HEADER PLANT PROTEIN 12-OCT-23 8WQP TITLE CRYO-EM STRUCTURE OF T. PSEUDONANA PYSHELL HELICAL TUBE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIATOM THE PYRENOID SHELL PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THALASSIOSIRA PSEUDONANA; SOURCE 3 ORGANISM_COMMON: MARINE DIATOM, CYCLOTELLA NANA; SOURCE 4 ORGANISM_TAXID: 35128; SOURCE 5 GENE: THAPSDRAFT_7881; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MARINE DIATOMS, PHOTOSYNTHESIS, CO2-CONCENTRATING MECHANISM, KEYWDS 2 PYRENOIDS, PLANT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.KAWAMOTO,R.TOHDA,C.GERLE,G.KURISU REVDAT 1 09-OCT-24 8WQP 0 JRNL AUTH G.SHIMAKAWA,M.DEMULDER,S.FLORI,A.KAWAMOTO,Y.TSUJI,H.NAWALY, JRNL AUTH 2 A.TANAKA,R.TOHDA,T.OTA,H.MATSUI,N.MORISHIMA,R.OKUBO, JRNL AUTH 3 W.WIETRZYNSKI,L.LAMM,D.R.RIGHETTO,C.UWIZEYE,B.GALLET, JRNL AUTH 4 H.P.JOUNEAU,C.GERLE,G.KURISU,G.FINAZZI,D.B.ENGEL,Y.MATSUDA JRNL TITL DIATOM PYRENOIDS ARE ENCASED IN A PROTEIN SHELL THAT ENABLES JRNL TITL 2 EFFICIENT CO2 FIXATION JRNL REF CELL V. 187 1 2024 JRNL DOI 10.1016/J.CELL.2024.09.013 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, SERIALEM, GCTF, COOT, UCSF REMARK 3 CHIMERA, CRYOSPARC, RELION, RELION, REMARK 3 RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 2.400 REMARK 3 NUMBER OF PARTICLES : 322887 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 8WQP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300040539. 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 : IN VITRO TUBE STRUCTURE OF T. REMARK 245 PSEUDONANA PYSHELL REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 5951 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1700.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 0.01 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 : 81000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 TRP B 85 OG1 THR B 147 2.16 REMARK 500 OD1 ASN A 197 OG1 THR A 199 2.17 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 GLU A 102 51.56 -94.46 REMARK 500 ASP A 117 26.15 -141.24 REMARK 500 GLN A 155 -179.03 -69.12 REMARK 500 ASN B 71 35.42 -98.70 REMARK 500 GLU B 102 51.37 -95.12 REMARK 500 ASP B 170 35.46 -99.55 REMARK 500 GLU B 265 30.74 -94.