HEADER ANTITUMOR PROTEIN 08-NOV-22 8F2I TITLE P53 MONOMER STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ANTIGEN NY-CO-13,PHOSPHOPROTEIN P53,TUMOR SUPPRESSOR P53; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 VARIANT: WILD-TYPE; SOURCE 6 CELL_LINE: U87 MG CELLS; SOURCE 7 ATCC: HTB-14; SOURCE 8 ORGAN: BRAIN TUMOR; SOURCE 9 TISSUE: BRAIN KEYWDS CANCER, TUMOR SUPPRESSOR, CELL CYCLE, APOPTOSIS, DNA REPAIR, KEYWDS 2 ANTITUMOR PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.SOLARES,D.F.KELLY REVDAT 2 01-MAY-24 8F2I 1 JRNL REVDAT 1 23-NOV-22 8F2I 0 JRNL AUTH M.J.SOLARES,G.M.JONAID,W.Y.LUQIU,S.BERRY,J.KHADELA,Y.LIANG, JRNL AUTH 2 M.C.EVANS,K.J.PRIDHAM,W.J.DEARNALEY,Z.SHENG,D.F.KELLY JRNL TITL HIGH-RESOLUTION IMAGING OF HUMAN CANCER PROTEINS USING JRNL TITL 2 MICROPROCESSOR MATERIALS. JRNL REF CHEMBIOCHEM V. 23 00310 2022 JRNL REFN ESSN 1439-7633 JRNL PMID 35789183 JRNL DOI 10.1002/CBIC.202200310 REMARK 2 REMARK 2 RESOLUTION. 5.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, PHENIX, RELION, RELION, RELION, REMARK 3 RELION, ISOLDE 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 : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 50.000 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) : 5.000 REMARK 3 NUMBER OF PARTICLES : 8000 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: VALIDATED IN RMEASURE REMARK 4 REMARK 4 8F2I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1000269573. 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 : P53 MONOMER ISOLATED FROM U87 REMARK 245 -MG CELLS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.20 REMARK 245 SAMPLE SUPPORT DETAILS : CLEANED MICROCHIPS WERE COATED REMARK 245 WITH 25% NI-NTA-CONTAINING REMARK 245 LIPID MONOLAYERS. ALIQUOTS (2 REMARK 245 MICROLITERS) OF P53 FRACTIONS REMARK 245 WERE ADDED TO THE NI-NTA-COATED REMARK 245 MICROCHIPS AND INCUBATED FOR 2 REMARK 245 MINUTE AT ROOM TEMPERATURE. REMARK 245 SAMPLE VITRIFICATION DETAILS : THE MICROCHIP SAMPLES WERE REMARK 245 LOADED INTO A FEI MARK III REMARK 245 VITROBOT AND FLASH-FROZEN INTO REMARK 245 LIQUID ETHANE. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NATIVE PROTEIN, WILD-TYPE WITH REMARK 245 NO TAGS REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 300 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS TALOS F200C REMARK 245 DETECTOR TYPE : FEI CETA (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 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) : 500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 142000 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 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 HG SER A 127 OE2 GLU A 286 1.59 REMARK 500 HG1 THR A 55 OE2 GLU A 68 1.60 REMARK 500 HG1 THR A 118 OE2 GLU A 286 1.60 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 ARG A 110 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 156 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 158 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 202 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 213 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 273 NE - CZ - NH2 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 ASP A 42 -151.60 58.60 REMARK 500 CYS A 124 -121.47 48.09 REMARK 500 THR A 125 -146.12 57.08 REMARK 500 MET A 237 19.67 53.86 REMARK 500 ARG A 290 -7.29 -141.66 REMARK 500 THR A 387 -44.27 -138.