HEADER PROTEIN TRANSPORT 13-JUN-17 5O8O TITLE N. CRASSA TOM40 MODEL BASED ON CRYO-EM STRUCTURE OF THE TOM CORE TITLE 2 COMPLEX AT 6.8 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM40; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN MOM38,TRANSLOCASE OF OUTER MEMBRANE 40 KDA SUBUNIT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEUROSPORA CRASSA (STRAIN ATCC 24698 / 74-OR23- SOURCE 3 1A / CBS 708.71 / DSM 1257 / FGSC 987); SOURCE 4 ORGANISM_TAXID: 5141; SOURCE 5 STRAIN: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 KEYWDS TOM-COMPLEX, PROTEIN IMPORT, MITOCHONDRIA, CRYO-EM, PROTEIN TRANSPORT EXPDTA ELECTRON MICROSCOPY AUTHOR T.BAUSEWEIN,D.J.MILLS,S.NUSSBERGER,B.NITSCHKE,W.KUEHLBRANDT REVDAT 2 24-OCT-18 5O8O 1 JRNL REVDAT 1 16-AUG-17 5O8O 0 JRNL AUTH T.BAUSEWEIN,D.J.MILLS,J.D.LANGER,B.NITSCHKE,S.NUSSBERGER, JRNL AUTH 2 W.KUHLBRANDT JRNL TITL CRYO-EM STRUCTURE OF THE TOM CORE COMPLEX FROM NEUROSPORA JRNL TITL 2 CRASSA. JRNL REF CELL V. 170 693 2017 JRNL REFN ISSN 1097-4172 JRNL PMID 28802041 JRNL DOI 10.1016/J.CELL.2017.07.012 REMARK 2 REMARK 2 RESOLUTION. 6.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, FOLDIT 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 : FLEXIBLE FIT 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) : 6.800 REMARK 3 NUMBER OF PARTICLES : 92144 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 5O8O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005365. 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 : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : TOM CORE COMPLEX CONSISTING OF REMARK 245 TOM40, TOM22, TOM5, TOM6 AND REMARK 245 TOM7 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.20 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 : JEOL 3200FSC REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 60.00 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 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: 19430 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 PHE A 4 REMARK 465 SER A 5 REMARK 465 THR A 6 REMARK 465 GLU A 7 REMARK 465 SER A 8 REMARK 465 PRO A 9 REMARK 465 LEU A 10 REMARK 465 ALA A 11 REMARK 465 MET A 12 REMARK 465 LEU A 13 REMARK 465 ARG A 14 REMARK 465 ASP A 15 REMARK 465 ASN A 16 REMARK 465 ALA A 17 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 H PHE A 73 O VAL A 81 1.46 REMARK 500 O ILE A 18 HG SER A 21 1.58 REMARK 500 O VAL A 194 HG1 THR A 206 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY A 64 O - C - N ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG A 128 O - C - N ANGL. DEV. = -11.3 DEGREES REMARK 500 PRO A 204 C - N - CA ANGL. DEV. = 13.1 DEGREES REMARK 500 PRO A 255 C - N - CA ANGL. DEV. = 9.3 DEGREES 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 GLN A 141 134.37 -170.