HEADER PEPTIDE BINDING PROTEIN 25-MAR-20 6YEU TITLE SECOND EH DOMAIN OF ATEH1/PAN1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALCIUM-BINDING EF HAND FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: F2D10.25; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AT1G20760, F2D10.25, F2D10_25; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B_EH11 KEYWDS ADAPTOR PROTEIN, EF-HAND, EH DOMAIN, CALCIUM-BINDING, PEPTIDE MOTIF KEYWDS 2 BINDING, PEPTIDE BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.YPERMAN,A.PAPAGEORGIOU,T.EVANGELIDIS,D.VAN DAMME,K.TRIPSIANES REVDAT 4 19-JUN-24 6YEU 1 REMARK REVDAT 3 14-JUN-23 6YEU 1 REMARK REVDAT 2 09-JUN-21 6YEU 1 JRNL REVDAT 1 31-MAR-21 6YEU 0 JRNL AUTH K.YPERMAN,A.C.PAPAGEORGIOU,R.MERCERON,S.DE MUNCK,Y.BLOCH, JRNL AUTH 2 D.EECKHOUT,Q.JIANG,P.TACK,R.GRIGORYAN,T.EVANGELIDIS, JRNL AUTH 3 J.VAN LEENE,L.VINCZE,P.VANDENABEELE,F.VANHAECKE,M.POTOCKY, JRNL AUTH 4 G.DE JAEGER,S.N.SAVVIDES,K.TRIPSIANES,R.PLESKOT,D.VAN DAMME JRNL TITL DISTINCT EH DOMAINS OF THE ENDOCYTIC TPLATE COMPLEX CONFER JRNL TITL 2 LIPID AND PROTEIN BINDING. JRNL REF NAT COMMUN V. 12 3050 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34031427 JRNL DOI 10.1038/S41467-021-23314-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YEU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107149. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 EH11, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D HC(CC TOCSY(CO))NH; 4D REMARK 210 13C,15N EDITED HMQC-NOESY-HSQC; REMARK 210 4D 13C,13C EDITED HMQC-NOESY- REMARK 210 HSQC; 3D 13C EDITED NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, 4D-CHAINS, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 GLY A 0 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 OE1 GLU A 12 HH21 ARG A 62 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 LEU A 105 -70.35 -120.25 REMARK 500 1 SER A 106 27.11 -148.83 REMARK 500 2 LEU A 105 -63.29 -93.72 REMARK 500 3 ALA A 2 36.61 -95.89 REMARK 500 4 ALA A 2 56.46 -94.11 REMARK 500 4 LEU A 105 -63.76 -93.32 REMARK 500 5 ALA A 2 -32.27 -152.62 REMARK 500 6 ALA A 2 -80.50 65.27 REMARK 500 6 SER A 106 48.60 -103.00 REMARK 500 8 ALA A 2 68.34 -115.96 REMARK 500 8 GLN A 4 108.67 -56.16 REMARK 500 11 SER A 106 104.72 -169.38 REMARK 500 12 ALA A 2 52.53 -155.44 REMARK 500 13 LEU A 105 -61.89 -96.39 REMARK 500 15 LEU A 105 -43.90 -130.95 REMARK 500 16 LYS A 78 33.90 70.13 REMARK 500 16 SER A 106 17.91 -142.51 REMARK 500 17 LEU A 105 -52.30 -120.81 REMARK 500 19 LEU A 105 -61.17 -107.53 REMARK 500 20 GLN A 4 29.03 -78.32 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 25 0.07 SIDE CHAIN REMARK 500 4 ARG A 79 0.08 SIDE CHAIN REMARK 500 7 ARG A 79 0.10 SIDE CHAIN REMARK 500 8 ARG A 25 0.09 SIDE CHAIN 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 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 19 OD1 REMARK 620 2 ASP A 21 OD1 79.7 REMARK 620 3 ASP A 23 OD1 89.6 73.2 REMARK 620 4 ARG A 25 O 86.1 144.9 74.7 REMARK 620 5 GLU A 30 OE1 86.2 77.3 150.5 133.9 REMARK 620 6 GLU A 30 OE2 89.2 132.2 153.7 79.0 55.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34504 RELATED DB: BMRB REMARK 900 SECOND EH DOMAIN OF ATEH1/PAN1 DBREF 6YEU A 1 107 UNP Q9LM78 Q9LM78_ARATH 1 107 SEQADV 6YEU GLY A -1 UNP Q9LM78 EXPRESSION TAG SEQADV 6YEU GLY A 0 UNP Q9LM78 EXPRESSION TAG SEQRES 1 A 109 GLY GLY MET ALA GLY GLN ASN PRO ASN MET ASP GLN PHE SEQRES 2 A 109 GLU ALA TYR PHE LYS ARG ALA ASP LEU ASP GLY ASP GLY SEQRES 3 A 109 ARG ILE SER GLY ALA GLU ALA VAL GLY PHE PHE GLN GLY SEQRES 4 A 109 SER GLY LEU SER LYS GLN VAL LEU ALA GLN ILE TRP SER SEQRES 5 A 109 LEU SER ASP ARG SER HIS SER GLY PHE LEU ASP ARG GLN SEQRES 6 A 109 ASN PHE TYR ASN SER LEU ARG LEU VAL THR VAL ALA GLN SEQRES 7 A 109 SER LYS ARG ASP LEU THR PRO GLU ILE VAL ASN ALA ALA SEQRES 8 A 109 LEU ASN THR PRO ALA ALA ALA LYS ILE PRO PRO PRO LYS SEQRES 9 A 109 ILE ASN LEU SER ALA HET CA A 201 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 AA1 ASN A 5 ASP A 19 1 15 HELIX 2 AA2 GLY A 28 GLN A 36 1 9 HELIX 3 AA3 SER A 41 ASP A 53 1 13 HELIX 4 AA4 ASP A 61 SER A 77 1 17 HELIX 5 AA5 THR A 82 ASN A 91 1 10 HELIX 6 AA6 THR A 92 LYS A 97 5 6 SHEET 1 AA1 2 ILE A 26 SER A 27 0 SHEET 2 AA1 2 PHE A 59 LEU A 60 -1 O LEU A 60 N ILE A 26 LINK OD1 ASP A 19 CA CA A 201 1555 1555 2.43 LINK OD1 ASP A 21 CA CA A 201 1555 1555 2.42 LINK OD1 ASP A 23 CA CA A 201 1555 1555 2.41 LINK O ARG A 25 CA CA A 201 1555 1555 2.38 LINK OE1 GLU A 30 CA CA A 201 1555 1555 2.42 LINK OE2 GLU A 30 CA CA A 201 1555 1555 2.39 SITE 1 AC1 6 ASP A 19 ASP A 21 ASP A 23 ARG A 25 SITE 2 AC1 6 SER A 27 GLU A 30 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