HEADER CONTRACTILE PROTEIN 03-APR-10 3MFP TITLE ATOMIC MODEL OF F-ACTIN BASED ON A 6.6 ANGSTROM RESOLUTION CRYOEM MAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACTIN, ALPHA SKELETAL MUSCLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: F-ACTIN, ALPHA-ACTIN-1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986 KEYWDS HELICAL FILAMENT, MUSCLE PROTEIN, CONTRACTILE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.FUJII,A.H.IWANE,T.YANAGIDA,K.NAMBA REVDAT 3 18-DEC-19 3MFP 1 REMARK LINK REVDAT 2 19-FEB-14 3MFP 1 JRNL VERSN REVDAT 1 29-SEP-10 3MFP 0 JRNL AUTH T.FUJII,A.H.IWANE,T.YANAGIDA,K.NAMBA JRNL TITL DIRECT VISUALIZATION OF SECONDARY STRUCTURES OF F-ACTIN BY JRNL TITL 2 ELECTRON CRYOMICROSCOPY JRNL REF NATURE V. 467 724 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20844487 JRNL DOI 10.1038/NATURE09372 REMARK 2 REMARK 2 RESOLUTION. 6.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : FLEX-EM, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1J6Z REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--FLEXIBLE FITTING 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) : 6.600 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 3MFP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1000058487. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : F-ACTIN 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 : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 21-MAR-09 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 50.00 REMARK 245 MICROSCOPE MODEL : JEOL 3200FSC REMARK 245 DETECTOR TYPE : TVIPS TEMCAM-F415 (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 1.60 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 20.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 100000 REMARK 245 CALIBRATED MAGNIFICATION : 172414 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = -166.66 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 27.60 ANGSTROMS 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 0.893465 0.449132 0.000000 0.00000 REMARK 350 BIOMT2 1 -0.449132 0.893465 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -55.20000 REMARK 350 BIOMT1 2 -0.973002 -0.230797 0.000000 0.00000 REMARK 350 BIOMT2 2 0.230797 -0.973002 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -27.60000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.973002 0.230797 0.000000 0.00000 REMARK 350 BIOMT2 4 -0.230797 -0.973002 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 27.60000 REMARK 350 BIOMT1 5 0.893465 -0.449132 0.000000 0.00000 REMARK 350 BIOMT2 5 0.449132 0.893465 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 55.20000 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 GLU A 2 -154.56 178.95 REMARK 500 ASP A 3 -133.71 -66.64 REMARK 500 GLU A 4 -159.85 40.47 REMARK 500 THR A 5 156.18 179.61 REMARK 500 LEU A 8 101.60 -58.79 REMARK 500 GLN A 41 97.31 21.83 REMARK 500 VAL A 43 -129.50 52.17 REMARK 500 MET A 44 -120.53 137.98 REMARK 500 VAL A 45 63.89 -150.18 REMARK 500 MET A 47 -143.78 -144.04 REMARK 500 VAL A 54 -82.08 61.51 REMARK 500 ALA A 58 -73.77 -40.72 REMARK 500 GLN A 59 -71.10 -31.84 REMARK 500 ALA A 181 -147.76 -161.41 REMARK 500 VAL A 201 -33.07 -135.48 REMARK 500 ASP A 222 118.74 -163.78 REMARK 500 GLU A 237 38.14 -73.67 REMARK 500 GLU A 334 78.10 -104.87 REMARK 500 ALA A 365 41.35 -107.64 REMARK 500 SER A 368 -39.79 -38.30 REMARK 500 VAL A 370 9.69 -64.72 REMARK 500 LYS A 373 38.61 71.92 REMARK 500 CYS A 374 -152.86 172.