HEADER TRANSFERASE 09-AUG-23 8TR9 TITLE CRYO-EM STRUCTURE OF TRANSGLUTAMINASE 2 BOUND TO GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ERYTHROCYTE TRANSGLUTAMINASE,HEART G ALPHA(H),HHG ALPHA(H), COMPND 5 ISOPEPTIDASE TGM2,PROTEIN G ALPHA(H),G(H),PROTEIN-GLUTAMINE DEAMIDASE COMPND 6 TGM2,PROTEIN-GLUTAMINE DOPAMINYLTRANSFERASE TGM2,PROTEIN-GLUTAMINE COMPND 7 HISTAMINYLTRANSFERASE TGM2,PROTEIN-GLUTAMINE COMPND 8 NORADRENALINYLTRANSFERASE TGM2,PROTEIN-GLUTAMINE SEROTONYLTRANSFERASE COMPND 9 TGM2,TISSUE TRANSGLUTAMINASE,TTG,TTGASE,TRANSGLUTAMINASE C,TG(C),TGC, COMPND 10 TGASE C,TRANSGLUTAMINASE H,TGASE H,TRANSGLUTAMINASE II,TGASE II, COMPND 11 TRANSGLUTAMINASE-2,TG2,TGASE-2,HTG2; COMPND 12 EC: 2.3.2.13,3.4.-.-,3.5.1.44,2.3.1.-; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TGM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GDP, COMPLEX, SIGNALING, G-PROTEIN, CANCER, CRYO-EM, TRANSFERASE EXPDTA ELECTRON MICROSCOPY AUTHOR C.APLIN,R.A.CERIONE REVDAT 1 31-JUL-24 8TR9 0 JRNL AUTH C.APLIN,K.A.ZIELINSKI,S.PABIT,D.OGUNRIBIDO,W.P.KATT, JRNL AUTH 2 L.POLLACK,R.A.CERIONE,S.K.MILANO JRNL TITL CONFORMATIONAL ACTIVATION AND INHIBITION OF TRANSGLUTAMINASE JRNL TITL 2 2 DETERMINED BY STATIC AND TIME RESOLVED SMALL-ANGLE X-RAY JRNL TITL 3 SCATTERING AND CRYOELECTRON MICROSCOPY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 136297 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8TR9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276487. 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 : TRANSGLUTAMINASE 2 BOUND TO GDP 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 : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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) : 5110.00 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) : 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 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 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 GLU A 3 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 ASN A 49 -114.01 59.01 REMARK 500 GLU A 85 65.48 -100.63 REMARK 500 TYR A 274 66.36 60.67 REMARK 500 ALA A 304 54.78 -93.55 REMARK 500 LEU A 462 0.62 -66.42 REMARK 500 LYS A 674 -167.29 -78.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-41574 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF TRANSGLUTAMINASE 2 BOUND TO GDP DBREF 8TR9 A 1 687 UNP P21980 TGM2_HUMAN 1 687 SEQRES 1 A 687 MET ALA GLU GLU LEU VAL LEU GLU ARG CYS ASP LEU GLU SEQRES 2 A 687 LEU GLU THR ASN GLY ARG ASP HIS HIS THR ALA ASP LEU SEQRES 3 A 687 CYS ARG GLU LYS LEU VAL VAL ARG ARG GLY GLN PRO PHE SEQRES 4 A 687 TRP LEU THR LEU HIS PHE GLU GLY ARG ASN TYR GLU ALA SEQRES 5 A 687 SER VAL ASP SER LEU THR PHE SER VAL VAL THR GLY PRO SEQRES 6 A 687 ALA PRO SER GLN GLU ALA GLY THR LYS ALA ARG PHE PRO SEQRES 7 A 687 LEU ARG ASP ALA VAL GLU GLU GLY ASP TRP THR ALA THR SEQRES 8 A 687 VAL VAL ASP GLN GLN ASP CYS THR LEU SER LEU GLN LEU SEQRES 9 A 687 THR THR PRO ALA