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37751 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF T. PSEUDONANA PYSHELL HELICAL TUBE DBREF 8WQP A 69 294 UNP B8C7S8 B8C7S8_THAPS 69 294 DBREF 8WQP B 69 294 UNP B8C7S8 B8C7S8_THAPS 69 294 SEQADV 8WQP UNK A 62 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK A 63 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK A 64 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK A 65 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK A 66 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK A 67 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK A 68 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK B 62 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK B 63 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK B 64 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK B 65 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK B 66 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK B 67 UNP B8C7S8 EXPRESSION TAG SEQADV 8WQP UNK B 68 UNP B8C7S8 EXPRESSION TAG SEQRES 1 A 233 UNK UNK UNK UNK UNK UNK UNK TRP ASP ASN SER SER PRO SEQRES 2 A 233 VAL ILE VAL GLN GLY GLY SER LEU ARG THR TRP SER PHE SEQRES 3 A 233 ALA ASN PRO ALA ILE GLU SER VAL GLN VAL LEU LEU LYS SEQRES 4 A 233 THR GLU GLY ARG PRO LEU ASP ALA ASP VAL GLU LEU TRP SEQRES 5 A 233 GLN GLY PRO ASP ASN THR PRO HIS LYS MET ARG VAL TYR SEQRES 6 A 233 VAL GLU ASP GLY ALA LEU ARG THR PHE ASN ALA VAL ILE SEQRES 7 A 233 GLY THR PRO ARG GLY PRO ASN THR VAL ALA ILE ARG ASN SEQRES 8 A 233 ILE GLY GLN LEU GLU PHE PRO LEU ASP ALA VAL VAL ARG SEQRES 9 A 233 PRO ASP ARG ASP ASP GLY LEU ALA ALA GLY ILE ALA SER SEQRES 10 A 233 VAL ALA THR ARG SER GLU THR ILE GLN GLY GLY ALA LEU SEQRES 11 A 233 ARG THR TYR PRO PHE ASN PRO THR VAL ASP SER VAL ALA SEQRES 12 A 233 ILE ILE LEU LYS THR ASP GLY ARG PRO LEU ASN ALA ARG SEQRES 13 A 233 ILE GLU LEU LEU GLN GLY PRO ASN ASN ASN LYS GLN VAL SEQRES 14 A 233 VAL GLU LEU TYR THR GLU ASP GLY LEU ASP ARG PRO PHE SEQRES 15 A 233 PHE ALA ILE VAL GLU THR PRO GLY SER GLY ASN VAL VAL SEQRES 16 A 233 ARG VAL VAL ASN THR ALA PRO VAL GLU PHE PRO LEU TYR SEQRES 17 A 233 ALA SER VAL ASP ALA TYR ARG VAL GLY GLY GLY GLY ASP SEQRES 18 A 233 TRP ALA ASP ASP GLY LEU MET ILE GLY ARG ALA PHE SEQRES 1 B 233 UNK UNK UNK UNK UNK UNK UNK TRP ASP ASN SER SER PRO SEQRES 2 B 233 VAL ILE VAL GLN GLY GLY SER LEU ARG THR TRP SER PHE SEQRES 3 B 233 ALA ASN PRO ALA ILE GLU SER VAL GLN VAL LEU LEU LYS SEQRES 4 B 233 THR GLU GLY ARG PRO LEU ASP ALA ASP VAL GLU LEU TRP SEQRES 5 B 233 GLN GLY PRO ASP ASN THR PRO HIS LYS MET ARG VAL TYR SEQRES 6 B 233 VAL GLU ASP GLY ALA LEU ARG THR PHE ASN ALA VAL ILE SEQRES 7 B 233 GLY THR PRO ARG GLY PRO ASN THR VAL ALA ILE ARG ASN SEQRES 8 B 233 ILE GLY GLN LEU GLU PHE PRO LEU ASP ALA VAL VAL ARG SEQRES 9 B 233 PRO ASP ARG ASP ASP GLY LEU ALA ALA GLY ILE ALA SER SEQRES 10 B 233 VAL ALA THR ARG SER GLU THR ILE GLN GLY GLY ALA LEU