HEADER LIPID BINDING PROTEIN 25-MAR-20 6YET 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_EH12 KEYWDS EF-HAND, EH DOMAIN, LIPID BINDING, ADAPTOR PROTEIN, CALCIUM BINDING, KEYWDS 2 LIPID BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.YPERMAN,A.PAPAGEORGIOU,T.EVANGELIDIS,D.VAN DAMME,K.TRIPSIANES REVDAT 4 19-JUN-24 6YET 1 REMARK REVDAT 3 14-JUN-23 6YET 1 REMARK REVDAT 2 09-JUN-21 6YET 1 JRNL REVDAT 1 31-MAR-21 6YET 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 6YET 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_1292107154. 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 EH12, 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 344 REMARK 465 GLY A 345 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 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 2 LYS A 374 44.07 38.54 REMARK 500 2 PRO A 434 150.50 -48.18 REMARK 500 5 PRO A 434 152.04 -48.38 REMARK 500 5 PHE A 443 36.14 -92.40 REMARK 500 6 ASN A 347 26.27 -146.82 REMARK 500 6 PHE A 443 34.32 -91.40 REMARK 500 7 PRO A 434 157.38 -48.80 REMARK 500 7 PHE A 443 42.65 -91.67 REMARK 500 10 ASP A 371 84.42 -69.47 REMARK 500 10 PHE A 443 30.71 -91.93 REMARK 500 11 PHE A 443 53.28 -112.45 REMARK 500 12 ASP A 371 74.43 -69.49 REMARK 500 12 PHE A 443 33.53 -87.06 REMARK 500 14 PHE A 443 42.44 -100.53 REMARK 500 16 ASN A 347 -73.90 -178.88 REMARK 500 16 ASN A 348 71.47 56.08 REMARK 500 16 ASP A 371 65.75 -69.73 REMARK 500 16 ASN A 408 25.84 47.35 REMARK 500 16 PHE A 443 38.49 -96.02 REMARK 500 18 ASN A 347 41.49 -88.19 REMARK 500 18 PHE A 443 36.08 -94.89 REMARK 500 19 PRO A 434 150.83 -48.24 REMARK 500 20 PRO A 434 154.32 -49.80 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 7 ARG A 428 0.11 SIDE CHAIN REMARK 500 8 ARG A 391 0.08 SIDE CHAIN REMARK 500 17 ARG A 428 0.07 SIDE CHAIN REMARK 500 18 ARG A 391 0.07 SIDE CHAIN REMARK 500 18 ARG A 426 0.08 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 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 405 OD1 REMARK 620 2 ASP A 407 OD1 92.4 REMARK 620 3 ASP A 409 OD1 94.8 73.8 REMARK 620 4 MET A 411 O 96.9 150.0 77.1 REMARK 620 5 SER A 413 OG 169.0 87.3 95.7 88.7 REMARK 620 6 GLU A 416 OE1 89.5 73.1 146.8 135.1 79.9 REMARK 620 7 GLU A 416 OE2 94.8 127.4 156.3 80.2 76.8 55.0 REMARK 620 N 1 2 3 4 5 6 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 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34503 RELATED DB: BMRB REMARK 900 SECOND EH DOMAIN OF ATEH1/PAN1 DBREF 6YET A 346 449 UNP Q9LM78 Q9LM78_ARATH 346 449 SEQADV 6YET GLY A 344 UNP Q9LM78 EXPRESSION TAG SEQADV 6YET GLY A 345 UNP Q9LM78 EXPRESSION TAG SEQRES 1 A 106 GLY GLY GLY ASN ASN GLN PRO PRO TRP PRO LYS MET LYS SEQRES 2 A 106 PRO SER ASP VAL GLN LYS TYR THR LYS VAL PHE MET GLU SEQRES 3 A 106 VAL ASP SER ASP LYS ASP GLY LYS ILE THR GLY GLU GLN SEQRES 4 A 106 ALA ARG ASN LEU PHE LEU SER TRP ARG LEU PRO ARG GLU SEQRES 5 A 106 VAL LEU LYS HIS VAL TRP GLU LEU SER ASP GLN ASP ASN SEQRES 6 A 106 ASP THR MET LEU SER LEU ARG GLU PHE CYS ILE SER LEU SEQRES 7 A 106 TYR LEU MET GLU ARG TYR ARG GLU GLY ARG PRO LEU PRO SEQRES 8 A 106 THR ALA LEU PRO SER SER ILE MET PHE ASP GLU THR LEU SEQRES 9 A 106 LEU SER HET CA A 501 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 AA1 LYS A 356 ASP A 371 1 16 HELIX 2 AA2 THR A 379 SER A 389 1 11 HELIX 3 AA3 PRO A 393 ASP A 405 1 13 HELIX 4 AA4 LEU A 414 GLY A 430 1 17 HELIX 5 AA5 PRO A 438 PHE A 443 1 6 HELIX 6 AA6 ASP A 444 SER A 449 1 6 SHEET 1 AA1 2 LYS A 377 ILE A 378 0 SHEET 2 AA1 2 LEU A 412 SER A 413 -1 O LEU A 412 N ILE A 378 LINK OD1 ASP A 405 CA CA A 501 1555 1555 2.46 LINK OD1 ASP A 407 CA CA A 501 1555 1555 2.44 LINK OD1 ASP A 409 CA CA A 501 1555 1555 2.42 LINK O MET A 411 CA CA A 501 1555 1555 2.43 LINK OG SER A 413 CA CA A 501 1555 1555 2.81 LINK OE1 GLU A 416 CA CA A 501 1555 1555 2.40 LINK OE2 GLU A 416 CA CA A 501 1555 1555 2.39 SITE 1 AC1 6 ASP A 405 ASP A 407 ASP A 409 MET A 411 SITE 2 AC1 6 SER A 413 GLU A 416 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