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-28817 RELATED DB: EMDB REMARK 900 P53 MONOMER STRUCTURE DBREF 8F2I A 1 393 UNP P04637 P53_HUMAN 1 393 SEQRES 1 A 393 MET GLU GLU PRO GLN SER ASP PRO SER VAL GLU PRO PRO SEQRES 2 A 393 LEU SER GLN GLU THR PHE SER ASP LEU TRP LYS LEU LEU SEQRES 3 A 393 PRO GLU ASN ASN VAL LEU SER PRO LEU PRO SER GLN ALA SEQRES 4 A 393 MET ASP ASP LEU MET LEU SER PRO ASP ASP ILE GLU GLN SEQRES 5 A 393 TRP PHE THR GLU ASP PRO GLY PRO ASP GLU ALA PRO ARG SEQRES 6 A 393 MET PRO GLU ALA ALA PRO PRO VAL ALA PRO ALA PRO ALA SEQRES 7 A 393 ALA PRO THR PRO ALA ALA PRO ALA PRO ALA PRO SER TRP SEQRES 8 A 393 PRO LEU SER SER SER VAL PRO SER GLN LYS THR TYR GLN SEQRES 9 A 393 GLY SER TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY SEQRES 10 A 393 THR ALA LYS SER VAL THR CYS THR TYR SER PRO ALA LEU SEQRES 11 A 393 ASN LYS MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL SEQRES 12 A 393 GLN LEU TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG SEQRES 13 A 393 VAL ARG ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET SEQRES 14 A 393 THR GLU VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SEQRES 15 A 393 SER ASP SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE SEQRES 16 A 393 ARG VAL GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP SEQRES 17 A 393 ARG ASN THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU SEQRES 18 A 393 PRO PRO GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR SEQRES 19 A 393 ASN TYR MET CYS ASN SER SER CYS MET GLY GLY MET ASN SEQRES 20 A 393 ARG ARG PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SEQRES 21 A 393 SER GLY ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG SEQRES 22 A 393 VAL CYS ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU SEQRES 23 A 393 GLU ASN LEU ARG LYS LYS GLY GLU PRO HIS HIS GLU LEU SEQRES 24 A 393 PRO PRO GLY SER THR LYS ARG ALA LEU PRO ASN ASN THR SEQRES 25 A 393 SER SER SER PRO GLN PRO LYS LYS LYS PRO LEU ASP GLY SEQRES 26 A 393 GLU TYR PHE THR LEU GLN ILE ARG GLY ARG GLU ARG PHE SEQRES 27 A 393 GLU MET PHE ARG GLU LEU ASN GLU ALA LEU GLU LEU LYS SEQRES 28 A 393 ASP ALA GLN ALA GLY LYS GLU PRO GLY GLY SER ARG ALA SEQRES 29 A 393 HIS SER SER HIS LEU LYS SER LYS LYS GLY GLN SER THR SEQRES 30 A 393 SER ARG HIS LYS LYS LEU MET PHE LYS THR GLU GLY PRO SEQRES 31 A 393 ASP SER ASP HELIX 1 AA1 SER A 15 SER A 20 1 6 HELIX 2 AA2 ASP A 21 LEU A 25 5 5 HELIX 3 AA3 ASP A 48 TRP A 53 1 6 HELIX 4 AA4 ARG A 65 ALA A 70 1 6 HELIX 5 AA5 CYS A 176 GLU A 180 5 5 HELIX 6 AA6 GLU A 198 ARG A 202 5 5 HELIX 7 AA7 CYS A 277 ASN A 288 1 12 HELIX 8 AA8 GLY A 293 GLU A 298 1 6 HELIX 9 AA9 GLY A 334 LEU A 350 1 17 HELIX 10 AB1 LYS A 351 ALA A 353 5 3 HELIX 11 AB2 GLY A 356 HIS A 365 1 10 HELIX 12 AB3 GLY A 374 THR A 377 5 4 HELIX 13 AB4 SER A 378 LEU A 383 1 6 SHEET 1 AA1 6 MET A 133 CYS A 135 0 SHEET 2 AA1 6 LEU A 264 VAL A 274 1 O GLU A 271 N MET A 133 SHEET 3 AA1 6 ILE A 251 GLU A 258 -1 N THR A 253 O PHE A 270 SHEET 4 AA1 6 ARG A 156 TYR A 163 -1 N ILE A 162 O LEU A 252 SHEET 5 AA1 6 SER A 215 PRO A 219 -1 O VAL A 218 N VAL A 157 SHEET 6 AA1 6 GLU A 204 LEU A 206 -1 N GLU A 204 O VAL A 217 SHEET 1 AA2 2 CYS A 141 VAL A 143 0 SHEET 2 AA2 2 ILE A 232 TYR A 234 -1 O TYR A 234 N CYS A 141 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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