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 376 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-5168 RELATED DB: EMDB DBREF 3MFP A 1 375 UNP P68135 ACTS_RABIT 3 377 SEQRES 1 A 375 ASP GLU ASP GLU THR THR ALA LEU VAL CYS ASP ASN GLY SEQRES 2 A 375 SER GLY LEU VAL LYS ALA GLY PHE ALA GLY ASP ASP ALA SEQRES 3 A 375 PRO ARG ALA VAL PHE PRO SER ILE VAL GLY ARG PRO ARG SEQRES 4 A 375 HIS GLN GLY VAL MET VAL GLY MET GLY GLN LYS ASP SER SEQRES 5 A 375 TYR VAL GLY ASP GLU ALA GLN SER LYS ARG GLY ILE LEU SEQRES 6 A 375 THR LEU LYS TYR PRO ILE GLU HIC GLY ILE ILE THR ASN SEQRES 7 A 375 TRP ASP ASP MET GLU LYS ILE TRP HIS HIS THR PHE TYR SEQRES 8 A 375 ASN GLU LEU ARG VAL ALA PRO GLU GLU HIS PRO THR LEU SEQRES 9 A 375 LEU THR GLU ALA PRO LEU ASN PRO LYS ALA ASN ARG GLU SEQRES 10 A 375 LYS MET THR GLN ILE MET PHE GLU THR PHE ASN VAL PRO SEQRES 11 A 375 ALA MET TYR VAL ALA ILE GLN ALA VAL LEU SER LEU TYR SEQRES 12 A 375 ALA SER GLY ARG THR THR GLY ILE VAL LEU ASP SER GLY SEQRES 13 A 375 ASP GLY VAL THR HIS ASN VAL PRO ILE TYR GLU GLY TYR SEQRES 14 A 375 ALA LEU PRO HIS ALA ILE MET ARG LEU ASP LEU ALA GLY SEQRES 15 A 375 ARG ASP LEU THR ASP TYR LEU MET LYS ILE LEU THR GLU SEQRES 16 A 375 ARG GLY TYR SER PHE VAL THR THR ALA GLU ARG GLU ILE SEQRES 17 A 375 VAL ARG ASP ILE LYS GLU LYS LEU CYS TYR VAL ALA LEU SEQRES 18 A 375 ASP PHE GLU ASN GLU MET ALA THR ALA ALA SER SER SER SEQRES 19 A 375 SER LEU GLU LYS SER TYR GLU LEU PRO ASP GLY GLN VAL SEQRES 20 A 375 ILE THR ILE GLY ASN GLU ARG PHE ARG CYS PRO GLU THR SEQRES 21 A 375 LEU PHE GLN PRO SER PHE ILE GLY MET GLU SER ALA GLY SEQRES 22 A 375 ILE HIS GLU THR THR TYR ASN SER ILE MET LYS CYS ASP SEQRES 23 A 375 ILE ASP ILE ARG LYS ASP LEU TYR ALA ASN ASN VAL MET SEQRES 24 A 375 SER GLY GLY THR THR MET TYR PRO GLY ILE ALA ASP ARG SEQRES 25 A 375 MET GLN LYS GLU ILE THR ALA LEU ALA PRO SER THR MET SEQRES 26 A 375 LYS ILE LYS ILE ILE ALA PRO PRO GLU ARG LYS TYR SER SEQRES 27 A 375 VAL TRP ILE GLY GLY SER ILE LEU ALA SER LEU SER THR SEQRES 28 A 375 PHE GLN GLN MET TRP ILE THR LYS GLN GLU TYR ASP GLU SEQRES 29 A 375 ALA GLY PRO SER ILE VAL HIS ARG LYS CYS PHE MODRES 3MFP HIC A 73 HIS 4-METHYL-HISTIDINE HET HIC A 73 11 HET ADP A 376 27 HETNAM HIC 4-METHYL-HISTIDINE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 1 HIC C7 H11 N3 O2 FORMUL 2 ADP C10 H15 N5 O10 P2 HELIX 1 1 VAL A 54 LYS A 61 1 8 HELIX 2 2 ASN A 78 ASN A 92 1 15 HELIX 3 3 ALA A 97 HIS A 101 5 5 HELIX 4 4 PRO A 112 THR A 126 1 15 HELIX 5 5 GLN A 137 GLY A 146 1 10 HELIX 6 6 ALA A 181 GLU A 195 1 15 HELIX 7 7 THR A 202 CYS A 217 1 16 HELIX 8 8 ASP A 222 ALA A 231 1 10 HELIX 9 9 ASN A 252 THR A 260 1 9 HELIX 10 10 LEU A 261 PHE A 262 5 2 HELIX 11 11 GLN A 263 GLY A 268 5 6 HELIX 12 12 GLY A 273 MET A 283 1 11 HELIX 13 13 LYS A 284 CYS A 285 5 2 HELIX 14 14 ASP A 286 ASP A 288 5 3 HELIX 15 15 ILE A 289 ALA A 295 1 7 HELIX 16 16 GLY A 301 MET A 305 5 5 HELIX 17 17 GLY A 308 ALA A 321 1 14 HELIX 18 18 TYR A 337 SER A 348 1 12 HELIX 19 19 LEU A 349 TRP A 356 5 8 HELIX 20 20 LYS A 359 GLY A 366 1 8 HELIX 21 21 PRO A 367 HIS A 371 5 5 SHEET 1 A 6 ALA A 29 PRO A 32 0 SHEET 2 A 6 LEU A 16 PHE A 21 -1 N VAL A 17 O PHE A 31 SHEET 3 A 6 LEU A 8 ASN A 12 -1 N ASP A 11 O LYS A 18 SHEET 4 A 6 THR A 103 GLU A 107 1 O LEU A 104 N LEU A 8 SHEET 5 A 6 ALA A 131 ILE A 136 1 O TYR A 133 N LEU A 105 SHEET 6 A 6 ILE A 357 THR A 358 -1 O ILE A 357 N MET A 132 SHEET 1 B 3 TYR A 169 ALA A 170 0 SHEET 2 B 3 THR A 160 TYR A 166 -1 N TYR A 166 O TYR A 169 SHEET 3 B 3 MET A 176 LEU A 178 -1 O LEU A 178 N THR A 160 SHEET 1 C 5 TYR A 169 ALA A 170 0 SHEET 2 C 5 THR A 160 TYR A 166 -1 N TYR A 166 O TYR A 169 SHEET 3 C 5 GLY A 150 SER A 155 -1 N GLY A 150 O ILE A 165 SHEET 4 C 5 ASN A 297 SER A 300 1 O VAL A 298 N LEU A 153 SHEET 5 C 5 ILE A 329 ILE A 330 1 O ILE A 330 N ASN A 297 SHEET 1 D 2 LYS A 238 GLU A 241 0 SHEET 2 D 2 VAL A 247 ILE A 250 -1 O ILE A 248 N TYR A 240 LINK C GLU A 72 N HIC A 73 1555 1555 1.34 LINK C HIC A 73 N GLY A 74 1555 1555 1.33 SITE 1 AC1 12 GLY A 156 ASP A 157 GLY A 158 GLY A 182 SITE 2 AC1 12 LYS A 213 GLU A 214 GLY A 301 GLY A 302 SITE 3 AC1 12 THR A 303 MET A 305 TYR A 306 LYS A 336 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