HEADER PROTEIN FIBRIL 18-MAY-18 6GK3 TITLE TWO PROTOFILAMENT BETA-2-MICROGLOBULIN AMYLOID FIBRIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 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: B2M, CDABP0092, HDCMA22P; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMYLOID, B2M, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR M.G.IADANZA,N.A.RANSON REVDAT 3 23-OCT-24 6GK3 1 REMARK REVDAT 2 30-MAR-22 6GK3 1 REMARK REVDAT 1 14-NOV-18 6GK3 0 JRNL AUTH M.G.IADANZA,R.SILVERS,J.BOARDMAN,H.I.SMITH,T.K.KARAMANOS, JRNL AUTH 2 G.T.DEBELOUCHINA,Y.SU,R.G.GRIFFIN,N.A.RANSON,S.E.RADFORD JRNL TITL THE STRUCTURE OF A BETA2-MICROGLOBULIN FIBRIL SUGGESTS A JRNL TITL 2 MOLECULAR BASIS FOR ITS AMYLOID POLYMORPHISM. JRNL REF NAT COMMUN V. 9 4517 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30375379 JRNL DOI 10.1038/S41467-018-06761-6 REMARK 2 REMARK 2 RESOLUTION. 3.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, RELION, GCTF, UCSF REMARK 3 CHIMERA, PHENIX, RELION, RELION, RELION, REMARK 3 RELION REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER 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) : 3.975 REMARK 3 NUMBER OF PARTICLES : 11035 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 6GK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1200010086. 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 : TWO PROTOFILAMENT BETA-2 REMARK 245 -MICROGLOBULIN AMYLOID FIBRIL REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.03 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 2.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 5549 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1.75 REMARK 245 MAXIMUM DEFOCUS (NM) : 3.25 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) : 3850.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 35320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -152.0 KCAL/MOL 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 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 CD2 TYR B 67 CE1 TYR C 67 2.08 REMARK 500 CE2 TYR A 67 OE2 GLU E 69 2.08 REMARK 500 CD2 TYR F 67 CE1 TYR G 67 2.08 REMARK 500 CD2 TYR B 63 CE1 TYR C 63 2.09 REMARK 500 CD2 TYR F 63 CE1 TYR G 63 2.09 REMARK 500 OE2 GLU A 69 CE2 TYR E 67 2.10 REMARK 500 CD2 TYR G 67 CE1 TYR H 67 2.10 REMARK 500 CD2 TYR C 67 CE1 TYR D 67 2.10 REMARK 500 CD2 TYR A 67 CE1 