HEADER ENDOCYTOSIS/EXOCYTOSIS 19-JAN-01 1HYI TITLE SOLUTION STRUCTURE OF THE EEA1 FYVE DOMAIN COMPLEXED WITH INOSITOL 1, TITLE 2 3-BISPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOSOME-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FYVE DOMAIN (RESIDUES 1346-1410); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS BETA SHEET, ALPHA HELIX, ZINC CLUSTER, PTDINS(3)P, ENDOCYTOSIS- KEYWDS 2 EXOCYTOSIS COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.KUTATELADZE,M.OVERDUIN REVDAT 3 23-FEB-22 1HYI 1 REMARK LINK REVDAT 2 24-FEB-09 1HYI 1 VERSN REVDAT 1 14-MAR-01 1HYI 0 JRNL AUTH T.KUTATELADZE,M.OVERDUIN JRNL TITL STRUCTURAL MECHANISM OF ENDOSOME DOCKING BY THE FYVE DOMAIN. JRNL REF SCIENCE V. 291 1793 2001 JRNL REFN ISSN 0036-8075 JRNL PMID 11230696 JRNL DOI 10.1126/SCIENCE.291.5509.1793 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 1, X-PLOR 3.84 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HYI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1000012687. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 200 MM KCL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM FYVE DOMAIN; 20 MM D-TRIS REMARK 210 BUFFER; PH 6.7; 200 MM KCL; 20 REMARK 210 MM D-DTT; 1 MM NAN3; 1MM FYVE REMARK 210 DOMAIN; 20 MM D-TRIS BUFFER; PH REMARK 210 6.7; 200 MM KCL; 20 MM D-DTT; 1 REMARK 210 MM NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.84 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 198 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: CLOSE CONTACTS 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 HIS A 26 H PHE A 35 1.57 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 1 GLU A 5 58.37 -98.96 REMARK 500 1 ASP A 6 18.73 58.48 REMARK 500 1 GLU A 8 32.95 174.68 REMARK 500 1 VAL A 9 -76.25 -86.60 REMARK 500 1 ASN A 11 112.07 -170.62 REMARK 500 1 CYS A 12 166.82 -47.87 REMARK 500 1 ALA A 14 -91.64 -69.69 REMARK 500 1 PHE A 19 132.93 -39.71 REMARK 500 1 GLN A 30 -72.92 -87.50 REMARK 500 1 ALA A 41 37.55 -81.75 REMARK 500 2 ASP A 6 35.03 -178.63 REMARK 500 2 GLU A 8 49.81 -156.91 REMARK 500 2 VAL A 9 -48.69 -132.00 REMARK 500 2 GLN A 10 37.23 28.51 REMARK 500 2 ASN A 11 123.61 -171.03 REMARK 500 2 ALA A 14 -82.06 -75.02 REMARK 500 2 PHE A 19 146.32 -39.78 REMARK 500 2 SER A 20 -145.46 -142.72 REMARK 500 2 GLN A 30 -72.85 -77.34 REMARK 500 2 SER A 49 -135.84 -110.40 REMARK 500 2 LYS A 50 49.10 -153.62 REMARK 500 3 LYS A 2 -82.02 57.32 REMARK 500 3 GLU A 5 -85.84 -93.11 REMARK 500 3 ASP A 6 24.43 -165.20 REMARK 500 3 GLU A 8 -18.33 -149.41 REMARK 500 3 ALA A 