HEADER CHAPERONE 15-APR-24 9BEE TITLE ALPHAB-CRYSTALLIN N-TERMINAL IXI VARIANT IN A FIBRIL STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-CRYSTALLIN B CHAIN; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: ALPHA(B)-CRYSTALLIN,HEAT SHOCK PROTEIN BETA-5,HSPB5,HEAT COMPND 5 SHOCK PROTEIN FAMILY B MEMBER 5,RENAL CARCINOMA ANTIGEN NY-REN-27, COMPND 6 ROSENTHAL FIBER COMPONENT; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ALPHA-CRYSTALLIN B CHAIN; COMPND 10 CHAIN: A; COMPND 11 SYNONYM: ALPHA(B)-CRYSTALLIN,HEAT SHOCK PROTEIN BETA-5,HSPB5,HEAT COMPND 12 SHOCK PROTEIN FAMILY B MEMBER 5,RENAL CARCINOMA ANTIGEN NY-REN-27, COMPND 13 ROSENTHAL FIBER COMPONENT; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: 7 RESIDUES ARE MODELED AS UNKNOWN AS THEY ARE COMPND 16 IDENTIFIABLE IN THE EM VOLUME WITH 1 BEING ABLE TO BE ASSIGNED AN COMPND 17 IDENTITY WITH INTERMEDIATE CONFIDENCE. WE CANNOT CLEARLY IDENTIFY COMPND 18 WHICH PROTOMER THE BOUND PEPTIDE CORRESPONDS TO THOUGH IT IS BELIEVED COMPND 19 TO PLAY A KEY ROLE IN THE OLIGOMERIZATION. WE HAVE OPTED TO INCLUDE COMPND 20 THE PEPTIDE AS PART OF CHAIN A WITH NUMBERING BASED ON OUR BEST COMPND 21 APPROXIMATION FROM RELATED PROTEIN SPECIES AND MASS SPEC DATA COMPND 22 PUBLISHED BY OTHERS. THE RESIDUES ARE LABELLED AS UNKNOWN TO REFLECT COMPND 23 OUR LOW CONFIDENCE OF THE IDENTITY OF THE PEPTIDE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CRYAB, CRYA2, HSPB5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SMALL HEAT-SHOCK PROTEIN FIBRIL PROTEOSTASIS CATARACT, CHAPERONE EXPDTA ELECTRON MICROSCOPY AUTHOR R.MCFARLAND,S.L.REICHOW REVDAT 1 11-DEC-24 9BEE 0 JRNL AUTH R.MCFARLAND,R.NOROOZI,A.P.MILLER,S.L.REICHOW JRNL TITL DYNAMIC FIBRILLAR ASSEMBLY OF ALPHA B-CRYSTALLIN INDUCED BY JRNL TITL 2 PERTURBATION OF THE CONSERVED NT-IXI MOTIF RESOLVED BY JRNL TITL 3 CRYO-EM. JRNL REF NAT COMMUN V. 15 10336 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39609421 JRNL DOI 10.1038/S41467-024-54647-7 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CTFFIND, UCSF REMARK 3 CHIMERAX, CRYOSPARC, CRYOSPARC, PHENIX, REMARK 3 COOT, ISOLDE REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2WJ7 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 139338 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 9BEE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-24. REMARK 100 THE DEPOSITION ID IS D_1000282448. 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 : ASYMMETRIC DIMER OF ALPHAB REMARK 245 -CRYSTALLIN FILAMENT STATE REMARK 245 FORMED BY AN N-TERMINAL IXI REMARK 245 VARIANT REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 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 : 10654 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) 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 : 2.30 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 : 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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: 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 UNK A 26 37.56 38.12 REMARK 500 ASP A 140 -8.82 90.80 REMARK 500 LYS A 150 -167.49 -116.79 REMARK 500 SER A 153 -161.74 -113.01 REMARK 500 PRO A 155 20.43 -77.08 REMARK 500 GLU A 156 -67.50 82.