HEADER STRUCTURAL PROTEIN 01-OCT-24 9JSU TITLE WILD-TYPE NATIVE PMEL AMYLOID - POLYMORPH 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: M-ALPHA; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 SYNONYM: 95 KDA MELANOCYTE-SPECIFIC SECRETED GLYCOPROTEIN,P26, COMPND 5 SECRETED MELANOMA-ASSOCIATED ME20 ANTIGEN,ME20-S,ME20S SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: HMV-II KEYWDS MELANOSOME, MELANOMA, PIGMENT, MELANIN, AMYLOID, GLAUCOMA, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.ODA,H.YANAGISAWA REVDAT 1 09-OCT-24 9JSU 0 JRNL AUTH H.YANAGISAWA,T.ODA JRNL TITL CRYO-EM OF PMEL AMYLOIDS REVEALS PATHOGENIC MECHANISM OF JRNL TITL 2 G175S IN PIGMENT DISPERSION SYNDROME. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 1.790 REMARK 3 NUMBER OF PARTICLES : 352878 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 9JSU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052120. 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 : FILAMENT REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : WILD-TYPE NATIVE PMEL AMYLOID REMARK 245 EXTRACTED FROM MELANOMA CELL REMARK 245 LINE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.30 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 4.40 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 CRYO ARM 300 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 : 2.70 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 : 60000 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61782 RELATED DB: EMDB REMARK 900 WILD-TYPE NATIVE PMEL AMYLOIDS - POLYMORPH 1 REMARK 900 RELATED ID: 9JST RELATED DB: PDB REMARK 900 WILD-TYPE NATIVE PMEL AMYLOIDS - POLYMORPH 1 REMARK 900 RELATED ID: EMD-61783 RELATED DB: EMDB REMARK 900 WILD-TYPE NATIVE PMEL AMYLOID - POLYMORPH 2 DBREF 9JSU A 151 183 UNP P40967 PMEL_HUMAN 151 183 DBREF 9JSU B 151 183 UNP P40967 PMEL_HUMAN 151 183 DBREF 9JSU C 151 183 UNP P40967 PMEL_HUMAN 151 183 DBREF 9JSU D 151 183 UNP P40967 PMEL_HUMAN 151 183 DBREF 9JSU E 151 183 UNP P40967 PMEL_HUMAN 151 183 DBREF 9JSU F 151 183 UNP P40967 PMEL_HUMAN 151 183 DBREF 9JSU G 151 183 UNP P40967 PMEL_HUMAN 151 183 DBREF 9JSU H 151 183 UNP P40967 PMEL_HUMAN 151 183 SEQRES 1 A 33 TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN VAL LEU SEQRES 2 A 33 GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR GLY ARG SEQRES 3 A 33 ALA MET LEU GLY THR HIS THR SEQRES 1 B 33 TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN VAL LEU SEQRES 2 B 33 GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR GLY ARG SEQRES 3 B 33 ALA MET LEU GLY THR HIS THR SEQRES 1 C 33 TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN VAL LEU SEQRES 2 C 33 GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR GLY ARG SEQRES 3 C 33 ALA MET LEU GLY THR HIS THR SEQRES 1 D 33 TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN VAL LEU SEQRES 2 D 33 GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR GLY ARG SEQRES 3 D 33 ALA MET LEU GLY THR HIS THR SEQRES 1 E 33 TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN VAL LEU SEQRES 2 E 33 GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR GLY ARG SEQRES 3 E 33 ALA MET LEU GLY THR HIS THR SEQRES 1 F 33 TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN VAL LEU SEQRES 2 F 33 GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR GLY ARG SEQRES 3 F 33 ALA MET LEU GLY THR HIS THR SEQRES 1 G 33 TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN VAL LEU SEQRES 2 G 33 GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR GLY ARG SEQRES 3 G 33 ALA MET LEU GLY THR HIS THR SEQRES 1 H 33 TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN VAL LEU SEQRES 2 H 33 GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR GLY ARG SEQRES 3 H 33 ALA MET LEU GLY THR HIS THR SHEET 1 AA1 4 VAL A 152 VAL A 162 0 SHEET 2 AA1 4 VAL B 152 VAL B 162 1 O VAL B 162 N GLN A 161 SHEET 3 AA1 4 VAL C 152 VAL C 162 1 O TRP C 156 N GLY B 157 SHEET 4 AA1 4 VAL D 152 VAL D 162 1 O TRP D 156 N GLY C 157 SHEET 1 AA2 4 VAL A 167 LEU A 179 0 SHEET 2 AA2 4 VAL B 167 LEU B 179 1 O LEU B 179 N MET A 178 SHEET 3 AA2 4 VAL C 167 LEU C 179 1 O VAL C 167 N SER B 168 SHEET 4 AA2 4 VAL D 167 LEU D 179 1 O GLY D 169 N SER C 168 SHEET 1 AA3 4 VAL E 152 VAL E 162 0 SHEET 2 AA3 4 VAL F 152 VAL F 162 1 O VAL F 162 N GLN E 161 SHEET 3 AA3 4 VAL G 152 VAL G 162 1 O TRP G 156 N GLY F 157 SHEET 4 AA3 4 VAL H 152 VAL H 162 1 O TRP H 156 N GLY G 157 SHEET 1 AA4 4 VAL E 167 LEU E 179 0 SHEET 2 AA4 4 VAL F 167 LEU F 179 1 O LEU F 179 N MET E 178 SHEET 3 AA4 4 VAL G 167 LEU G 179 1 O VAL G 167 N SER F 168 SHEET 4 AA4 4 VAL H 167 LEU H 179 1 O VAL H 167 N SER G 168 CISPEP 1 GLY A 165 PRO A 166 0 -8.35 CISPEP 2 GLY B 165 PRO B 166 0 -9.68 CISPEP 3 GLY C 165 PRO C 166 0 -10.74 CISPEP 4 GLY D 165 PRO D 166 0 -4.83 CISPEP 5 GLY E 165 PRO E 166 0 -7.10 CISPEP 6 GLY F 165 PRO F 166 0 -10.07 CISPEP 7 GLY G 165 PRO G 166 0 -9.29 CISPEP 8 GLY H 165 PRO H 166 0 -5.31 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