HEADER LIPID BINDING PROTEIN 24-AUG-23 8QBF TITLE COMPACT STATE - PIL1 DIMER WITH LIPID HEADGROUPS FITTED IN NATIVE TITLE 2 EISOSOME LATTICE BOUND TO PLASMA MEMBRANE MICRODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPHINGOLIPID LONG CHAIN BASE-RESPONSIVE PROTEIN PIL1; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 STRAIN: TB50 KEYWDS BAR DOMAIN, LIPID RECONSTITUTION, MEMBRANE MICRODOMAIN, LIPID BINDING KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.M.KEFAUVER,L.ZOU,A.DESFOSSES,R.J.LOEWITH REVDAT 4 28-AUG-24 8QBF 1 JRNL REVDAT 3 07-AUG-24 8QBF 1 JRNL REVDAT 2 31-JUL-24 8QBF 1 JRNL REVDAT 1 24-JUL-24 8QBF 0 JRNL AUTH J.M.KEFAUVER,M.HAKALA,L.ZOU,J.ALBA,J.ESPADAS,M.G.TETTAMANTI, JRNL AUTH 2 J.GAJIC,C.GABUS,P.CAMPOMANES,L.F.ESTROZI,N.E.SEN,S.VANNI, JRNL AUTH 3 A.ROUX,A.DESFOSSES,R.LOEWITH JRNL TITL CRYO-EM ARCHITECTURE OF A NEAR-NATIVE STRETCH-SENSITIVE JRNL TITL 2 MEMBRANE MICRODOMAIN. JRNL REF NATURE V. 632 664 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 39048819 JRNL DOI 10.1038/S41586-024-07720-6 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE,B.K.POON,R.J.READ,O.V.SOBOLEV,T.C.TERWILLIGER, REMARK 1 AUTH 2 A.URZHUMTSEV,P.D.ADAMS REMARK 1 TITL REAL-SPACE REFINEMENT IN PHENIX FOR CRYO-EM AND REMARK 1 TITL 2 CRYSTALLOGRAPHY. REMARK 1 REF ACTA CRYSTALLOGR D STRUCT V. 74 531 2018 REMARK 1 REF 2 BIOL REMARK 1 REFN ISSN 2059-7983 REMARK 1 PMID 29872004 REMARK 1 DOI 10.1107/S2059798318006551 REMARK 2 REMARK 2 RESOLUTION. 3.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, GCTF, UCSF CHIMERA, COOT, REMARK 3 RELION, CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.670 REMARK 3 NUMBER OF PARTICLES : 63118 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8QBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132985. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : HELICAL ARRAY REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : HELICAL LATTICE OF NATIVE REMARK 245 PIL1/LSP1 PROTEIN BOUND TO REMARK 245 PLASMA MEMBRANE MICRODOMAIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 IN SAME ASYMMETRIC UNIT 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 NZ LYS B 130 O41 I3P B 301 1.63 REMARK 500 CD ARG A 43 O3P SEP A 302 2.01 REMARK 500 CE LYS B 130 O41 I3P B 301 2.13 REMARK 500 NZ LYS A 130 O51 I3P A 301 2.15 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 PHE A 32 -169.11 -166.53 REMARK 500 PHE B 32 -169.08 -166.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-18311 RELATED DB: EMDB DBREF 8QBF A 1 271 UNP P53252 PIL1_YEAST 1 271 DBREF 8QBF B 1 271 UNP P53252 PIL1_YEAST 1 271 SEQRES 1 A 271 MET HIS ARG THR TYR SER LEU ARG ASN SER ARG ALA PRO SEQRES 2 A 271 THR ALA SER GLN LEU GLN ASN PRO PRO PRO PRO PRO SER SEQRES 3 A 271 THR THR LYS GLY ARG PHE PHE GLY LYS GLY GLY LEU ALA SEQRES 4 A 271 TYR SER PHE ARG ARG SER ALA ALA GLY ALA PHE GLY PRO SEQRES 5 A 271 GLU LEU SER ARG LYS LEU SER GLN LEU VAL LYS ILE GLU SEQRES 6 A 271 LYS ASN VAL LEU ARG SER MET GLU LEU THR ALA ASN GLU SEQRES 7 A 271 ARG ARG ASP ALA ALA LYS GLN LEU