HEADER OXIDOREDUCTASE 17-JUL-23 8PVF TITLE STRUCTURE OF GAPDH DETERMINED BY CRYOEM AT 100 KEV COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.2.1.12; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRYPTOSPORIDIUM PARVUM; SOURCE 3 ORGANISM_TAXID: 5807; SOURCE 4 GENE: CGD6_3790, 1MB.519, CPATCC_002941; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GAPDH, OXIDOREDUCTASE EXPDTA ELECTRON MICROSCOPY AUTHOR G.MCMULLAN,K.NAYDENOVA,D.MIHAYLOV,M.J.PEET,H.WILSON,K.YAMASHITA, AUTHOR 2 J.L.DICKERSON,S.CHEN,G.CANNONE,Y.LEE,K.A.HUTCHINGS,O.GITTINS, AUTHOR 3 M.SOBHY,T.WELLS,M.M.EL-GOMATI,J.DALBY,M.MEFFERT,C.SCHULZE-BRIESE, AUTHOR 4 R.HENDERSON,C.J.RUSSO REVDAT 2 06-DEC-23 8PVF 1 JRNL REVDAT 1 29-NOV-23 8PVF 0 JRNL AUTH G.MCMULLAN,K.NAYDENOVA,D.MIHAYLOV,K.YAMASHITA,M.J.PEET, JRNL AUTH 2 H.WILSON,J.L.DICKERSON,S.CHEN,G.CANNONE,Y.LEE,K.A.HUTCHINGS, JRNL AUTH 3 O.GITTINS,M.A.SOBHY,T.WELLS,M.M.EL-GOMATI,J.DALBY,M.MEFFERT, JRNL AUTH 4 C.SCHULZE-BRIESE,R.HENDERSON,C.J.RUSSO JRNL TITL STRUCTURE DETERMINATION BY CRYOEM AT 100 KEV. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 05120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 38011573 JRNL DOI 10.1073/PNAS.2312905120 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERVALCAT REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3CPS REMARK 3 REFINEMENT SPACE : RECIPROCAL 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 19411 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 8PVF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292131854. 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 : GLYCERALDEHYDE 3-PHOSPHATE REMARK 245 DEHYDROGENASE 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 : 7.40 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 1400/HR + YPS FEG REMARK 245 DETECTOR TYPE : DECTRIS SINGLA (1K X 1K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 4000.00 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) : 100 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 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 215.42400 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 215.42400 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 215.42400 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 215.42400 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 215.42400 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 215.42400 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 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 SER A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 ARG A 11 REMARK 465 GLU A 12 REMARK 465 ASN A 13 REMARK 465 LEU A 14 REMARK 465 TYR A 15 REMARK 465 PHE A 16 REMARK 465 GLN A 17 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 79 CG CD CE NZ REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 VAL A 87 CG1 CG2 REMARK 470 ASN A 200 CG OD1 ND2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 LYS A 212 CG CD CE NZ 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 ARG A 215 NE - CZ - NH1 ANGL. DEV. = 3.5 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 PHE A 25 55.60 -100.70 REMARK 500 SER A 136 40.44 -96.62 REMARK 500 ASP A 141 -156.38 -125.00 REMARK 500 ALA A 166 -161.44 62.69 REMARK 500 LYS A 212 -51.98 -122.56 REMARK 500 VAL A 258 132.68 95.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17964 RELATED DB: EMDB REMARK 900 STRUCTURE OF GAPDH DETERMINED BY CRYOEM AT 100 KEV DBREF 8PVF A 19 354 UNP Q7YYQ9 Q7YYQ9_CRYPV 4 339 SEQADV 8PVF MET A 1 UNP Q7YYQ9 INITIATING METHIONINE SEQADV 8PVF HIS A 2 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF HIS A 3 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF HIS A 4 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF HIS A 5 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF HIS A 6 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF HIS A 7 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF SER A 8 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF SER A 9 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF GLY A 10 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF ARG A 11 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF GLU A 12 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF ASN A 13 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF LEU A 14 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF