HEADER STRUCTURAL PROTEIN 01-OCT-24 9JSX TITLE G175S PMEL CAF AMYLOID - IN VITRO POLYMERIZED COMPND MOL_ID: 1; COMPND 2 MOLECULE: M-ALPHA; COMPND 3 CHAIN: A, E, B, F, C, G, D, H; COMPND 4 SYNONYM: 95 KDA MELANOCYTE-SPECIFIC SECRETED GLYCOPROTEIN,P26, COMPND 5 SECRETED MELANOMA-ASSOCIATED ME20 ANTIGEN,ME20-S,ME20S; 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: PMEL, D12S53E, PMEL17, SILV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MELANOSOME, MELANOMA, PIGMENT, MELANIN, AMYLOID, GLAUCOMA, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.ODA,H.YANAGISAWA REVDAT 1 09-OCT-24 9JSX 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 : 781124 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 9JSX 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_1300052127. 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 : G175S MUTANT PMEL CAF DOMAIN, REMARK 245 EXPRESSED IN E. COLI 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, E, B, F, C, G, D, 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 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 B 168 O VAL C 167 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER E 168 CB SER E 168 OG -0.130 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 TYR A 159 74.32 56.98 REMARK 500 TYR E 159 78.19 60.43 REMARK 500 TYR B 159 71.22 58.54 REMARK 500 TYR F 159 78.83 59.09 REMARK 500 TYR C 159 72.99 58.38 REMARK 500 TYR G 159 79.15 59.20 REMARK 500 TYR D 159 73.20 58.48 REMARK 500 TYR H 159 75.89 56.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61782 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-61783 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-61784 RELATED DB: EMDB REMARK 900 RELATED ID: 9JST RELATED DB: PDB REMARK 900 RELATED ID: 9JSU RELATED DB: PDB REMARK 900 RELATED ID: 9JSV RELATED DB: PDB REMARK 900 RELATED ID: EMD-61785 RELATED DB: EMDB REMARK 900 RELATED ID: 9JSW RELATED DB: PDB REMARK 900 RELATED ID: EMD-61786 RELATED DB: EMDB REMARK 900 G175S PMEL CAF AMYLOID - IN VITRO POLYMERIZED DBREF 9JSX A 149 182 UNP P40967 PMEL_HUMAN 149 182 DBREF 9JSX E 149 182 UNP P40967 PMEL_HUMAN 149 182 DBREF 9JSX B 149 182 UNP P40967 PMEL_HUMAN 149 182 DBREF 9JSX F 149 182 UNP P40967 PMEL_HUMAN 149 182 DBREF 9JSX C 149 182 UNP P40967 PMEL_HUMAN 149 182 DBREF 9JSX G 149 182 UNP P40967 PMEL_HUMAN 149 182 DBREF 9JSX D 149 182 UNP P40967 PMEL_HUMAN 149 182 DBREF 9JSX H 149 182 UNP P40967 PMEL_HUMAN 149 182 SEQADV 9JSX SER A 175 UNP P40967 GLY 175 VARIANT SEQADV 9JSX SER E 175 UNP P40967 GLY 175 VARIANT SEQADV 9JSX SER B 175 UNP P40967 GLY 175 VARIANT SEQADV 9JSX SER F 175 UNP P40967 GLY 175 VARIANT SEQADV 9JSX SER C 175 UNP P40967 GLY 175 VARIANT SEQADV 9JSX SER G 175 UNP P40967 GLY 175 VARIANT SEQADV 9JSX SER D 175 UNP P40967 GLY 175 VARIANT SEQADV 9JSX SER H 175 UNP P40967 GLY 175 VARIANT SEQRES 1 A 34 PHE VAL TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN SEQRES 2 A 34 VAL LEU GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR SEQRES 3 