HEADER TRANSPORT PROTEIN 18-DEC-23 8VE0 TITLE HUMAN TRANSTHYRETIN COVALENTLY MODIFIED WITH A2-DERIVED STILBENE IN TITLE 2 THE COMPRESSED CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSTHYRETIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: ATTR,PREALBUMIN,TBPA; COMPND 5 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: TTR, PALB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMYLOIDOSIS, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR B.BASANTA,K.NUGROHO,N.YAN,G.M.KLINE,F.J.TSAI,M.WU,J.W.KELLY, AUTHOR 2 G.C.LANDER REVDAT 2 13-MAR-24 8VE0 1 SOURCE REVDAT 1 31-JAN-24 8VE0 0 JRNL AUTH B.BASANTA,K.NUGROHO,N.YAN,G.M.KLINE,E.T.POWERS,F.J.TSAI, JRNL AUTH 2 M.WU,A.HANSEL-HARRIS,J.CHEN,S.FORLI,J.W.KELLY,G.C.LANDER JRNL TITL THE CONFORMATIONAL LANDSCAPE OF HUMAN TRANSTHYRETIN REVEALED JRNL TITL 2 BY CRYO-EM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX, LEGINON, RELION 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 105961 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 8VE0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279409. 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 : TRANSTHYRETIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.41 REMARK 245 SAMPLE SUPPORT DETAILS : GRAPHENE GRIDS WERE TREATED REMARK 245 WITH UV/OZONE USING THE UVOCS REMARK 245 T10XT10 SYSTEM. A 10-MINUTE REMARK 245 WARMUP RUN WAS PERFORMED REMARK 245 IMMEDIATELY PRIOR TO INSERTING REMARK 245 AND TREATING THE GRIDS FOR 4 REMARK 245 MINUTES. REMARK 245 SAMPLE VITRIFICATION DETAILS : 3 UL OF SAMPLE WERE APPLIED REMARK 245 ONTO THE GRAPHENE SIDE OF THE REMARK 245 GRID AFTER IT WAS MOUNTED ON REMARK 245 THE PLUNGER (ALWAYS AT THE SAME REMARK 245 HEIGHT), AND IMMEDIATELY REMARK 245 BLOTTED FOR 6 SECONDS BY REMARK 245 HOLDING A 1 X 6 CM PIECE OF REMARK 245 WHATMAN 1 FILTER PAPER PARALLEL REMARK 245 TO THE GRID, IN FULL CONTACT. REMARK 245 TIMING WAS KEPT WITH THE HELP REMARK 245 OF A METRONOME. THE BLOTTING REMARK 245 COUNTDOWN WAS STARTED AFTER THE REMARK 245 BLOTTED LIQUID SPOT ON THE REMARK 245 FILTER PAPER STOPPED SPREADING REMARK 245 AND THE GRID WAS PLUNGED IN REMARK 245 LIQUID ETHANE AT THE SAME TIME REMARK 245 THE BLOTTING PAPER WAS PULLED REMARK 245 BACK, IN A SINGLE MOTION. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.60 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4536 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 73000 REMARK 245 CALIBRATED MAGNIFICATION : 88968 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 0 REMARK 465 GLY A 1 REMARK 465 PRO A 2 REMARK 465 THR A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 GLU A 7 REMARK 465 SER A 8 REMARK 465 LYS A 126 REMARK 465 GLU A 127 REMARK 465 MET B 0 REMARK 465 GLY B 1 REMARK 465 PRO B 2 REMARK 465 THR B 3 REMARK 465 GLY B 4 REMARK 465 THR B 5 REMARK 465 GLY B 6 REMARK 465 GLU B 7 REMARK 465 SER B 8 REMARK 465 LYS B 9 REMARK 465 LYS B 126 REMARK 465 GLU B 127 REMARK 465 MET C 0 REMARK 465 GLY C 1 REMARK 465 PRO C 2 REMARK 465 THR C 3 REMARK 465 GLY C 4 REMARK 465 THR C 5 REMARK 465 GLY C 6 REMARK 465 GLU C 7 REMARK 465 SER C 8 REMARK 465 LYS C 126 REMARK 465 GLU C 127 REMARK 465 MET D 0 REMARK 465 GLY D 1 REMARK 465 PRO D 2 REMARK 465 THR D 3 REMARK 465 GLY D 4 REMARK 465 THR D 5 REMARK 465 GLY D 6 REMARK 465 GLU D 7 REMARK 465 SER D 8 REMARK 465 PRO D 125 REMARK 465 LYS D 126 REMARK 465 GLU D 127 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 ILE A 26 CG1 CG2 CD1 REMARK 470 ASN A 27 CG OD1 ND2 REMARK 470 ASP A 38 CG OD1 OD2 