14 -76.96 -78.84 REMARK 500 3 PHE A 19 161.37 -41.29 REMARK 500 3 SER A 20 -146.13 -157.47 REMARK 500 3 GLN A 30 -73.46 -82.25 REMARK 500 3 ALA A 41 44.12 -80.49 REMARK 500 3 LYS A 50 17.22 57.90 REMARK 500 4 TRP A 3 -134.19 -123.32 REMARK 500 4 ALA A 4 74.07 -61.46 REMARK 500 4 GLU A 5 -58.33 63.93 REMARK 500 4 ASN A 7 -44.77 -176.42 REMARK 500 4 ASN A 11 115.50 -165.36 REMARK 500 4 CYS A 12 155.75 -41.34 REMARK 500 4 ALA A 14 -81.05 -84.82 REMARK 500 4 PHE A 19 163.04 -41.49 REMARK 500 4 SER A 20 -153.67 -168.10 REMARK 500 4 SER A 49 -112.01 -74.85 REMARK 500 4 LYS A 50 30.62 -177.83 REMARK 500 5 LYS A 2 -73.87 -116.98 REMARK 500 5 TRP A 3 -161.97 -104.38 REMARK 500 5 ASP A 6 29.84 43.90 REMARK 500 5 GLU A 8 24.11 -166.00 REMARK 500 5 GLN A 10 29.15 35.13 REMARK 500 5 ASN A 11 114.50 -171.11 REMARK 500 5 ALA A 14 -80.00 -84.10 REMARK 500 5 PHE A 19 121.37 -39.77 REMARK 500 REMARK 500 THIS ENTRY HAS 208 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 1 0.09 SIDE CHAIN REMARK 500 1 ARG A 24 0.22 SIDE CHAIN REMARK 500 1 ARG A 25 0.13 SIDE CHAIN REMARK 500 1 ARG A 29 0.30 SIDE CHAIN REMARK 500 1 ARG A 54 0.22 SIDE CHAIN REMARK 500 2 ARG A 1 0.32 SIDE CHAIN REMARK 500 2 ARG A 24 0.24 SIDE CHAIN REMARK 500 2 ARG A 25 0.27 SIDE CHAIN REMARK 500 2 ARG A 29 0.08 SIDE CHAIN REMARK 500 2 ARG A 54 0.24 SIDE CHAIN REMARK 500 3 ARG A 1 0.31 SIDE CHAIN REMARK 500 3 ARG A 25 0.19 SIDE CHAIN REMARK 500 3 ARG A 54 0.19 SIDE CHAIN REMARK 500 4 ARG A 1 0.25 SIDE CHAIN REMARK 500 4 ARG A 24 0.26 SIDE CHAIN REMARK 500 4 ARG A 25 0.23 SIDE CHAIN REMARK 500 4 ARG A 29 0.20 SIDE CHAIN REMARK 500 4 ARG A 54 0.29 SIDE CHAIN REMARK 500 5 ARG A 1 0.17 SIDE CHAIN REMARK 500 5 ARG A 24 0.20 SIDE CHAIN REMARK 500 5 ARG A 25 0.29 SIDE CHAIN REMARK 500 5 ARG A 29 0.11 SIDE CHAIN REMARK 500 5 ARG A 54 0.31 SIDE CHAIN REMARK 500 6 ARG A 1 0.13 SIDE CHAIN REMARK 500 6 ARG A 24 0.22 SIDE CHAIN REMARK 500 6 ARG A 25 0.18 SIDE CHAIN REMARK 500 6 ARG A 29 0.28 SIDE CHAIN REMARK 500 6 ARG A 54 0.22 SIDE CHAIN REMARK 500 7 ARG A 1 0.25 SIDE CHAIN REMARK 500 7 ARG A 24 0.30 SIDE CHAIN REMARK 500 7 ARG A 25 0.23 SIDE CHAIN REMARK 500 7 ARG A 29 0.24 SIDE CHAIN REMARK 500 7 ARG A 54 0.32 SIDE CHAIN REMARK 500 8 ARG A 1 0.18 SIDE CHAIN REMARK 500 8 ARG A 24 0.31 SIDE CHAIN REMARK 500 8 ARG A 25 0.29 SIDE CHAIN REMARK 500 8 ARG A 29 0.29 SIDE CHAIN REMARK 500 8 ARG A 54 0.08 SIDE CHAIN REMARK 500 9 ARG A 1 0.21 SIDE CHAIN REMARK 500 9 ARG A 24 0.32 SIDE CHAIN REMARK 500 9 ARG A 25 0.12 SIDE CHAIN REMARK 500 9 ARG A 29 0.20 SIDE CHAIN REMARK 500 10 ARG A 1 0.29 SIDE CHAIN REMARK 500 10 ARG A 24 0.24 SIDE CHAIN REMARK 500 10 ARG A 25 0.27 SIDE CHAIN REMARK 500 10 ARG A 54 0.23 SIDE CHAIN REMARK 500 11 ARG A 1 0.21 SIDE CHAIN REMARK 500 11 ARG A 24 0.10 SIDE CHAIN REMARK 500 11 ARG A 25 0.25 SIDE CHAIN REMARK 500 11 ARG A 29 0.17 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 92 PLANE DEVIATIONS. 