HEADER STRUCTURAL PROTEIN 21-APR-23 8J5A TITLE SINGLE-PARTICLE CRYO-EM STRUCTURE OF MOUSE APOFERRITIN AT 1.19 TITLE 2 ANGSTROM RESOLUTION (DATASET A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERRITIN HEAVY CHAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: FTH1, FTH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SINGLE-PARTICLE CRYO-EM, COLD FIELD EMISSION, CFEG, APOFERRITIN, CRYO KEYWDS 2 ARM, STRUCTURAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.KAWAKAMI,S.MAKI-YONEKURA,T.HAMAGUCHI,K.TAKABA,K.YONEKURA REVDAT 1 12-JUL-23 8J5A 0 JRNL AUTH S.MAKI-YONEKURA,K.KAWAKAMI,K.TAKABA,T.HAMAGUCHI,K.YONEKURA JRNL TITL MEASUREMENT OF CHARGES AND CHEMICAL BONDING IN A CRYO-EM JRNL TITL 2 STRUCTURE. JRNL REF COMMUN CHEM V. 6 98 2023 JRNL REFN ESSN 2399-3669 JRNL PMID 37258702 JRNL DOI 10.1038/S42004-023-00900-X REMARK 2 REMARK 2 RESOLUTION. 1.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, COOT, REFMAC, 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) : 1.190 REMARK 3 NUMBER OF PARTICLES : 223586 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 8J5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300037218. 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 : APOFERRITIN FROM MUS MUSCULUS 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 : JEOL CRYO ARM 300 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1000.00 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) : 3647.00 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) : 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 OCTAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = O). 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 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 126.72000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT1 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 6 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT3 6 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT1 7 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT2 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 7 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT1 8 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT2 8 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT3 8 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 9 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 10 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT2 10 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT3 10 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 11 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 11 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT3 11 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT1 12 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT2 12 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT1 13 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 13 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT3 13 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 14 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT2 14 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT3 14 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT1 15 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 15 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 15 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT1 16 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT2 16 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 16 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 17 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 17 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT3 17 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 18 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT2 18 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 18 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 19 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT2 19 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT3 19 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT1 20 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 20 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 20 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT1 21 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 21 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 22 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 22 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 22 0.000000 0.000000 -1.000000 126.72000 REMARK 350 BIOMT1 23 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT2 23 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 23 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 24 0.000000 -1.000000 0.000000 126.72000 REMARK 350 BIOMT2 24 -1.000000 0.000000 0.000000 126.72000 REMARK 350 BIOMT3 24 0.000000 0.000000 -1.000000 126.72000 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 GLN A 14 CG CD OE1 NE2 REMARK 470 ASP A 42 CG OD1 OD2 REMARK 470 LYS A 49 CG CD CE NZ REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 LYS A 71 CG CD CE NZ REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 ASP A 89 CG OD1 OD2 REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 91 CG OD1 OD2 REMARK 470 GLU A 94 CG CD OE1 OE2 REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 GLU A 140 CG CD OE1 OE2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 GLU A 147 CG CD OE1 OE2 REMARK 470 LYS A 157 CG CD CE NZ REMARK 470 GLU A 162 CG CD OE1 OE2 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 ND1 HIS A 173 O HOH A 301 2.14 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 VAL A 46 -60.64 -123.02 REMARK 500 GLU A 94 -52.72 79.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 62 OE1 REMARK 620 2 HOH A 321 O 149.5 REMARK 620 3 HOH A 332 O 79.2 76.0 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35981 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-35984 RELATED DB: EMDB REMARK 900 STRUCTURE OF APOFERRITIN FROM MUS MUSCULUS BY CRYO-ELECTRON REMARK 900 MICROSCOPY DBREF 8J5A A 5 176 UNP P09528 FRIH_MOUSE 6 177 SEQRES 1 A 172 PRO SER GLN VAL ARG GLN ASN TYR HIS GLN ASP ALA GLU SEQRES 2 A 172 ALA ALA ILE ASN ARG GLN ILE ASN LEU GLU LEU TYR ALA SEQRES 3 A 172 SER TYR VAL TYR LEU SER MET SER CYS TYR PHE ASP ARG SEQRES 4 A 172 ASP ASP VAL ALA LEU LYS ASN PHE ALA LYS TYR PHE LEU SEQRES 5 A 172 HIS GLN SER HIS GLU GLU ARG GLU HIS ALA GLU LYS LEU SEQRES 6 A 172 MET LYS LEU GLN ASN GLN ARG GLY GLY ARG ILE PHE LEU SEQRES 7 A 172 GLN ASP ILE LYS LYS PRO ASP ARG ASP ASP TRP GLU SER SEQRES 8 A 172 GLY LEU ASN ALA MET GLU CYS ALA LEU HIS LEU GLU LYS SEQRES 9 A 172 SER VAL ASN GLN SER LEU LEU GLU LEU HIS LYS LEU ALA SEQRES 10 A 172 THR ASP LYS ASN ASP PRO HIS LEU CYS ASP PHE ILE GLU SEQRES 11 A 172 THR TYR TYR LEU SER GLU GLN VAL LYS SER ILE LYS GLU SEQRES 12 A 172 LEU GLY ASP HIS VAL THR ASN LEU ARG LYS MET GLY ALA SEQRES 13 A 172 PRO GLU ALA GLY MET ALA GLU TYR LEU PHE ASP LYS HIS SEQRES 14 A 172 THR LEU GLY HET NA A 201 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *141(H2 O) HELIX 1 AA1 HIS A 13 ASP A 42 1 30 HELIX 2 AA2 LEU A 48 ARG A 76 1 29 HELIX 3 AA3 SER A 95 LYS A 124 1 30 HELIX 4 AA4 ASP A 126 TYR A 137 1 12 HELIX 5 AA5 TYR A 137 GLY A 159 1 23 HELIX 6 AA6 ALA A 163 THR A 174 1 12 LINK OE1 GLU A 62 NA NA A 201 1555 1555 1.98 LINK NA NA A 201 O HOH A 321 1555 1555 2.31 LINK NA NA A 201 O HOH A 332 1555 1555 2.19 CISPEP 1 ALA A 160 PRO A 161 0 -6.07 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