HEADER EXOCYTOSIS 07-DEC-20 7B6E TITLE DROSOPHILA MELANOGASTER TRAPP C8 SUBUNITS REGION 355 TO 661 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FI18195P1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LETHAL (3) 76BDM,ISOFORM A,ISOFORM B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: L(3)76BDM, DMEL\CG8793, L(3)76BDM-RA, L(3)L3809, TRAPPC8, SOURCE 6 CG8793, DMEL_CG8793; SOURCE 7 EXPRESSION_SYSTEM: SPODOPTERA AFF. FRUGIPERDA 1 BOLD-2017; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 2449148 KEYWDS GOLGI, GEFS, RAB1, TRAPP, EXOCYTOSIS EXPDTA ELECTRON MICROSCOPY AUTHOR A.GALINDO,S.MUNRO,V.J.PLANELLES-HERRERO,G.DEGLIESPOSTI REVDAT 4 07-JUL-21 7B6E 1 JRNL REVDAT 3 23-JUN-21 7B6E 1 COMPND SOURCE JRNL REMARK REVDAT 3 2 1 DBREF SEQRES HELIX ATOM REVDAT 2 16-JUN-21 7B6E 1 JRNL REVDAT 1 09-JUN-21 7B6E 0 JRNL AUTH A.GALINDO,V.J.PLANELLES-HERRERO,G.DEGLIESPOSTI,S.MUNRO JRNL TITL CRYO-EM STRUCTURE OF METAZOAN TRAPPIII, THE MULTI-SUBUNIT JRNL TITL 2 COMPLEX THAT ACTIVATES THE GTPASE RAB1. JRNL REF EMBO J. V. 40 07608 2021 JRNL REFN ESSN 1460-2075 JRNL PMID 34018214 JRNL DOI 10.15252/EMBJ.2020107608 REMARK 2 REMARK 2 RESOLUTION. 4.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOLO, EPU, CTFFIND, UCSF CHIMERA, REMARK 3 COOT, RELION, RELION, 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 : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 302.400 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) : 4.500 REMARK 3 NUMBER OF PARTICLES : 353400 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 7B6E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292112706. 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 : TRAPPIII COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.05 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : PARTIAL MODEL OF THE TRAPP C8 REMARK 245 SUBUNITS FROM THE TRAPP C8, C12 AND C13 MAP. PART OF THE REMARK 245 TRAPPIII COMPLEX REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 3671 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 2200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 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) : 3000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 75000 REMARK 245 CALIBRATED MAGNIFICATION : 75000 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : 32% OF THE IMAGES WERE REMARK 245 ACQUIRING TILTED THE STAGE 19 DEGREES. 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: 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: 16590 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 ASN A 386 REMARK 465 LYS A 387 REMARK 465 LYS A 388 REMARK 465 GLY A 389 REMARK 465 VAL A 390 REMARK 465 SER A 391 REMARK 465 LYS A 392 REMARK 465 SER A 393 REMARK 465 LEU A 394 REMARK 465 LEU A 395 REMARK 465 SER A 396 REMARK 465 ALA A 397 REMARK 465 THR A 398 REMARK 465 LYS A 399 REMARK 465 ARG A 400 REMARK 465 TRP A 401 REMARK 465 PHE A 402 REMARK 465 VAL A 403 REMARK 465 THR A 404 REMARK 465 SER A 405 REMARK 465 LYS A 406 REMARK 465 PRO A 407 REMARK 465 GLY A 408 REMARK 465 ALA A 409 REMARK 465 GLY A 410 REMARK 465 ALA A 411 REMARK 465 ASN A 412 REMARK 465 ASN A 413 REMARK 465 GLN A 414 REMARK 465 ASN A 415 REMARK 465 ALA A 416 REMARK 465 VAL A 417 REMARK 465 ILE A 418 REMARK 465 TYR A 419 REMARK 465 THR A 