TYR B 67 2.10 REMARK 500 CD2 TYR E 67 CE1 TYR F 67 2.10 REMARK 500 CD2 TYR A 63 CE1 TYR B 63 2.18 REMARK 500 CD2 TYR E 63 CE1 TYR F 63 2.18 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 67 73.07 47.94 REMARK 500 PRO A 72 156.78 -49.66 REMARK 500 TYR B 67 73.34 47.98 REMARK 500 PRO B 72 156.85 -49.60 REMARK 500 TYR C 67 73.43 48.35 REMARK 500 PRO C 72 156.74 -49.63 REMARK 500 TYR D 67 73.61 48.06 REMARK 500 PRO D 72 156.79 -49.57 REMARK 500 TYR E 67 73.08 47.92 REMARK 500 PRO E 72 156.77 -49.68 REMARK 500 TYR F 67 73.34 47.95 REMARK 500 PRO F 72 156.86 -49.67 REMARK 500 TYR G 67 73.43 48.33 REMARK 500 PRO G 72 156.75 -49.65 REMARK 500 TYR H 67 73.61 48.02 REMARK 500 PRO H 72 156.81 -49.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-0014 RELATED DB: EMDB REMARK 900 TWO PROTOFILAMENT BETA-2-MICROGLOBULIN AMYLOID FIBRIL DBREF 6GK3 A 22 85 UNP P61769 B2MG_HUMAN 42 105 DBREF 6GK3 B 22 85 UNP P61769 B2MG_HUMAN 42 105 DBREF 6GK3 C 22 85 UNP P61769 B2MG_HUMAN 42 105 DBREF 6GK3 D 22 85 UNP P61769 B2MG_HUMAN 42 105 DBREF 6GK3 E 22 85 UNP P61769 B2MG_HUMAN 42 105 DBREF 6GK3 F 22 85 UNP P61769 B2MG_HUMAN 42 105 DBREF 6GK3 G 22 85 UNP P61769 B2MG_HUMAN 42 105 DBREF 6GK3 H 22 85 UNP P61769 B2MG_HUMAN 42 105 SEQRES 1 A 64 PHE LEU ASN CYS TYR VAL SER GLY PHE HIS PRO SER ASP SEQRES 2 A 64 ILE GLU VAL ASP LEU LEU LYS ASN GLY GLU ARG ILE GLU SEQRES 3 A 64 LYS VAL GLU HIS SER ASP LEU SER PHE SER LYS ASP TRP SEQRES 4 A 64 SER PHE TYR LEU LEU TYR TYR THR GLU PHE THR PRO THR SEQRES 5 A 64 GLU LYS ASP GLU TYR ALA CYS ARG VAL ASN HIS VAL SEQRES 1 B 64 PHE LEU ASN CYS TYR VAL SER GLY PHE HIS PRO SER ASP SEQRES 2 B 64 ILE GLU VAL ASP LEU LEU LYS ASN GLY GLU ARG ILE GLU SEQRES 3 B 64 LYS VAL GLU HIS SER ASP LEU SER PHE SER LYS ASP TRP SEQRES 4 B 64 SER PHE TYR LEU LEU TYR TYR THR GLU PHE THR PRO THR SEQRES 5 B 64 GLU LYS ASP GLU TYR ALA CYS ARG VAL ASN HIS VAL SEQRES 1 C 64 PHE LEU ASN CYS TYR VAL SER GLY PHE HIS PRO SER ASP SEQRES 2 C 64 ILE GLU VAL ASP LEU LEU LYS ASN GLY GLU ARG ILE GLU SEQRES 3 C 64 LYS VAL GLU HIS SER ASP LEU SER PHE SER LYS ASP TRP SEQRES 4 C 64 SER PHE TYR LEU LEU TYR TYR THR GLU PHE THR PRO THR SEQRES 5 C 64 GLU LYS ASP GLU TYR ALA CYS ARG VAL ASN HIS VAL SEQRES 1 D 64 PHE LEU ASN CYS TYR VAL SER GLY PHE HIS PRO SER ASP SEQRES 2 D 64 ILE GLU VAL ASP LEU LEU LYS ASN GLY GLU ARG ILE GLU SEQRES 3 D 64 