYS A 66 HIS A 75 1 10 SHEET 1 AA1 2 ARG A 33 HIS A 35 0 SHEET 2 AA1 2 LEU A 42 CYS A 44 -1 O PHE A 43 N HIS A 34 SHEET 1 AA2 2 SER A 52 ILE A 54 0 SHEET 2 AA2 2 ILE A 59 VAL A 63 -1 O VAL A 63 N SER A 52 LINK SG CYS A 20 ZN ZN A 101 1555 1555 2.30 LINK SG CYS A 23 ZN ZN A 101 1555 1555 2.30 LINK SG CYS A 36 ZN ZN A 102 1555 1555 2.40 LINK SG CYS A 39 ZN ZN A 102 1555 1555 2.40 LINK SG CYS A 44 ZN ZN A 101 1555 1555 2.30 LINK SG CYS A 47 ZN ZN A 101 1555 1555 2.30 LINK SG CYS A 66 ZN ZN A 102 1555 1555 2.35 LINK SG CYS A 69 ZN ZN A 102 1555 1555 2.36 SITE 1 AC1 4 CYS A 20 CYS A 23 CYS A 44 CYS A 47 SITE 1 AC2 5 CYS A 36 ASN A 38 CYS A 39 CYS A 66 SITE 2 AC2 5 CYS A 69 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1