ASN ALA PRO ILE GLY LEU TYR ARG LEU SEQRES 10 A 687 SER LEU GLU ALA SER THR GLY TYR GLN GLY SER SER PHE SEQRES 11 A 687 VAL LEU GLY HIS PHE ILE LEU LEU PHE ASN ALA TRP CYS SEQRES 12 A 687 PRO ALA ASP ALA VAL TYR LEU ASP SER GLU GLU GLU ARG SEQRES 13 A 687 GLN GLU TYR VAL LEU THR GLN GLN GLY PHE ILE TYR GLN SEQRES 14 A 687 GLY SER ALA LYS PHE ILE LYS ASN ILE PRO TRP ASN PHE SEQRES 15 A 687 GLY GLN PHE GLU ASP GLY ILE LEU ASP ILE CYS LEU ILE SEQRES 16 A 687 LEU LEU ASP VAL ASN PRO LYS PHE LEU LYS ASN ALA GLY SEQRES 17 A 687 ARG ASP CYS SER ARG ARG SER SER PRO VAL TYR VAL GLY SEQRES 18 A 687 ARG VAL VAL SER GLY MET VAL ASN CYS ASN ASP ASP GLN SEQRES 19 A 687 GLY VAL LEU LEU GLY ARG TRP ASP ASN ASN TYR GLY ASP SEQRES 20 A 687 GLY VAL SER PRO MET SER TRP ILE GLY SER VAL ASP ILE SEQRES 21 A 687 LEU ARG ARG TRP LYS ASN HIS GLY CYS GLN ARG VAL LYS SEQRES 22 A 687 TYR GLY GLN CYS TRP VAL PHE ALA ALA VAL ALA CYS THR SEQRES 23 A 687 VAL LEU ARG CYS LEU GLY ILE PRO THR ARG VAL VAL THR SEQRES 24 A 687 ASN TYR ASN SER ALA HIS ASP GLN ASN SER ASN LEU LEU SEQRES 25 A 687 ILE GLU TYR PHE ARG ASN GLU PHE GLY GLU ILE GLN GLY SEQRES 26 A 687 ASP LYS SER GLU MET ILE TRP ASN PHE HIS CYS TRP VAL SEQRES 27 A 687 GLU SER TRP MET THR ARG PRO ASP LEU GLN PRO GLY TYR SEQRES 28 A 687 GLU GLY TRP GLN ALA LEU ASP PRO THR PRO GLN GLU LYS SEQRES 29 A 687 SER GLU GLY THR TYR CYS CYS GLY PRO VAL PRO VAL ARG SEQRES 30 A 687 ALA ILE LYS GLU GLY ASP LEU SER THR LYS TYR ASP ALA SEQRES 31 A 687 PRO PHE VAL PHE ALA GLU VAL ASN ALA ASP VAL VAL ASP SEQRES 32 A 687 TRP ILE GLN GLN ASP ASP GLY SER VAL HIS LYS SER ILE SEQRES 33 A 687 ASN ARG SER LEU ILE VAL GLY LEU LYS ILE SER THR LYS SEQRES 34 A 687 SER VAL GLY ARG ASP GLU ARG GLU ASP ILE THR HIS THR SEQRES 35 A 687 TYR LYS TYR PRO GLU GLY SER SER GLU GLU ARG GLU ALA SEQRES 36 A 687 PHE THR ARG ALA ASN HIS LEU ASN LYS LEU ALA GLU LYS SEQRES 37 A 687 GLU GLU THR GLY MET ALA MET ARG ILE ARG VAL GLY GLN SEQRES 38 A 687 SER MET ASN MET GLY SER ASP PHE ASP VAL PHE ALA HIS SEQRES 39 A 687 ILE THR ASN ASN THR ALA GLU GLU TYR VAL CYS ARG LEU SEQRES 40 A 687 LEU LEU CYS ALA ARG THR VAL SER TYR ASN GLY ILE LEU SEQRES 41 A 687 GLY PRO GLU CYS GLY THR LYS TYR LEU LEU ASN LEU ASN SEQRES 42 A 687 LEU GLU PRO PHE SER GLU LYS SER VAL PRO LEU CYS ILE SEQRES 43 A 687 LEU TYR GLU LYS TYR ARG ASP CYS LEU THR GLU SER ASN SEQRES 44 A 687 LEU ILE LYS VAL ARG ALA LEU LEU VAL GLU PRO VAL ILE SEQRES 45 A 687 ASN SER TYR LEU LEU ALA GLU ARG ASP LEU TYR LEU GLU SEQRES 46 A 687 ASN PRO GLU ILE LYS ILE ARG ILE LEU GLY GLU PRO LYS SEQRES 47 A 687 GLN LYS ARG LYS LEU VAL ALA GLU VAL SER LEU GLN ASN SEQRES 48 A 687 PRO LEU PRO VAL ALA LEU GLU GLY CYS THR PHE THR VAL SEQRES 49 A 687 GLU GLY ALA GLY LEU THR GLU GLU GLN LYS THR VAL GLU SEQRES 50 A 687 ILE PRO ASP PRO VAL GLU ALA GLY GLU GLU VAL LYS VAL SEQRES 51 A 687 ARG MET ASP LEU LEU PRO LEU HIS MET GLY LEU HIS LYS SEQRES 52 A 687 LEU VAL VAL ASN PHE GLU SER ASP LYS LEU LYS ALA VAL SEQRES 