HEADER PROTEIN FIBRIL 05-NOV-21 7Q67 TITLE CRYO-EM STRUCTURE OF THE NUP98 FIBRIL POLYMORPH 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR PORE COMPLEX PROTEIN NUP98; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J, K; COMPND 4 SYNONYM: 98 KDA NUCLEOPORIN,NUCLEOPORIN NUP98,NUP98; COMPND 5 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: NUP98, ADAR2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NUCLEAR PORE COMPLEX PROTEIN NUP98 FUNCTIONAL AMYLOID FIBRIL PROTEIN KEYWDS 2 FIBRIL, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR A.IBANEZ DE OPAKUA,J.A.GERAETS,B.FRIEG,C.DIENEMANN,A.SAVASTANO, AUTHOR 2 M.RANKOVIC,M.-S.CIMA-OMORI,G.F.SCHROEDER,M.ZWECKSTETTER REVDAT 3 17-JUL-24 7Q67 1 REMARK REVDAT 2 16-NOV-22 7Q67 1 JRNL REVDAT 1 12-OCT-22 7Q67 0 JRNL AUTH A.IBANEZ DE OPAKUA,J.A.GERAETS,B.FRIEG,C.DIENEMANN, JRNL AUTH 2 A.SAVASTANO,M.RANKOVIC,M.S.CIMA-OMORI,G.F.SCHRODER, JRNL AUTH 3 M.ZWECKSTETTER JRNL TITL MOLECULAR INTERACTIONS OF FG NUCLEOPORIN REPEATS AT HIGH JRNL TITL 2 RESOLUTION. JRNL REF NAT.CHEM. V. 14 1278 2022 JRNL REFN ESSN 1755-4349 JRNL PMID 36138110 JRNL DOI 10.1038/S41557-022-01035-7 REMARK 2 REMARK 2 RESOLUTION. 3.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX, COOT, RELION 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) : 3.370 REMARK 3 NUMBER OF PARTICLES : 12674 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 7Q67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292119063. 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 : THE NUCLEAR PORE COMPLEX REMARK 245 PROTEIN NUP98 FIBRIL POLYMORPH 4 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : THE NUP98 POLYMORPH 4 FIBRIL IS REMARK 245 FORMED BY TWO PROTOFILAMENTS, CONSISTING OF NUP98 MONOMERS. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4180 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 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) : 4100.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 81000 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: UNDECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K 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 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 THR A 82 REMARK 465 GLY A 83 REMARK 465 THR A 84 REMARK 465 ALA A 85 REMARK 465 ASN A 86 REMARK 465 SER A 120 REMARK 465 THR A 121 REMARK 465 THR B 82 REMARK 465 GLY B 83 REMARK 465 THR B 84 REMARK 465 ALA B 85 REMARK 465 ASN B 86 REMARK 465 SER B 120 REMARK 465 THR B 121 REMARK 465 THR C 82 REMARK 465 GLY C 83 REMARK 465 THR C 84 REMARK 465 ALA C 85 REMARK 465 ASN C 86 REMARK 465 SER C 120 REMARK 465 THR C 121 REMARK 465 THR D 82 REMARK 465 GLY D 83 REMARK 465 THR D 84 REMARK 465 ALA D 85 REMARK 465 ASN D 86 REMARK 465 SER D 120 REMARK 465 THR D 121 REMARK 465 THR E 82 REMARK 465 GLY E 83 REMARK 465 THR E 84 REMARK 465 ALA E 85 REMARK 465 ASN E 86 REMARK 465 SER E 120 REMARK 465 THR E 121 REMARK 465 THR F 82 REMARK 465 GLY F 83 REMARK 465 THR F 84 REMARK 465 ALA F 85 REMARK 465 ASN F 86 REMARK 465 SER F 120 REMARK 465 THR F 121 REMARK 465 THR G 82 REMARK 465 GLY G 83 REMARK 465 THR G 84 REMARK 465 ALA G 85 REMARK 465 ASN G 86 REMARK 465 SER G 120 REMARK 465 THR G 121 REMARK 465 THR H 82 REMARK 465 GLY H 83 REMARK 465 THR H 84 REMARK 465 ALA H 85 REMARK 465 ASN H 86 REMARK 465 SER H 120 REMARK 465 THR H 121 REMARK 465 THR I 82 REMARK 465 GLY I 83 REMARK 465 THR I 84 REMARK 465 ALA I 85 REMARK 465 ASN I 86 REMARK 465 SER I 120 REMARK 465 THR I 121 REMARK 465 THR J 82 REMARK 465 GLY J 83 REMARK 465 THR J 84 REMARK 465 ALA J 85 REMARK 465 ASN J 86 REMARK 465 SER J 120 REMARK 465 THR J 121 REMARK 465 THR K 82 REMARK 465 GLY K 83 REMARK 465 THR K 84 REMARK 465 ALA K 85 REMARK 465 ASN K 86 REMARK 465 SER K 120 REMARK 465 THR K 121 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 88 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU B 88 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU C 88 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU D 88 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU E 88 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU F 88 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU G 88 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU H 88 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU I 88 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU J 88 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU K 88 CA - CB - CG ANGL. DEV. = 16.9 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 THR A 96 58.47 29.67 REMARK 500 ASN A 116 81.62 53.04 