REMARK 470 ASP A 39 CG OD1 OD2 REMARK 470 THR A 40 OG1 CG2 REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 THR A 59 OG1 CG2 REMARK 470 THR A 60 OG1 CG2 REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 GLU A 62 CG CD OE1 OE2 REMARK 470 ASP A 99 CG OD1 OD2 REMARK 470 SER A 100 OG REMARK 470 MET B 13 CG SD CE REMARK 470 ASP B 39 CG OD1 OD2 REMARK 470 GLU B 61 CG CD OE1 OE2 REMARK 470 GLU B 62 CG CD OE1 OE2 REMARK 470 GLU B 92 CG CD OE1 OE2 REMARK 470 THR B 96 OG1 CG2 REMARK 470 SER B 100 OG REMARK 470 LYS C 9 CG CD CE NZ REMARK 470 ASP C 39 CG OD1 OD2 REMARK 470 SER C 46 OG REMARK 470 GLU C 51 CG CD OE1 OE2 REMARK 470 GLU C 62 CG CD OE1 OE2 REMARK 470 GLU C 63 CG CD OE1 OE2 REMARK 470 VAL C 65 CG1 CG2 REMARK 470 GLU C 66 CG CD OE1 OE2 REMARK 470 SER C 77 OG REMARK 470 LYS D 9 CG CD CE NZ REMARK 470 ASP D 39 CG OD1 OD2 REMARK 470 THR D 60 OG1 CG2 REMARK 470 GLU D 62 CG CD OE1 OE2 REMARK 470 GLU D 63 CG CD OE1 OE2 REMARK 470 VAL D 65 CG1 CG2 REMARK 470 GLU D 92 CG CD OE1 OE2 REMARK 470 ARG D 104 CG CD NE CZ NH1 NH2 REMARK 470 THR D 123 OG1 CG2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-43160 RELATED DB: EMDB REMARK 900 HUMAN TRANSTHYRETIN COVALENTLY MODIFIED WITH A2-DERIVED STILBENE IN REMARK 900 THE CANONICAL CONFORMATION DBREF 8VE0 A 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 8VE0 B 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 8VE0 C 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 8VE0 D 1 127 UNP P02766 TTHY_HUMAN 21 147 SEQADV 8VE0 MET A 0 UNP P02766 INITIATING METHIONINE SEQADV 8VE0 MET B 0 UNP P02766 INITIATING METHIONINE SEQADV 8VE0 MET C 0 UNP P02766 INITIATING METHIONINE SEQADV 8VE0 MET D 0 UNP P02766 INITIATING METHIONINE SEQRES 1 A 128 MET GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU SEQRES 2 A 128 MET VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA SEQRES 3 A 128 ILE ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP SEQRES 4 A 128 ASP THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SEQRES 5 A 128 SER GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE SEQRES 6 A 128 VAL GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER SEQRES 7 A 128 TYR TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS SEQRES 8 A 128 ALA GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG SEQRES 9 A 128 ARG TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SEQRES 10 A 128 SER THR THR ALA VAL VAL THR ASN PRO LYS GLU SEQRES 1 B 128 MET GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU SEQRES 2 B 128 MET VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA SEQRES 3 B 128 ILE ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP SEQRES 4 B 128 ASP THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SEQRES 5 B 128 SER GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE SEQRES 6 B 128 VAL GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER SEQRES 7 B 128 TYR TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS SEQRES 8 B 128 ALA GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG SEQRES 9 B 128 ARG TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SEQRES 10 B 128 SER THR THR ALA VAL VAL THR ASN PRO LYS GLU SEQRES 1 C 128 MET GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU SEQRES 2 C 128 MET VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA SEQRES 3 C 128 ILE ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP SEQRES 4 C 128 ASP THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SEQRES 5 C 128 SER GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE SEQRES 6 C 128 VAL GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER SEQRES 7 C 128 TYR TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS SEQRES 8 C 128 ALA GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG SEQRES 9 C 128 ARG TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SEQRES 10 C 128 SER THR THR ALA VAL VAL THR ASN PRO LYS GLU SEQRES 1 D 128 MET GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU SEQRES 2 D 128 MET VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA SEQRES 3 D 128 ILE ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP SEQRES 4 D 128 ASP THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SEQRES 5 D 128 SER GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLU PHE SEQRES 6 D 128 VAL GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER SEQRES 7 D 128 TYR TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS SEQRES 8 D 128 ALA GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG SEQRES 9 D 128 ARG TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SEQRES 10 D 128 SER THR THR ALA VAL VAL THR ASN PRO LYS GLU HET 1WZ B 201 22 HET 1WZ C 201 22 HETNAM 1WZ 3-(DIMETHYLAMINO)-5-[(E)-2-(4-HYDROXY-3,5- HETNAM 2 1WZ DIMETHYLPHENYL)ETHENYL]BENZOIC ACID HETSYN 1WZ (E)-3-(DIMETHYLAMINO)-5-(4-HYDROXY-3,5-DIMETHYLSTYRYL) HETSYN 2 1WZ BENZOIC ACID FORMUL 5 1WZ 2(C19 H21 N O3) HELIX 1 AA1 ASP A 74 GLY A 83 1 10 HELIX 2 AA2 ASP B 74 GLY B 83 1 10 HELIX 3 AA3 THR C 75 GLY C 83 1 9 HELIX 4 AA4 ASP D 74 GLY D 83 1 10 SHEET 1 AA1 3 SER A 23 PRO A 24 0 SHEET 2 AA1 3 LEU A 12 ASP A 18 -1 N ASP A 18 O SER A 23 SHEET 3 AA1 3 GLU A 54 LEU A 55 -1 O LEU A 55 N VAL A 14 SHEET 1 AA2 7 SER A 23 PRO A 24 0 SHEET 2 AA2 7 LEU A 12 ASP A 18 -1 N ASP A 18 O SER A 23 SHEET 3 AA2 7 ARG A 104 LEU A 111 1 O LEU A 111 N LEU A 17 SHEET 4 AA2 7 SER A 115 THR A 123 -1 O SER A 117 N LEU A 110 SHEET 5 AA2 7 SER B 115 THR B 123 -1 O TYR B 116 N THR A 118 SHEET 6 AA2 7 ARG B 104 LEU B 111 -1 N ARG B 104 O THR B 123 SHEET 7 AA2 7 LEU B 12 ASP B 18 1 N LYS B 15 O ALA B 109 SHEET 1 AA3 8 TRP A 41 LYS A 48 0 SHEET 2 AA3 8 ALA A 29 LYS A 35 -1 N VAL A 32 O PHE A 44 SHEET 3 AA3 8 GLY A 67 ILE A 73 -1 O GLU A 72 N HIS A 31 SHEET 4 AA3 8 HIS A 88 ALA A 97 -1 O ALA A 91 N ILE A 73 SHEET 5 AA3 8 HIS B 88 ALA B 97 -1 O VAL B 94 N GLU A 89 SHEET 6 AA3 8 GLY B 67 ILE B 73 -1 N VAL B 71 O VAL B 93 SHEET 7 AA3 8 ALA B 29 LYS B 35 -1 N HIS B 31 O GLU B 72 SHEET 8 AA3 8 TRP B 41 LYS B 48 -1 O PHE B 44 N VAL B 32 SHEET 1 AA4 8 SER C 23 PRO C 24 0 SHEET 2 AA4 8 LEU C 12 ASP C 18 -1 N ASP C 18 O SER C 23 SHEET 3 AA4 8 ARG C 104 LEU C 111 1 O LEU C 111 N LEU C 17 SHEET 4 AA4 8 SER C 115 THR C 123 -1 O SER C 117 N LEU C 110 SHEET 5 AA4 8 SER D 115 THR D 123 -1 O THR D 118 N TYR C 116 SHEET 6 AA4 8 ARG D 104 SER D 112 -1 N SER D 112 O SER D 115 SHEET 7 AA4 8 LEU D 12 ASP D 18 1 N LEU D 17 O LEU D 111 SHEET 8 AA4 8 GLU D 54 LEU D 55 -1 O LEU D 55 N VAL D 14 SHEET 1 AA5 8 TRP C 41 LYS C 48 0 SHEET 2 AA5 8 ALA C 29 LYS C 35 -1 N VAL C 32 O ALA C 45 SHEET 3 AA5 8 GLY C 67 ASP C 74 -1 O GLU C 72 N HIS C 31 SHEET 4 AA5 8 HIS C 88 ALA C 97 -1 O ALA C 91 N ILE C 73 SHEET 5 AA5 8 HIS D 88 ALA D 97 -1 O GLU D 89 N VAL C 94 SHEET 6 AA5 8 GLY D 67 ILE D 73 -1 N GLY D 67 O ALA D 97 SHEET 7 AA5 8 ALA D 29 LYS D 35 -1 N HIS D 31 O GLU D 72 SHEET 8 AA5 8 TRP D 41 LYS D 48 -1 O ALA D 45 N VAL D 32 LINK NZ LYS B 15 CAO 1WZ B 201 1555 1555 1.47 LINK NZ LYS C 15 CAO 1WZ C 201 1555 1555 1.48 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