53 A 687 LYS GLY PHE ARG ASN VAL ILE ILE GLY PRO ALA HET GDP A 701 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 GDP C10 H15 N5 O11 P2 HELIX 1 AA1 GLU A 13 HIS A 21 1 9 HELIX 2 AA2 GLU A 153 LEU A 161 1 9 HELIX 3 AA3 GLY A 188 ASP A 198 1 11 HELIX 4 AA4 ASN A 200 ASN A 206 1 7 HELIX 5 AA5 ASN A 206 ARG A 214 1 9 HELIX 6 AA6 SER A 216 MET A 227 1 12 HELIX 7 AA7 ASN A 244 GLY A 248 5 5 HELIX 8 AA8 SER A 250 TRP A 254 5 5 HELIX 9 AA9 GLY A 256 HIS A 267 1 12 HELIX 10 AB1 GLN A 276 GLY A 292 1 17 HELIX 11 AB2 VAL A 376 GLU A 381 1 6 HELIX 12 AB3 ASP A 389 ALA A 399 1 11 HELIX 13 AB4 SER A 449 ALA A 459 1 11 HELIX 14 AB5 LEU A 547 ARG A 552 1 6 SHEET 1 AA1 4 LEU A 7 ASP A 11 0 SHEET 2 AA1 4 PHE A 39 PHE A 45 -1 O THR A 42 N ASP A 11 SHEET 3 AA1 4 THR A 99 THR A 105 -1 O LEU A 102 N LEU A 41 SHEET 4 AA1 4 THR A 89 GLN A 96 -1 N ASP A 94 O SER A 101 SHEET 1 AA2 5 LEU A 31 ARG A 34 0 SHEET 2 AA2 5 HIS A 134 LEU A 138 1 O ILE A 136 N VAL A 33 SHEET 3 AA2 5 GLY A 113 THR A 123 -1 N TYR A 115 O PHE A 135 SHEET 4 AA2 5 ASP A 55 THR A 63 -1 N SER A 56 O SER A 122 SHEET 5 AA2 5 ALA A 75 PRO A 78 -1 O ALA A 75 N VAL A 61 SHEET 1 AA3 4 LEU A 31 ARG A 34 0 SHEET 2 AA3 4 HIS A 134 LEU A 138 1 O ILE A 136 N VAL A 33 SHEET 3 AA3 4 GLY A 113 THR A 123 -1 N TYR A 115 O PHE A 135 SHEET 4 AA3 4 GLN A 126 SER A 129 -1 O GLN A 126 N THR A 123 SHEET 1 AA4 2 GLN A 164 GLY A 170 0 SHEET 2 AA4 2 ILE A 175 ASN A 181 -1 O ILE A 178 N ILE A 167 SHEET 1 AA5 2 LEU A 237 GLY A 239 0 SHEET 2 AA5 2 VAL A 272 GLY A 275 1 O VAL A 272 N LEU A 238 SHEET 1 AA6 6 VAL A 374 PRO A 375 0 SHEET 2 AA6 6 GLY A 353 LEU A 357 -1 N ALA A 356 O VAL A 374 SHEET 3 AA6 6 TRP A 332 MET A 342 -1 N MET A 342 O GLY A 353 SHEET 4 AA6 6 THR A 295 SER A 303 -1 N ASN A 302 O ASN A 333 SHEET 5 AA6 6 ILE A 426 LYS A 429 -1 O SER A 427 N THR A 299 SHEET 6 AA6 6 ARG A 436 ASP A 438 -1 O GLU A 437 N THR A 428 SHEET 1 AA7 7 LEU A 312 ARG A 317 0 SHEET 2 AA7 7 ASP A 400 GLN A 406 1 O ASP A 400 N ILE A 313 SHEET 3 AA7 7 VAL A 412 ASN A 417 -1 O HIS A 413 N ILE A 405 SHEET 4 AA7 7 TYR A 575 TYR A 583 1 O TYR A 575 N ILE A 416 SHEET 5 AA7 7 LEU A 560 VAL A 568 -1 N ILE A 561 O LEU A 582 SHEET 6 AA7 7 TYR A 503 VAL A 514 -1 N CYS A 510 O ARG A 564 SHEET 7 AA7 7 LEU A 520 LEU A 534 -1 O CYS A 524 N ALA A 511 SHEET 1 AA8 3 ALA A 474 ARG A 478 0 SHEET 2 AA8 3 PHE A 489 THR A 496 -1 O HIS A 494 N ARG A 476 SHEET 3 AA8 3 GLU A 539 ILE A 546 -1 O LYS A 540 N ILE A 495 SHEET 1 AA9 3 LYS A 590 LEU A 594 0 SHEET 2 AA9 3 LEU A 603 GLN A 610 -1 O VAL A 604 N LEU A 594 SHEET 3 AA9 3 GLU A 647 LEU A 654 -1 O VAL A 650 N VAL A 607 SHEET 1 AB1 4 LYS A 634 GLU A 637 0 SHEET 2 AB1 4 THR A 621 GLU A 625 -1 N VAL A 624 O LYS A 634 SHEET 3 AB1 4 VAL A 665 PHE A 668 -1 O VAL A 665 N GLU A 625 SHEET 4 AB1 4 VAL A 676 GLY A 678 -1 O GLY A 678 N VAL A 666 SHEET 1 AB2 2 GLY A 660 LYS A 663 0 SHEET 2 AB2 2 ASN A 681 ILE A 684 -1 O ILE A 684 N GLY A 660 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