420 REMARK 465 ASN A 421 REMARK 465 GLU A 422 REMARK 465 SER A 423 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 O ALA A 471 OG SER A 474 2.13 REMARK 500 OE1 GLN A 482 NZ LYS A 484 2.16 REMARK 500 O CYS A 516 OG1 THR A 519 2.18 REMARK 500 O GLU A 382 OG1 THR A 385 2.19 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 LEU A 468 CA - CB - CG ANGL. DEV. = 15.0 DEGREES REMARK 500 PRO A 559 CA - N - CD ANGL. DEV. = -9.6 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 MET A 477 48.54 -92.09 REMARK 500 ALA A 481 12.53 54.87 REMARK 500 GLN A 482 58.55 37.99 REMARK 500 ARG A 521 -6.75 69.09 REMARK 500 LEU A 522 51.31 -92.33 REMARK 500 GLU A 537 -12.55 77.93 REMARK 500 SER A 538 -178.42 179.64 REMARK 500 PRO A 559 -164.44 -79.72 REMARK 500 TRP A 600 72.91 43.50 REMARK 500 LEU A 632 75.31 58.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 598 GLU A 599 -145.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-12053 RELATED DB: EMDB REMARK 900 DROSOPHILA MELANOGASTER TRAPP C8 SUBUNITS REGION 355 TO 661 DBREF 7B6E A 355 661 UNP Q9VW22 Q9VW22_DROME 355 661 SEQRES 1 A 307 ASP ASN LEU ARG HIS PHE VAL GLN ASP TYR ALA VAL ARG SEQRES 2 A 307 ALA LEU ILE PRO TYR ILE GLU HIS LEU VAL ALA ILE LEU SEQRES 3 A 307 ALA GLU GLY VAL THR ASN LYS LYS GLY VAL SER LYS SER SEQRES 4 A 307 LEU LEU SER ALA THR LYS ARG TRP PHE VAL THR SER LYS SEQRES 5 A 307 PRO GLY ALA GLY ALA ASN ASN GLN ASN ALA VAL ILE TYR SEQRES 6 A 307 THR ASN GLU SER ALA GLU LEU GLN THR ARG LYS LEU GLY SEQRES 7 A 307 ASP LEU TYR PHE MET PHE GLY HIS TYR ASN LEU ALA PHE SEQRES 8 A 307 GLN SER TYR HIS GLN ALA LYS ARG ASP PHE ASN ALA ASP SEQRES 9 A 307 SER ALA TRP GLN TYR TYR ALA GLY ALA LEU GLU MET ALA SEQRES 10 A 307 ALA LEU SER ALA PHE MET LEU GLY THR ALA GLN ARG LYS SEQRES 11 A 307 THR TYR ASP TYR MET GLU ASP ALA ILE VAL CYS TYR LEU SEQRES 12 A 307 THR VAL CYS LYS LEU GLN GLN PHE ALA THR ARG ALA THR SEQRES 13 A 307 LEU LEU SER MET GLU CYS LEU LYS THR ALA ARG LEU TYR SEQRES 14 A 307 SER GLU VAL ALA LYS GLN LEU ILE ARG MET THR ASN GLU SEQRES 15 A 307 GLU SER ASP LEU ARG SER ALA LEU LEU LEU GLU GLN ALA SEQRES 16 A 307 ALA TYR CYS PHE LEU VAL THR GLN PRO PRO MET HIS ARG SEQRES 17 A 307 LYS TYR ALA PHE HIS ILE VAL LEU ALA GLY ASN ARG TYR SEQRES 18 A 307 SER ARG ALA GLY GLN ARG LYS HIS ALA TYR ARG CYS TYR SEQRES 19 A 307 ARG GLN ALA TYR GLN VAL PHE GLN LYS ARG GLU TRP SER SEQRES 20 A 307 LEU ALA GLU ASP HIS ILE GLN TYR THR VAL ALA LYS GLN SEQRES 21 A 307 ALA TYR MET LEU LYS GLN LEU GLU GLU ALA SER ARG SER SEQRES 22 A 307 PHE ALA HIS LEU LEU ARG PRO GLY SER LEU GLN SER ALA SEQRES 23 A 307 GLN GLN GLN THR SER PHE LEU LYS GLU TYR ILE GLN THR SEQRES 24 A 307 GLN ASN GLU LEU VAL LYS ARG SER HELIX 1 AA1 ASP A 355 VAL A 384 1 30 HELIX 2 AA2 GLU A 425 PHE A 438 1 14 HELIX 3 AA3 ASN A 442 ASN A 456 1 15 HELIX 4 AA4 TRP A 461 MET A 477 1 17 HELIX 5 AA5 ARG A 483 CYS A 500 1 18 HELIX 6 AA6 LEU A 502 THR A 519 1 18 HELIX 7 AA7 TYR A 523 ASN A 535 1 13 HELIX 8 AA8 LEU A 540 GLN A 557 1 18 HELIX 9 AA9 HIS A 561 GLY A 579 1 19 HELIX 10 AB1 GLN A 580 ARG A 598 1 19 HELIX 11 AB2 TRP A 600 GLN A 614 1 15 HELIX 12 AB3 GLN A 620 LEU A 632 1 13 HELIX 13 AB4 SER A 639 SER A 661 1 23 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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