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 66 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 12 SG REMARK 620 2 CYS A 15 SG 79.1 REMARK 620 3 CYS A 36 SG 134.5 87.1 REMARK 620 4 CYS A 39 SG 110.3 128.9 112.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 67 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 28 SG REMARK 620 2 CYS A 31 SG 93.5 REMARK 620 3 CYS A 56 SG 116.8 149.7 REMARK 620 4 CYS A 59 SG 76.0 122.4 68.2 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 66 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 67 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ITP A 68 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HYJ RELATED DB: PDB REMARK 900 1HYJ CONTAINS THE FYVE DOMAIN WITHOUT INOSITOL 1,3-BISPHOSPHATE DBREF 1HYI A 1 65 UNP Q15075 EEA1_HUMAN 1346 1410 SEQRES 1 A 65 ARG LYS TRP ALA GLU ASP ASN GLU VAL GLN ASN CYS MET SEQRES 2 A 65 ALA CYS GLY LYS GLY PHE SER VAL THR VAL ARG ARG HIS SEQRES 3 A 65 HIS CYS ARG GLN CYS GLY ASN ILE PHE CYS ALA GLU CYS SEQRES 4 A 65 SER ALA LYS ASN ALA LEU THR PRO SER SER LYS LYS PRO SEQRES 5 A 65 VAL ARG VAL CYS ASP ALA CYS PHE ASN ASP LEU GLN GLY HET ZN A 66 1 HET ZN A 67 1 HET ITP A 68 30 HETNAM ZN ZINC ION HETNAM ITP PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5- HETNAM 2 ITP PHOSPHONOOXY-CYCLOHEXYL) ESTER HETSYN ITP INOSITOL 1,3-BISPHOSPHATE FORMUL 2 ZN 2(ZN 2+) FORMUL 4 ITP C6 H14 O12 P2 HELIX 1 1 CYS A 56 GLN A 64 1 9 SHEET 1 A 2 ARG A 25 HIS A 27 0 SHEET 2 A 2 ILE A 34 CYS A 36 -1 N PHE A 35 O HIS A 26 SHEET 1 B 2 LYS A 42 THR A 46 0 SHEET 2 B 2 LYS A 51 VAL A 55 -1 O LYS A 51 N THR A 46 LINK SG CYS A 12 ZN ZN A 66 1555 1555 2.38 LINK SG CYS A 15 ZN ZN A 66 1555 1555 2.54 LINK SG CYS A 28 ZN ZN A 67 1555 1555 2.84 LINK SG CYS A 31 ZN ZN A 67 1555 1555 2.88 LINK SG CYS A 36 ZN ZN A 66 1555 1555 2.37 LINK SG CYS A 39 ZN ZN A 66 1555 1555 2.38 LINK SG CYS A 56 ZN ZN A 67 1555 1555 2.89 LINK SG CYS A 59 ZN ZN A 67 1555 1555 2.67 SITE 1 AC1 4 CYS A 12 CYS A 15 CYS A 36 CYS A 39 SITE 1 AC2 4 CYS A 28 CYS A 31 CYS A 56 CYS A 59 SITE 1 AC3 5 ARG A 25 HIS A 26 HIS A 27 ARG A 29 SITE 2 AC3 5 ARG A 54 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