LYS VAL GLU HIS SER ASP LEU SER PHE SER LYS ASP TRP SEQRES 4 D 64 SER PHE TYR LEU LEU TYR TYR THR GLU PHE THR PRO THR SEQRES 5 D 64 GLU LYS ASP GLU TYR ALA CYS ARG VAL ASN HIS VAL SEQRES 1 E 64 PHE LEU ASN CYS TYR VAL SER GLY PHE HIS PRO SER ASP SEQRES 2 E 64 ILE GLU VAL ASP LEU LEU LYS ASN GLY GLU ARG ILE GLU SEQRES 3 E 64 LYS VAL GLU HIS SER ASP LEU SER PHE SER LYS ASP TRP SEQRES 4 E 64 SER PHE TYR LEU LEU TYR TYR THR GLU PHE THR PRO THR SEQRES 5 E 64 GLU LYS ASP GLU TYR ALA CYS ARG VAL ASN HIS VAL SEQRES 1 F 64 PHE LEU ASN CYS TYR VAL SER GLY PHE HIS PRO SER ASP SEQRES 2 F 64 ILE GLU VAL ASP LEU LEU LYS ASN GLY GLU ARG ILE GLU SEQRES 3 F 64 LYS VAL GLU HIS SER ASP LEU SER PHE SER LYS ASP TRP SEQRES 4 F 64 SER PHE TYR LEU LEU TYR TYR THR GLU PHE THR PRO THR SEQRES 5 F 64 GLU LYS ASP GLU TYR ALA CYS ARG VAL ASN HIS VAL SEQRES 1 G 64 PHE LEU ASN CYS TYR VAL SER GLY PHE HIS PRO SER ASP SEQRES 2 G 64 ILE GLU VAL ASP LEU LEU LYS ASN GLY GLU ARG ILE GLU SEQRES 3 G 64 LYS VAL GLU HIS SER ASP LEU SER PHE SER LYS ASP TRP SEQRES 4 G 64 SER PHE TYR LEU LEU TYR TYR THR GLU PHE THR PRO THR SEQRES 5 G 64 GLU LYS ASP GLU TYR ALA CYS ARG VAL ASN HIS VAL SEQRES 1 H 64 PHE LEU ASN CYS TYR VAL SER GLY PHE HIS PRO SER ASP SEQRES 2 H 64 ILE GLU VAL ASP LEU LEU LYS ASN GLY GLU ARG ILE GLU SEQRES 3 H 64 LYS VAL GLU HIS SER ASP LEU SER PHE SER LYS ASP TRP SEQRES 4 H 64 SER PHE TYR LEU LEU TYR TYR THR GLU PHE THR PRO THR SEQRES 5 H 64 GLU LYS ASP GLU TYR ALA CYS ARG VAL ASN HIS VAL SHEET 1 AA1 4 ASN A 24 VAL A 27 0 SHEET 2 AA1 4 ASN B 24 VAL B 27 1 O ASN B 24 N CYS A 25 SHEET 3 AA1 4 ASN C 24 VAL C 27 1 O ASN C 24 N CYS B 25 SHEET 4 AA1 4 ASN D 24 VAL D 27 1 O ASN D 24 N CYS C 25 SHEET 1 AA2 4 ILE A 35 LEU A 39 0 SHEET 2 AA2 4 ILE B 35 LEU B 39 1 O VAL B 37 N GLU A 36 SHEET 3 AA2 4 ILE C 35 LEU C 39 1 O VAL C 37 N GLU B 36 SHEET 4 AA2 4 ILE D 35 LEU D 39 1 O VAL D 37 N GLU C 36 SHEET 1 AA3 4 ARG A 45 GLU A 50 0 SHEET 2 AA3 4 ARG B 45 GLU B 50 1 O ILE B 46 N ARG A 45 SHEET 3 AA3 4 ARG C 45 GLU C 50 1 O ILE C 46 N ARG B 45 SHEET 4 AA3 4 ARG D 45 GLU D 50 1 O ILE D 46 N ARG C 45 SHEET 1 AA4 4 ASP A 53 SER A 55 0 SHEET 2 AA4 4 ASP B 53 SER B 55 1 O LEU B 54 N SER A 55 SHEET 3 AA4 4 ASP C 53 SER C 55 1 O LEU C 54 N SER B 55 SHEET 4 AA4 4 ASP D 53 SER D 55 1 O LEU D 54 N SER C 55 SHEET 1 AA5 4 ASP A 59 TRP A 60 0 SHEET 2 AA5 4 ASP B 59 