SEQRES 11 B 233 ARG THR TYR PRO PHE ASN PRO THR VAL ASP SER VAL ALA SEQRES 12 B 233 ILE ILE LEU LYS THR ASP GLY ARG PRO LEU ASN ALA ARG SEQRES 13 B 233 ILE GLU LEU LEU GLN GLY PRO ASN ASN ASN LYS GLN VAL SEQRES 14 B 233 VAL GLU LEU TYR THR GLU ASP GLY LEU ASP ARG PRO PHE SEQRES 15 B 233 PHE ALA ILE VAL GLU THR PRO GLY SER GLY ASN VAL VAL SEQRES 16 B 233 ARG VAL VAL ASN THR ALA PRO VAL GLU PHE PRO LEU TYR SEQRES 17 B 233 ALA SER VAL ASP ALA TYR ARG VAL GLY GLY GLY GLY ASP SEQRES 18 B 233 TRP ALA ASP ASP GLY LEU MET ILE GLY ARG ALA PHE HELIX 1 AA1 UNK A 64 ASN A 71 1 8 HELIX 2 AA2 GLY A 171 ALA A 180 1 10 HELIX 3 AA3 UNK B 64 ASN B 71 1 8 HELIX 4 AA4 GLY B 171 ALA B 180 1 10 SHEET 1 AA1 8 VAL A 75 VAL A 77 0 SHEET 2 AA1 8 LEU A 160 PRO A 166 -1 O LEU A 160 N VAL A 77 SHEET 3 AA1 8 SER A 94 LYS A 100 -1 N LYS A 100 O ASP A 161 SHEET 4 AA1 8 PHE A 135 GLY A 140 -1 O ILE A 139 N VAL A 95 SHEET 5 AA1 8 PHE A 243 GLU A 248 -1 O PHE A 244 N VAL A 138 SHEET 6 AA1 8 VAL A 200 LYS A 208 -1 N ILE A 205 O ALA A 245 SHEET 7 AA1 8 LEU A 268 VAL A 277 -1 O ARG A 276 N ASP A 201 SHEET 8 AA1 8 GLU A 184 ILE A 186 -1 N GLU A 184 O ALA A 270 SHEET 1 AA2 8 LEU A 82 PHE A 87 0 SHEET 2 AA2 8 ASN A 146 ASN A 152 -1 O VAL A 148 N TRP A 85 SHEET 3 AA2 8 LEU A 106 TRP A 113 -1 N ASP A 109 O ARG A 151 SHEET 4 AA2 8 HIS A 121 VAL A 127 -1 O HIS A 121 N LEU A 112 SHEET 5 AA2 8 ASN A 227 THR A 235 -1 O GLU A 232 N ARG A 124 SHEET 6 AA2 8 LEU A 214 LEU A 221 -1 N LEU A 220 O LYS A 228 SHEET 7 AA2 8 VAL A 255 ASN A 260 -1 O ARG A 257 N GLU A 219 SHEET 8 AA2 8 LEU A 191 PRO A 195 -1 N ARG A 192 O VAL A 258 SHEET 1 AA3 8 VAL B 75 VAL B 77 0 SHEET 2 AA3 8 LEU B 160 PRO B 166 -1 O LEU B 160 N VAL B 77 SHEET 3 AA3 8 SER B 94 LYS B 100 -1 N LEU B 98 O VAL B 163 SHEET 4 AA3 8 PHE B 135 GLY B 140 -1 O ALA B 137 N VAL B 97 SHEET 5 AA3 8 PHE B 243 GLU B 248 -1 O PHE B 244 N VAL B 138 SHEET 6 AA3 8 VAL B 200 LYS B 208 -1 N VAL B 203 O VAL B 247 SHEET 7 AA3 8 LEU B 268 VAL B 277 -1 O ASP B 273 N ALA B 204 SHEET 8 AA3 8 GLU B 184 ILE B 186 -1 N GLU B 184 O ALA B 270 SHEET 1 AA4 8 LEU B 82 PHE B 87 0 SHEET 2 AA4 8 ASN B 146 ASN B 152 -1 O ASN B 146 N PHE B 87 SHEET 3 AA4 8 LEU B 106 TRP B 113 -1 N ASP B 109 O ARG B 151 SHEET 4 AA4 8 HIS B 121 VAL B 127 -1 O VAL B 127 N LEU B 106 SHEET 5 AA4 8 ASN B 227 THR B 235 -1 O GLU B 232 N ARG B 124 SHEET 6 AA4 8 LEU B 214 LEU B 221 -1 N LEU B 220 O LYS B 228 SHEET 7 AA4 8 VAL B 255 ASN B 260 -1 O ARG B 257 N GLU B 219 SHEET 8 AA4 8 LEU B 191 PRO B 195 -1 N ARG B 192 O VAL B 258 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