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-3761 RELATED DB: EMDB REMARK 900 N. CRASSA TOM40 MODEL BASED ON CRYO-EM STRUCTURE OF THE TOM CORE REMARK 900 COMPLEX AT 6.8 A DBREF 5O8O A 1 349 UNP P24391 TOM40_NEUCR 1 349 SEQRES 1 A 349 MET ALA SER PHE SER THR GLU SER PRO LEU ALA MET LEU SEQRES 2 A 349 ARG ASP ASN ALA ILE TYR SER SER LEU SER ASP ALA PHE SEQRES 3 A 349 ASN ALA PHE GLN GLU ARG ARG LYS GLN PHE GLY LEU SER SEQRES 4 A 349 ASN PRO GLY THR ILE GLU THR ILE ALA ARG GLU VAL GLN SEQRES 5 A 349 ARG ASP THR LEU LEU THR ASN TYR MET PHE SER GLY LEU SEQRES 6 A 349 ARG ALA ASP VAL THR LYS ALA PHE SER LEU ALA PRO LEU SEQRES 7 A 349 PHE GLN VAL SER HIS GLN PHE ALA MET GLY GLU ARG LEU SEQRES 8 A 349 ASN PRO TYR ALA PHE ALA ALA LEU TYR GLY THR ASN GLN SEQRES 9 A 349 ILE PHE ALA GLN GLY ASN LEU ASP ASN GLU GLY ALA LEU SEQRES 10 A 349 SER THR ARG PHE ASN TYR ARG TRP GLY ASP ARG THR ILE SEQRES 11 A 349 THR LYS THR GLN PHE SER ILE GLY GLY GLY GLN ASP MET SEQRES 12 A 349 ALA GLN PHE GLU HIS GLU HIS LEU GLY ASP ASP PHE SER SEQRES 13 A 349 ALA SER LEU LYS ALA ILE ASN PRO SER PHE LEU ASP GLY SEQRES 14 A 349 GLY LEU THR GLY ILE PHE VAL GLY ASP TYR LEU GLN ALA SEQRES 15 A 349 VAL THR PRO ARG LEU GLY LEU GLY LEU GLN ALA VAL TRP SEQRES 16 A 349 GLN ARG GLN GLY LEU THR GLN GLY PRO ASP THR ALA ILE SEQRES 17 A 349 SER TYR PHE ALA ARG TYR LYS ALA GLY ASP TRP VAL ALA SEQRES 18 A 349 SER ALA GLN LEU GLN ALA GLN GLY ALA LEU ASN THR SER SEQRES 19 A 349 PHE TRP LYS LYS LEU THR ASP ARG VAL GLN ALA GLY VAL SEQRES 20 A 349 ASP MET THR LEU SER VAL ALA PRO SER GLN SER MET MET SEQRES 21 A 349 GLY GLY LEU THR LYS GLU GLY ILE THR THR PHE GLY ALA SEQRES 22 A 349 LYS TYR ASP PHE ARG MET SER THR PHE ARG ALA GLN ILE SEQRES 23 A 349 ASP SER LYS GLY LYS LEU SER CYS LEU LEU GLU LYS ARG SEQRES 24 A 349 LEU GLY ALA ALA PRO VAL THR LEU THR PHE ALA ALA ASP SEQRES 25 A 349 VAL ASP HIS VAL THR GLN GLN ALA LYS LEU GLY MET SER SEQRES 26 A 349 VAL SER ILE GLU ALA SER ASP VAL ASP LEU GLN GLU GLN SEQRES 27 A 349 GLN GLU GLY ALA GLN SER LEU ASN ILE PRO PHE HELIX 1 AA1 TYR A 19 GLY A 37 1 19 HELIX 2 AA2 THR A 43 MET A 61 1 19 HELIX 3 AA3 ASP A 332 ALA A 342 1 11 SHEET 1 AA120 ALA A 67 ALA A 76 0 SHEET 2 AA120 PHE A 79 PHE A 85 -1 O VAL A 81 N PHE A 73 SHEET 3 AA120 ALA A 95 THR A 102 -1 O ALA A 95 N GLN A 84 SHEET 4 AA120 ILE A 105 ASN A 113 -1 O ALA A 107 N TYR A 100 SHEET 5 AA120 LEU A 117 ARG A 124 -1 O SER A 118 N ASP A 112 SHEET 6 AA120 THR A 131 ILE A 137 -1 O PHE A 135 N PHE A 121 SHEET 7 AA120 MET A 143 LEU A 151 -1 O MET A 143 N SER A 136 SHEET 8 AA120 PHE A 155 ILE A 162 -1 O LEU A 159 N HIS A 148 SHEET 9 AA120 GLY A 173 ALA A 182 -1 O VAL A 176 N LYS A 160 SHEET 10 AA120 LEU A 187 ARG A 197 -1 O TRP A 195 N PHE A 175 SHEET 11 AA120 PRO A 204 LYS A 215 -1 O ASP A 205 N GLN A 196 SHEET 12 AA120 VAL A 220 LEU A 225 -1 O ALA A 221 N TYR A 214 SHEET 13 AA120 LEU A 231 LYS A 238 -1 O TRP A 236 N VAL A 220 SHEET 14 AA120 VAL A 243 SER A 252 -1 O MET A 249 N THR A 233 SHEET 15 AA120 GLU A 266 TYR A 275 -1 O ILE A 268 N THR A 250 SHEET 16 AA120 SER A 280 SER A 288 -1 O ILE A 286 N PHE A 271 SHEET 17 AA120 LYS A 291 ARG A 299 -1 O LEU A 295 N ARG A 283 SHEET 18 AA120 VAL A 305 ASP A 314 -1 O LEU A 307 N LYS A 298 SHEET 19 AA120 GLN A 319 GLU A 329 -1 O GLN A 319 N ASP A 314 SHEET 20 AA120 ALA A 67 ALA A 76 1 N THR A 70 O ILE A 328 SHEET 1 AA2 2 PHE A 166 LEU A 167 0 SHEET 2 AA2 2 GLY A 170 LEU A 171 -1 O GLY A 170 N LEU A 167 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