TRP B 60 1 O TRP B 60 N ASP A 59 SHEET 3 AA5 4 ASP C 59 TRP C 60 1 O TRP C 60 N ASP B 59 SHEET 4 AA5 4 ASP D 59 TRP D 60 1 O TRP D 60 N ASP C 59 SHEET 1 AA6 4 LEU A 65 GLU A 69 0 SHEET 2 AA6 4 LEU B 65 GLU B 69 1 O LEU B 65 N TYR A 66 SHEET 3 AA6 4 LEU C 65 GLU C 69 1 O LEU C 65 N TYR B 66 SHEET 4 AA6 4 LEU D 65 GLU D 69 1 O LEU D 65 N TYR C 66 SHEET 1 AA7 4 ASP A 76 ASN A 83 0 SHEET 2 AA7 4 ASP B 76 ASN B 83 1 O CYS B 80 N ALA A 79 SHEET 3 AA7 4 ASP C 76 ASN C 83 1 O CYS C 80 N ALA B 79 SHEET 4 AA7 4 ASP D 76 ASN D 83 1 O CYS D 80 N ALA C 79 SHEET 1 AA8 4 ASN E 24 VAL E 27 0 SHEET 2 AA8 4 ASN F 24 VAL F 27 1 O ASN F 24 N CYS E 25 SHEET 3 AA8 4 ASN G 24 VAL G 27 1 O ASN G 24 N CYS F 25 SHEET 4 AA8 4 ASN H 24 VAL H 27 1 O ASN H 24 N CYS G 25 SHEET 1 AA9 4 ILE E 35 LEU E 39 0 SHEET 2 AA9 4 ILE F 35 LEU F 39 1 O VAL F 37 N GLU E 36 SHEET 3 AA9 4 ILE G 35 LEU G 39 1 O VAL G 37 N GLU F 36 SHEET 4 AA9 4 ILE H 35 LEU H 39 1 O VAL H 37 N GLU G 36 SHEET 1 AB1 4 ARG E 45 GLU E 50 0 SHEET 2 AB1 4 ARG F 45 GLU F 50 1 O ILE F 46 N ARG E 45 SHEET 3 AB1 4 ARG G 45 GLU G 50 1 O ILE G 46 N ARG F 45 SHEET 4 AB1 4 ARG H 45 GLU H 50 1 O ILE H 46 N ARG G 45 SHEET 1 AB2 4 ASP E 53 SER E 55 0 SHEET 2 AB2 4 ASP F 53 SER F 55 1 O LEU F 54 N SER E 55 SHEET 3 AB2 4 ASP G 53 SER G 55 1 O LEU G 54 N SER F 55 SHEET 4 AB2 4 ASP H 53 SER H 55 1 O LEU H 54 N SER G 55 SHEET 1 AB3 4 ASP E 59 TRP E 60 0 SHEET 2 AB3 4 ASP F 59 TRP F 60 1 O TRP F 60 N ASP E 59 SHEET 3 AB3 4 ASP G 59 TRP G 60 1 O TRP G 60 N ASP F 59 SHEET 4 AB3 4 ASP H 59 TRP H 60 1 O TRP H 60 N ASP G 59 SHEET 1 AB4 4 LEU E 65 GLU E 69 0 SHEET 2 AB4 4 LEU F 65 GLU F 69 1 O LEU F 65 N TYR E 66 SHEET 3 AB4 4 LEU G 65 GLU G 69 1 O LEU G 65 N TYR F 66 SHEET 4 AB4 4 LEU H 65 GLU H 69 1 O LEU H 65 N TYR G 66 SHEET 1 AB5 4 ASP E 76 ASN E 83 0 SHEET 2 AB5 4 ASP F 76 ASN F 83 1 O CYS F 80 N ALA E 79 SHEET 3 AB5 4 ASP G 76 ASN G 83 1 O CYS G 80 N ALA F 79 SHEET 4 AB5 4 ASP H 76 ASN H 83 1 O CYS H 80 N ALA G 79 SSBOND 1 CYS A 25 CYS A 80 1555 1555 2.02 SSBOND 2 CYS B 25 CYS B 80 1555 1555 2.02 SSBOND 3 CYS C 25 CYS C 80 1555 1555 2.02 SSBOND 4 CYS D 25 CYS D 80 1555 1555 2.02 SSBOND 5 CYS E 25 CYS E 80 1555 1555 2.02 SSBOND 6 CYS F 25 CYS F 80 1555 1555 2.02 SSBOND 7 CYS G 25 CYS G 80 1555 1555 2.02 SSBOND 8 CYS H 25 CYS H 80 1555 1555 2.02 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