REMARK 500 THR B 96 58.46 29.72 REMARK 500 ASN B 116 81.64 52.97 REMARK 500 THR C 96 58.48 29.66 REMARK 500 ASN C 116 81.62 53.05 REMARK 500 THR D 96 58.49 29.69 REMARK 500 ASN D 116 81.65 52.98 REMARK 500 THR E 96 58.50 29.67 REMARK 500 ASN E 116 81.63 53.02 REMARK 500 THR F 96 58.48 29.66 REMARK 500 ASN F 116 81.61 53.00 REMARK 500 THR G 96 58.52 29.64 REMARK 500 ASN G 116 81.69 52.93 REMARK 500 THR H 96 58.44 29.69 REMARK 500 ASN H 116 81.69 52.99 REMARK 500 THR I 96 58.45 29.68 REMARK 500 ASN I 116 81.66 52.97 REMARK 500 THR J 96 58.45 29.72 REMARK 500 ASN J 116 81.66 52.99 REMARK 500 THR K 96 58.45 29.72 REMARK 500 ASN K 116 81.67 52.91 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 GLY A 113 PHE A 114 -138.13 REMARK 500 GLY B 113 PHE B 114 -138.10 REMARK 500 GLY C 113 PHE C 114 -138.15 REMARK 500 GLY D 113 PHE D 114 -138.10 REMARK 500 GLY E 113 PHE E 114 -138.08 REMARK 500 GLY F 113 PHE F 114 -138.14 REMARK 500 GLY G 113 PHE G 114 -138.09 REMARK 500 GLY H 113 PHE H 114 -138.14 REMARK 500 GLY I 113 PHE I 114 -138.13 REMARK 500 GLY J 113 PHE J 114 -138.09 REMARK 500 GLY K 113 PHE K 114 -138.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13854 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE NUP98 FIBRIL POLYMORPH 4 DBREF 7Q67 A 82 121 UNP P52948 NUP98_HUMAN 85 124 DBREF 7Q67 B 82 121 UNP P52948 NUP98_HUMAN 85 124 DBREF 7Q67 C 82 121 UNP P52948 NUP98_HUMAN 85 124 DBREF 7Q67 D 82 121 UNP P52948 NUP98_HUMAN 85 124 DBREF 7Q67 E 82 121 UNP P52948 NUP98_HUMAN 85 124 DBREF 7Q67 F 82 121 UNP P52948 NUP98_HUMAN 85 124 DBREF 7Q67 G 82 121 UNP P52948 NUP98_HUMAN 85 124 DBREF 7Q67 H 82 121 UNP P52948 NUP98_HUMAN 85 124 DBREF 7Q67 I 82 121 UNP P52948 NUP98_HUMAN 85 124 DBREF 7Q67 J 82 121 UNP P52948 NUP98_HUMAN 85 124 DBREF 7Q67 K 82 121 UNP P52948 NUP98_HUMAN 85 124 SEQRES 1 A 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 A 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 A 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 A 40 THR SEQRES 1 B 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 B 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 B 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 B 40 THR SEQRES 1 C 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 C 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 C 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 C 40 THR SEQRES 1 D 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 D 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 D 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 D 40 THR SEQRES 1 E 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 E 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 E 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 E 40 THR SEQRES 1 F 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 F 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 F 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 F 40 THR SEQRES 1 G 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 G 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 G 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 G 40 THR SEQRES 1 H 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 H 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 H 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 H 40 THR SEQRES 1 I 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 I 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 I 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 I 40 THR SEQRES 1 J 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 J 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 J 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 J 40 THR SEQRES 1 K 40 THR GLY THR ALA ASN THR LEU PHE GLY THR ALA SER THR SEQRES 2 K 40 GLY THR SER LEU PHE SER SER GLN ASN ASN ALA PHE ALA SEQRES 3 K 40 GLN ASN LYS PRO THR GLY PHE GLY ASN PHE GLY THR SER SEQRES 4 K 40 THR SHEET 1 AA1 6 ASN A 103 ASN A 109 0 SHEET 2 AA1 6 ASN C 103 ASN C 109 1 O ASN C 104 N ALA A 105 SHEET 3 AA1 6 ASN E 103 ASN E 109 1 O ASN E 104 N ALA C 105 SHEET 4 AA1 6 ASN G 103 ASN G 109 1 O ASN G 104 N ALA E 105 SHEET 5 AA1 6 ASN I 103 ASN I 109 1 O ASN I 104 N ALA G 105 SHEET 6 AA1 6 ASN K 103 ASN K 109 1 O ASN K 104 N ALA I 105 SHEET 1 AA2 5 ASN B 103 ASN B 109 0 SHEET 2 AA2 5 ASN D 103 ASN D 109 1 O ASN D 104 N ALA B 105 SHEET 3 AA2 5 ASN F 103 ASN F 109 1 O ASN F 104 N ALA D 105 SHEET 4 AA2 5 ASN H 103 ASN H 109 1 O ASN H 104 N ALA F 105 SHEET 5 AA2 5 ASN J 103 ASN J 109 1 O ASN J 104 N ALA H 105 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