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-44477 RELATED DB: EMDB REMARK 900 ALPHAB-CRYSTALLIN N-TERMINAL IXI VARIANT IN A FIBRIL STATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE COMPLETE SAMPLE SEQUENCE IS REMARK 999 MDAAAHHPWIRRPFFPFHSPSRLFDQFFGEHLLESDLFPTSTSLSPFYLRPPSFLRAPSW REMARK 999 FDTGLSEMRLEKDRFSVNLDVKHFSPEELKVKVLGDVIEVHGKHEERQDEHGFISREFHR REMARK 999 KYRIPADVDPLTITSSLSSDGVLTVNGPRKQVSGPERTIPITREEKPAVTAAPKK DBREF 9BEE B 76 163 UNP P02511 CRYAB_HUMAN 76 163 DBREF 9BEE A 22 163 PDB 9BEE 9BEE 22 163 SEQRES 1 B 88 SER VAL ASN LEU ASP VAL LYS HIS PHE SER PRO GLU GLU SEQRES 2 B 88 LEU LYS VAL LYS VAL LEU GLY ASP VAL ILE GLU VAL HIS SEQRES 3 B 88 GLY LYS HIS GLU GLU ARG GLN ASP GLU HIS GLY PHE ILE SEQRES 4 B 88 SER ARG GLU PHE HIS ARG LYS TYR ARG ILE PRO ALA ASP SEQRES 5 B 88 VAL ASP PRO LEU THR ILE THR SER SER LEU SER SER ASP SEQRES 6 B 88 GLY VAL LEU THR VAL ASN GLY PRO ARG LYS GLN VAL SER SEQRES 7 B 88 GLY PRO GLU ARG THR ILE PRO ILE THR ARG SEQRES 1 A 108 UNK UNK UNK UNK UNK UNK UNK THR GLY LEU SER GLU MET SEQRES 2 A 108 ARG LEU GLU LYS ASP ARG PHE SER VAL ASN LEU ASP VAL SEQRES 3 A 108 LYS HIS PHE SER PRO GLU GLU LEU LYS VAL LYS VAL LEU SEQRES 4 A 108 GLY ASP VAL ILE GLU VAL HIS GLY LYS HIS GLU GLU ARG SEQRES 5 A 108 GLN ASP GLU HIS GLY PHE ILE SER ARG GLU PHE HIS ARG SEQRES 6 A 108 LYS TYR ARG ILE PRO ALA ASP VAL ASP PRO LEU THR ILE SEQRES 7 A 108 THR SER SER LEU SER SER ASP GLY VAL LEU THR VAL ASN SEQRES 8 A 108 GLY PRO ARG LYS GLN VAL SER GLY PRO GLU ARG THR ILE SEQRES 9 A 108 PRO ILE THR ARG HELIX 1 AA1 SER A 85 GLU A 87 5 3 SHEET 1 AA1 3 VAL B 77 ASP B 80 0 SHEET 2 AA1 3 VAL B 142 ASN B 146 -1 O VAL B 145 N VAL B 77 SHEET 3 AA1 3 THR B 134 LEU B 137 -1 N SER B 136 O THR B 144 SHEET 1 AA2 4 LYS B 90 LEU B 94 0 SHEET 2 AA2 4 VAL B 97 LYS B 103 -1 O VAL B 97 N LEU B 94 SHEET 3 AA2 4 GLY B 112 ARG B 123 -1 O ARG B 120 N VAL B 100 SHEET 4 AA2 4 GLN B 108 ASP B 109 -1 N ASP B 109 O GLY B 112 SHEET 1 AA3 6 LYS B 90 LEU B 94 0 SHEET 2 AA3 6 VAL B 97 LYS B 103 -1 O VAL B 97 N LEU B 94 SHEET 3 AA3 6 GLY B 112 ARG B 123 -1 O ARG B 120 N VAL B 100 SHEET 4 AA3 6 PHE A 113 TYR A 122 -1 O HIS A 119 N SER B 115 SHEET 5 AA3 6 ILE A 98 GLN A 108 -1 N ARG A 107 O ILE A 114 SHEET 6 AA3 6 LEU A 89 LYS A 92 -1 N LYS A 90 O HIS A 101 SHEET 1 AA4 4 GLU A 67 LEU A 70 0 SHEET 2 AA4 4 ARG A 74 LEU A 79 -1 O SER A 76 N ARG A 69 SHEET 3 AA4 4 VAL A 142 PRO A 148 -1 O LEU A 143 N LEU A 79 SHEET 4 AA4 4 THR A 134 SER A 138 -1 N THR A 134 O ASN A 146 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 TER 1409 ARG B 163 TER 3085 ARG A 163 MASTER 133 0 0 1 17 0 0 6 1545 2 0 16 END