SER ILE TRP GLY LEU SEQRES 8 A 271 GLU ASN ASP ASP ASP VAL SER ASP ILE THR ASP LYS LEU SEQRES 9 A 271 GLY VAL LEU ILE TYR GLU VAL SER GLU LEU ASP ASP GLN SEQRES 10 A 271 PHE ILE ASP ARG TYR ASP GLN TYR ARG LEU THR LEU LYS SEQRES 11 A 271 SER ILE ARG ASP ILE GLU GLY SER VAL GLN PRO SER ARG SEQRES 12 A 271 ASP ARG LYS ASP LYS ILE THR ASP LYS ILE ALA TYR LEU SEQRES 13 A 271 LYS TYR LYS ASP PRO GLN SER PRO LYS ILE GLU VAL LEU SEQRES 14 A 271 GLU GLN GLU LEU VAL ARG ALA GLU ALA GLU SER LEU VAL SEQRES 15 A 271 ALA GLU ALA GLN LEU SER ASN ILE THR ARG SER LYS LEU SEQRES 16 A 271 ARG ALA ALA PHE ASN TYR GLN PHE ASP SER ILE ILE GLU SEQRES 17 A 271 HIS SER GLU LYS ILE ALA LEU ILE ALA GLY TYR GLY LYS SEQRES 18 A 271 ALA LEU LEU GLU LEU LEU ASP ASP SER PRO VAL THR PRO SEQRES 19 A 271 GLY GLU THR ARG PRO ALA TYR ASP GLY TYR GLU ALA SER SEQRES 20 A 271 LYS GLN ILE ILE ILE ASP ALA GLU SER ALA LEU ASN GLU SEQRES 21 A 271 TRP THR LEU ASP SER ALA GLN VAL LYS PRO THR SEQRES 1 B 271 MET HIS ARG THR TYR SER LEU ARG ASN SER ARG ALA PRO SEQRES 2 B 271 THR ALA SER GLN LEU GLN ASN PRO PRO PRO PRO PRO SER SEQRES 3 B 271 THR THR LYS GLY ARG PHE PHE GLY LYS GLY GLY LEU ALA SEQRES 4 B 271 TYR SER PHE ARG ARG SER ALA ALA GLY ALA PHE GLY PRO SEQRES 5 B 271 GLU LEU SER ARG LYS LEU SER GLN LEU VAL LYS ILE GLU SEQRES 6 B 271 LYS ASN VAL LEU ARG SER MET GLU LEU THR ALA ASN GLU SEQRES 7 B 271 ARG ARG ASP ALA ALA LYS GLN LEU SER ILE TRP GLY LEU SEQRES 8 B 271 GLU ASN ASP ASP ASP VAL SER ASP ILE THR ASP LYS LEU SEQRES 9 B 271 GLY VAL LEU ILE TYR GLU VAL SER GLU LEU ASP ASP GLN SEQRES 10 B 271 PHE ILE ASP ARG TYR ASP GLN TYR ARG LEU THR LEU LYS SEQRES 11 B 271 SER ILE ARG ASP ILE GLU GLY SER VAL GLN PRO SER ARG SEQRES 12 B 271 ASP ARG LYS ASP LYS ILE THR ASP LYS ILE ALA TYR LEU SEQRES 13 B 271 LYS TYR LYS ASP PRO GLN SER PRO LYS ILE GLU VAL LEU SEQRES 14 B 271 GLU GLN GLU LEU VAL ARG ALA GLU ALA GLU SER LEU VAL SEQRES 15 B 271 ALA GLU ALA GLN LEU SER ASN ILE THR ARG SER LYS LEU SEQRES 16 B 271 ARG ALA ALA PHE ASN TYR GLN PHE ASP SER ILE ILE GLU SEQRES 17 B 271 HIS SER GLU LYS ILE ALA LEU ILE ALA GLY TYR GLY LYS SEQRES 18 B 271 ALA LEU LEU GLU LEU LEU ASP ASP SER PRO VAL THR PRO SEQRES 19 B 271 GLY GLU THR ARG PRO ALA TYR ASP GLY TYR GLU ALA SER SEQRES 20 B 271 LYS GLN ILE ILE ILE ASP ALA GLU SER ALA LEU ASN GLU SEQRES 21 B 271 TRP THR LEU ASP SER ALA GLN VAL LYS PRO THR HET I3P A 301 24 HET SEP A 302 11 HET I3P B 301 24 HET SEP B 302 11 HETNAM I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 3 I3P 2(C6 H15 O15 P3) FORMUL 4 SEP 2(C3 H8 N O6 P) HELIX 1 AA1 THR A 14 ASN A 20 1 7 HELIX 2 AA2 LEU A 38 GLY A 48 1 11 HELIX 3 AA3 PRO A 52 GLU A 92 1 41 HELIX 4 AA4 ASP A 94 ASP A 160 1 67 HELIX 5 AA5 PRO A 164 LEU A 227 1 64 HELIX 6 AA6 GLY A 243 TRP A 261 1 19 HELIX 7 AA7 THR B 14 ASN B 20 1 7 HELIX 8 AA8 LEU B 38 GLY B 48 1 11 HELIX 9 AA9 PRO B 52 GLU B 92 1 41 HELIX 10 AB1 ASP B 94 ASP B 160 1 67 HELIX 11 AB2 PRO B 164 LEU B 227 1 64 HELIX 12 AB3 GLY B 243 TRP B 261 1 19 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