A 34 SER ARG ALA MET LEU GLY THR HIS SEQRES 1 E 34 PHE VAL TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN SEQRES 2 E 34 VAL LEU GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR SEQRES 3 E 34 SER ARG ALA MET LEU GLY THR HIS SEQRES 1 B 34 PHE VAL TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN SEQRES 2 B 34 VAL LEU GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR SEQRES 3 B 34 SER ARG ALA MET LEU GLY THR HIS SEQRES 1 F 34 PHE VAL TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN SEQRES 2 F 34 VAL LEU GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR SEQRES 3 F 34 SER ARG ALA MET LEU GLY THR HIS SEQRES 1 C 34 PHE VAL TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN SEQRES 2 C 34 VAL LEU GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR SEQRES 3 C 34 SER ARG ALA MET LEU GLY THR HIS SEQRES 1 G 34 PHE VAL TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN SEQRES 2 G 34 VAL LEU GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR SEQRES 3 G 34 SER ARG ALA MET LEU GLY THR HIS SEQRES 1 D 34 PHE VAL TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN SEQRES 2 D 34 VAL LEU GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR SEQRES 3 D 34 SER ARG ALA MET LEU GLY THR HIS SEQRES 1 H 34 PHE VAL TYR VAL TRP LYS THR TRP GLY GLN TYR TRP GLN SEQRES 2 H 34 VAL LEU GLY GLY PRO VAL SER GLY LEU SER ILE GLY THR SEQRES 3 H 34 SER ARG ALA MET LEU GLY THR HIS SHEET 1 AA1 4 VAL A 150 LEU A 163 0 SHEET 2 AA1 4 VAL B 150 LEU B 163 1 O LEU B 163 N VAL A 162 SHEET 3 AA1 4 VAL C 150 LEU C 163 1 O GLN C 161 N VAL B 162 SHEET 4 AA1 4 VAL D 150 LEU D 163 1 O GLN D 161 N VAL C 162 SHEET 1 AA2 4 VAL A 167 ILE A 172 0 SHEET 2 AA2 4 VAL B 167 ILE B 172 1 O LEU B 170 N GLY A 169 SHEET 3 AA2 4 VAL C 167 ILE C 172 1 O GLY C 169 N SER B 168 SHEET 4 AA2 4 VAL D 167 LEU D 170 1 O GLY D 169 N SER C 168 SHEET 1 AA3 4 SER A 175 LEU A 179 0 SHEET 2 AA3 4 SER B 175 LEU B 179 1 O ALA B 177 N MET A 178 SHEET 3 AA3 4 SER C 175 LEU C 179 1 O ALA C 177 N ARG B 176 SHEET 4 AA3 4 SER D 175 LEU D 179 1 O ALA D 177 N ARG C 176 SHEET 1 AA4 4 VAL E 150 TRP E 153 0 SHEET 2 AA4 4 VAL F 150 TRP F 153 1 O TYR F 151 N VAL E 150 SHEET 3 AA4 4 VAL G 150 TRP G 153 1 O TYR G 151 N VAL F 150 SHEET 4 AA4 4 VAL H 150 TRP H 153 1 O TYR H 151 N VAL G 150 SHEET 1 AA5 4 TRP E 156 LEU E 163 0 SHEET 2 AA5 4 TRP F 156 LEU F 163 1 O GLN F 161 N VAL E 162 SHEET 3 AA5 4 TRP G 156 LEU G 163 1 O GLN G 161 N VAL F 162 SHEET 4 AA5 4 TRP H 156 LEU H 163 1 O GLN H 161 N VAL G 162 SHEET 1 AA6 4 VAL E 167 ILE E 172 0 SHEET 2 AA6 4 VAL F 167 ILE F 172 1 O GLY F 169 N SER E 168 SHEET 3 AA6 4 VAL G 167 ILE G 172 1 O GLY G 169 N SER F 168 SHEET 4 AA6 4 VAL H 167 ILE H 172 1 O GLY H 169 N SER G 168 SHEET 1 AA7 4 SER E 175 LEU E 179 0 SHEET 2 AA7 4 SER F 175 LEU F 179 1 O ALA F 177 N ARG E 176 SHEET 3 AA7 4 SER G 175 LEU G 179 1 O ALA G 177 N ARG F 176 SHEET 4 AA7 4 SER H 175 LEU H 179 1 O ALA H 177 N ARG G 176 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