TYR A 15 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF PHE A 16 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF GLN A 17 UNP Q7YYQ9 EXPRESSION TAG SEQADV 8PVF GLY A 18 UNP Q7YYQ9 EXPRESSION TAG SEQRES 1 A 354 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 354 LEU TYR PHE GLN GLY THR LEU GLY ILE ASN GLY PHE GLY SEQRES 3 A 354 ARG ILE GLY ARG LEU VAL LEU ARG ALA CYS MET GLU ARG SEQRES 4 A 354 ASN ASP ILE THR VAL VAL ALA ILE ASN ASP PRO PHE MET SEQRES 5 A 354 ASP VAL GLU TYR MET ALA TYR LEU LEU LYS TYR ASP SER SEQRES 6 A 354 VAL HIS GLY ASN PHE ASN GLY THR VAL GLU VAL SER GLY SEQRES 7 A 354 LYS ASP LEU CYS ILE ASN GLY LYS VAL VAL LYS VAL PHE SEQRES 8 A 354 GLN ALA LYS ASP PRO ALA GLU ILE PRO TRP GLY ALA SER SEQRES 9 A 354 GLY ALA GLN ILE VAL CYS GLU SER THR GLY VAL PHE THR SEQRES 10 A 354 THR GLU GLU LYS ALA SER LEU HIS LEU LYS GLY GLY ALA SEQRES 11 A 354 LYS LYS VAL ILE ILE SER ALA PRO PRO LYS ASP ASN VAL SEQRES 12 A 354 PRO MET TYR VAL MET GLY VAL ASN ASN THR GLU TYR ASP SEQRES 13 A 354 PRO SER LYS PHE ASN VAL ILE SER ASN ALA SER CYS THR SEQRES 14 A 354 THR ASN CYS LEU ALA PRO LEU ALA LYS ILE ILE ASN ASP SEQRES 15 A 354 LYS PHE GLY ILE VAL GLU GLY LEU MET THR THR VAL HIS SEQRES 16 A 354 SER LEU THR ALA ASN GLN LEU THR VAL ASP GLY PRO SER SEQRES 17 A 354 LYS GLY GLY LYS ASP TRP ARG ALA GLY ARG CYS ALA GLY SEQRES 18 A 354 ASN ASN ILE ILE PRO ALA SER THR GLY ALA ALA LYS ALA SEQRES 19 A 354 VAL GLY LYS VAL ILE PRO ALA LEU ASN GLY LYS LEU THR SEQRES 20 A 354 GLY MET ALA ILE ARG VAL PRO THR PRO ASP VAL SER VAL SEQRES 21 A 354 VAL ASP LEU THR CYS LYS LEU ALA LYS PRO ALA SER ILE SEQRES 22 A 354 GLU GLU ILE TYR GLN ALA VAL LYS GLU ALA SER ASN GLY SEQRES 23 A 354 PRO MET LYS GLY ILE MET GLY TYR THR SER ASP ASP VAL SEQRES 24 A 354 VAL SER THR ASP PHE ILE GLY CYS LYS TYR SER SER ILE SEQRES 25 A 354 PHE ASP LYS ASN ALA CYS ILE ALA LEU ASN ASP SER PHE SEQRES 26 A 354 VAL LYS LEU ILE SER TRP TYR ASP ASN GLU SER GLY TYR SEQRES 27 A 354 SER ASN ARG LEU VAL ASP LEU ALA VAL TYR VAL ALA SER SEQRES 28 A 354 ARG GLY LEU HET NAD A 401 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 2 NAD C21 H27 N7 O14 P2 HELIX 1 AA1 GLY A 26 GLU A 38 1 13 HELIX 2 AA2 ASP A 53 TYR A 63 1 11 HELIX 3 AA3 ASP A 95 ILE A 99 5 5 HELIX 4 AA4 PRO A 100 GLY A 105 1 6 HELIX 5 AA5 THR A 118 SER A 123 1 6 HELIX 6 AA6 LEU A 124 LYS A 127 5 4 HELIX 7 AA7 ASN A 151 TYR A 155 5 5 HELIX 8 AA8 SER A 167 PHE A 184 1 18 HELIX 9 AA9 GLY A 230 ILE A 239 1 10 HELIX 10 AB1 PRO A 240 ASN A 243 5 4 HELIX 11 AB2 SER A 272 ASN A 285 1 14 HELIX 12 AB3 VAL A 300 ILE A 305 5 6 HELIX 13 AB4 ASN A 316 CYS A 318 5 3 HELIX 14 AB5 GLU A 335 ARG A 352 1 18 SHEET 1 AA1 8 VAL A 74 VAL A 76 0 SHEET 2 AA1 8 ASP A 80 ILE A 83 -1 O CYS A 82 N GLU A 75 SHEET 3 AA1 8 LYS A 86 PHE A 91 -1 O VAL A 88 N LEU A 81 SHEET 4 AA1 8 THR A 43 ASN A 48 1 N ILE A 47 O LYS A 89 SHEET 5 AA1 8 THR A 19 ASN A 23 1 N LEU A 20 O VAL A 45 SHEET 6 AA1 8 ILE A 108 GLU A 111 1 O CYS A 110 N GLY A 21 SHEET 7 AA1 8 LYS A 132 ILE A 135 1 O ILE A 134 N VAL A 109 SHEET 8 AA1 8 VAL A 162 SER A 164 1 O ILE A 163 N ILE A 135 SHEET 1 AA2 7 ILE A 225 SER A 228 0 SHEET 2 AA2 7 LEU A 246 ARG A 252 -1 O ARG A 252 N ILE A 225 SHEET 3 AA2 7 ILE A 186 HIS A 195 1 N THR A 193 O ILE A 251 SHEET 4 AA2 7 SER A 259 LEU A 267 -1 O LYS A 266 N VAL A 187 SHEET 5 AA2 7 PHE A 325 TYR A 332 -1 O SER A 330 N VAL A 261 SHEET 6 AA2 7 SER A 311 ASP A 314 -1 N ASP A 314 O ILE A 329 SHEET 7 AA2 7 MET A 292 THR A 295 1 N GLY A 293 O SER A 311 SHEET 1 AA3 6 ILE A 225 SER A 228 0 SHEET 2 AA3 6 LEU A 246 ARG A 252 -1 O ARG A 252 N ILE A 225 SHEET 3 AA3 6 ILE A 186 HIS A 195 1 N THR A 193 O ILE A 251 SHEET 4 AA3 6 SER A 259 LEU A 267 -1 O LYS A 266 N VAL A 187 SHEET 5 AA3 6 PHE A 325 TYR A 332 -1 O SER A 330 N VAL A 261 SHEET 6 AA3 6 ILE A 319 ASN A 322 -1 N ILE A 319 O LYS A 327 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 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -1.000000 0.000000 0.000000 215.42400 MTRIX2 2 0.000000 -1.000000 0.000000 215.42400 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 1.000000 0.000000 0.000000 0.00000 MTRIX2 3 0.000000 -1.000000 0.000000 215.42400 MTRIX3 3 0.000000 0.000000 -1.000000 215.42400 MTRIX1 4 -1.000000 0.000000 0.000000 215.42400 MTRIX2 4 0.000000 1.000000 0.000000 0.00000 MTRIX3 4 0.000000 0.000000 -1.000000 215.42400