HEADER LYASE 17-FEB-21 7E55 TITLE CRYO-EM STRUCTURE OF ALPHA 7 HOMO-TETRADECAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASOME SUBUNIT ALPHA TYPE-3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MACROPAIN SUBUNIT C8,MULTICATALYTIC ENDOPEPTIDASE COMPLEX COMPND 5 SUBUNIT C8,PROTEASOME COMPONENT C8; COMPND 6 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: PSMA3, HC8, PSC8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CONFORMATIONAL FLUCTUATION, DOUBLE-RING, PROTEASOME, D7 SYMMETRY, KEYWDS 2 CHAPERONE, LYASE EXPDTA ELECTRON MICROSCOPY AUTHOR C.SONG,K.MURATA REVDAT 2 19-MAY-21 7E55 1 JRNL REVDAT 1 05-MAY-21 7E55 0 JRNL AUTH C.SONG,T.SATOH,T.SEKIGUCHI,K.KATO,K.MURATA JRNL TITL STRUCTURAL FLUCTUATIONS OF THE HUMAN PROTEASOME ALPHA 7 JRNL TITL 2 HOMO-TETRADECAMER DOUBLE RING IMPLY THE PROTEASOMAL JRNL TITL 3 ALPHA-RING ASSEMBLY MECHANISM. JRNL REF INT J MOL SCI V. 22 2021 JRNL REFN ESSN 1422-0067 JRNL PMID 33926037 JRNL DOI 10.3390/IJMS22094519 REMARK 2 REMARK 2 RESOLUTION. 5.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, RELION, CTFFIND, PHENIX, REMARK 3 RELION, RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 5DSV REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 531.000 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) : 5.900 REMARK 3 NUMBER OF PARTICLES : 18388 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7E55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1300020771. 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 : PROTEASOME SUBUNIT ALPHA TYPE-7 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 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 2200FS REMARK 245 DETECTOR TYPE : DIRECT ELECTRON DE-20 (5K X REMARK 245 3K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 4.20 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 : 40000 REMARK 245 CALIBRATED MAGNIFICATION : 45065 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 DIHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = D7). 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 0.623490 0.781831 0.000000 -57.55555 REMARK 350 BIOMT2 2 -0.781831 0.623490 0.000000 164.48456 REMARK 350 BIOMT3 2 0.000000 0.000001 1.000000 -0.00008 REMARK 350 BIOMT1 3 -0.222521 0.974928 -0.000001 35.15835 REMARK 350 BIOMT2 3 -0.974928 -0.222521 0.000000 312.03774 REMARK 350 BIOMT3 3 0.000000 0.000001 1.000000 -0.00008 REMARK 350 BIOMT1 4 -0.900969 0.433884 -0.000001 208.32625 REMARK 350 BIOMT2 4 -0.433884 -0.900969 0.000000 331.54900 REMARK 350 BIOMT3 4 -0.000001 0.000001 1.000000 0.00001 REMARK 350 BIOMT1 5 -0.900969 -0.433884 -0.000001 331.54919 REMARK 350 BIOMT2 5 0.433884 -0.900969 0.000001 208.32595 REMARK 350 BIOMT3 5 -0.000001 0.000000 1.000000 0.00012 REMARK 350 BIOMT1 6 -0.222521 -0.974928 0.000000 312.03777 REMARK 350 BIOMT2 6 0.974928 -0.222521 0.000001 35.15807 REMARK 350 BIOMT3 6 -0.000001 0.000000 1.000000 0.00016 REMARK 350 BIOMT1 7 0.623490 -0.781831 0.000000 164.48450 REMARK 350 BIOMT2 7 0.781831 0.623490 0.000001 -57.55570 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00011 REMARK 350 BIOMT1 8 1.000000 0.000002 0.000001 -0.00037 REMARK 350 BIOMT2 8 0.000002 -1.000000 0.000000 283.99977 REMARK 350 BIOMT3 8 0.000001 0.000000 -1.000000 283.99989 REMARK 350 BIOMT1 9 0.623489 0.781832 0.000001 -57.55568 REMARK 350 BIOMT2 9 0.781832 -0.623489 0.000000 119.51513 REMARK 350 BIOMT3 9 0.000001 0.000000 -1.000000 283.99991 REMARK 350 BIOMT1 10 -0.222522 0.974928 0.000000 35.15845 REMARK 350 BIOMT2 10 0.974928 0.222522 0.000000 -28.03792 REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 284.00001 REMARK 350 BIOMT1 11 -0.900970 0.433882 0.000000 208.32638 REMARK 350 BIOMT2 11 0.433882 0.900970 0.000000 -47.54892 REMARK 350 BIOMT3 11 0.000000 0.000000 -1.000000 284.00011 REMARK 350 BIOMT1 12 -0.900968 -0.433885 0.000000 331.54913 REMARK 350 BIOMT2 12 -0.433885 0.900968 -0.000001 75.67431 REMARK 350 BIOMT3 12 0.000000 -0.000001 -1.000000 284.00014 REMARK 350 BIOMT1 13 -0.222519 -0.974928 0.000001 312.03745 REMARK 350 BIOMT2 13 -0.974928 0.222519 -0.000001 248.84217 REMARK 350 BIOMT3 13 0.000001 -0.000001 -1.000000 284.00008 REMARK 350 BIOMT1 14 0.623491 -0.781831 0.000001 164.48405 REMARK 350 BIOMT2 14 -0.781831 -0.623491 -0.000001 341.55572 REMARK 350 BIOMT3 14 0.000001 -0.000001 -1.000000 283.99996 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 SER A 1 REMARK 465 GLU A 246 REMARK 465 ASP A 247 REMARK 465 GLU A 248 REMARK 465 SER A 249 REMARK 465 ASP A 250 REMARK 465 ASP A 251 REMARK 465 ASP A 252 REMARK 465 ASN A 253 REMARK 465 MET A 254 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 LEU A 213 CA - CB - CG ANGL. DEV. = 15.3 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 70 -169.49 -129.95 REMARK 500 TYR A 122 31.64 -95.50 REMARK 500 TYR A 125 -169.09 -117.47 REMARK 500 SER A 126 17.30 -140.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 215 VAL A 216 139.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30990 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ALPHA 7 HOMO-TETRADECAMER DBREF 7E55 A 0 254 UNP P25788 PSA3_HUMAN 1 255 SEQRES 1 A 255 MET SER SER ILE GLY THR GLY TYR ASP LEU SER ALA SER SEQRES 2 A 255 THR PHE SER PRO ASP GLY ARG VAL PHE GLN VAL GLU TYR SEQRES 3 A 255 ALA MET LYS ALA VAL GLU ASN SER SER THR ALA ILE GLY SEQRES 4 A 255 ILE ARG CYS LYS ASP GLY VAL VAL PHE GLY VAL GLU LYS SEQRES 5 A 255 LEU VAL LEU SER LYS LEU TYR GLU GLU GLY SER ASN LYS SEQRES 6 A 255 ARG LEU PHE ASN VAL ASP ARG HIS VAL GLY MET ALA VAL SEQRES 7 A 255 ALA GLY LEU LEU ALA ASP ALA ARG SER LEU ALA ASP ILE SEQRES 8 A 255 ALA ARG GLU GLU ALA SER ASN PHE ARG SER ASN PHE GLY SEQRES 9 A 255 TYR ASN ILE PRO LEU LYS HIS LEU ALA ASP ARG VAL ALA SEQRES 10 A 255 MET TYR VAL HIS ALA TYR THR LEU TYR SER ALA VAL ARG SEQRES 11 A 255 PRO PHE GLY CYS SER PHE MET LEU GLY SER TYR SER VAL SEQRES 12 A 255 ASN ASP GLY ALA GLN LEU TYR MET ILE ASP PRO SER GLY SEQRES 13 A 255 VAL SER TYR GLY TYR TRP GLY CYS ALA ILE GLY LYS ALA SEQRES 14 A 255 ARG GLN ALA ALA LYS THR GLU ILE GLU LYS LEU GLN MET SEQRES 15 A 255 LYS GLU MET THR CYS ARG ASP ILE VAL LYS GLU VAL ALA SEQRES 16 A 255 LYS ILE ILE TYR ILE VAL HIS ASP GLU VAL LYS ASP LYS SEQRES 17 A 255 ALA PHE GLU LEU GLU LEU SER TRP VAL GLY GLU LEU THR SEQRES 18 A 255 ASN GLY ARG HIS GLU ILE VAL PRO LYS ASP ILE ARG GLU SEQRES 19 A 255 GLU ALA GLU LYS TYR ALA LYS GLU SER LEU LYS GLU GLU SEQRES 20 A 255 ASP GLU SER ASP ASP ASP ASN MET HELIX 1 1 PHE A 21 ASN A 32 1 12 HELIX 2 2 LEU A 81 PHE A 102 1 22 HELIX 3 3 LEU A 108 THR A 123 1 16 HELIX 4 4 ARG A 169 LYS A 178 1 10 HELIX 5 5 CYS A 186 VAL A 200 1 15 HELIX 6 6 GLU A 218 THR A 220 1 3 HELIX 7 7 LYS A 229 LYS A 244 1 16 SHEET 1 1 1 ALA A 36 ILE A 39 0 SHEET 1 2 1 GLY A 44 VAL A 49 0 SHEET 1 3 1 LEU A 66 ASN A 68 0 SHEET 1 4 1 VAL A 73 GLY A 79 0 SHEET 1 5 1 CYS A 133 SER A 141 0 SHEET 1 6 1 GLY A 145 ILE A 151 0 SHEET 1 7 1 SER A 157 GLY A 159 0 SHEET 1 8 1 GLY A 162 ILE A 165 0 SHEET 1 9 1 GLU A 212 GLY A 217 0 SSBOND 1 CYS A 41 CYS A 186 1555 1555 2.02 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