HEADER PROTEIN FIBRIL 07-MAR-25 9M6M TITLE ATOMIC-LEVEL ARCHITECTURE AND ASSEMBLY MECHANISM OF HIGH-ORDER TITLE 2 STRUCTURES OF RIPK1 FIBRIL NETWORK REVEALED BY INTEGRATED STRUCTURAL TITLE 3 BIOLOGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 1; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: CELL DEATH PROTEIN RIP,RECEPTOR-INTERACTING PROTEIN 1,RIP-1; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: DDLIKYTIFNSSGIQIGNHNYMDVG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RIPK1, RINP, RIP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSSETADE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASIMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS NECROPTOSIS, RIPK1, RHIM, SSNMR, PROTEIN, FIBRIL, HIGH-ORDER FIBRIL KEYWDS 2 STRUCTURE, PROTEIN FIBRIL EXPDTA SOLID-STATE NMR NUMMDL 10 AUTHOR J.LIU,X.WU,J.LU REVDAT 2 01-APR-26 9M6M 1 JRNL REVDAT 1 22-OCT-25 9M6M 0 JRNL AUTH J.LIU,A.MU,S.MA,Y.LIU,J.ZHANG,J.Z.ZHAO,J.WANG,X.L.WU,J.X.LU JRNL TITL ATOMIC-LEVEL ARCHITECTURE AND ASSEMBLY MECHANISM OF JRNL TITL 2 HIGH-ORDER STRUCTURES OF RIPK1 FIBRIL REVEALED BY INTEGRATED JRNL TITL 3 STRUCTURAL BIOLOGY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 123 57123 2026 JRNL REFN ESSN 1091-6490 JRNL PMID 41855259 JRNL DOI 10.1073/PNAS.2529157123 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9M6M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 11-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057236. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 263; 293; 279 REMARK 210 PH : 5.0; 5.0; 5.0 REMARK 210 IONIC STRENGTH : 0; 0; 0 REMARK 210 PRESSURE : 1 PA; 1 PA; 1 PA REMARK 210 SAMPLE CONTENTS : 4.0 MG/UL [U-100% 13C] GLUCOSE, REMARK 210 1.5 MG/L [U-100% 15N] AMMONIUM REMARK 210 CHLORIDE, 50MM ACETIC ACID REMARK 210 BUFFER PH 5.0; 4.0 MG/L [2-13C] REMARK 210 GLYCEROL, 1.5 MG/L [U-100% 15N] REMARK 210 AMMONIUM CHLORIDE, 50MM ACETIC REMARK 210 ACID BUFFER PH 5.0; 4.0 MG/L [2- REMARK 210 13C] GLYCEROL, 1.5 MG/L [U-100% REMARK 210 15N] AMMONIUM CHLORIDE, 50MM REMARK 210 ACETIC ACID BUFFER PH 5.0; 4.0 REMARK 210 MG/L [2-13C] GLUCOSE, 1.5 MG/L REMARK 210 [U-100% 15N] AMMONIUM CHLORIDE, REMARK 210 99 % [2H] 99% D2O, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D CH; 3D CANH; 3D COCACONH; 3D REMARK 210 HNCACX; 3D HCANCOCX; 2D TEDOR; REMARK 210 2D DARR 50MS; 2D DARR 200MS; 2D REMARK 210 DARR 500MS; 2D [2]-13C-DARR 50MS; REMARK 210 2D [2]-13C-DARR 200MS; 2D [2]- REMARK 210 13C-DARR 500MS; 2D NCACX; 2D REMARK 210 NCOCX REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : 3.2 MM HCN E-FREE PROBE; 0.7 MM REMARK 210 HCN PROBE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 192 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 THESE RECORDS ARE MEANINGLESS. 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 2 PHE A 9 117.55 -165.01 REMARK 500 4 ASN C 10 74.59 60.97 REMARK 500 4 ASN D 10 81.51 62.09 REMARK 500 4 SER D 12 -78.08 -77.37 REMARK 500 5 ASN C 10 77.06 60.73 REMARK 500 5 ASN D 10 70.34 58.68 REMARK 500 8 ILE A 4 85.28 65.22 REMARK 500 8 ILE B 4 83.86 63.79 REMARK 500 8 ILE C 4 81.73 63.99 REMARK 500 8 ASN C 10 76.96 61.75 REMARK 500 8 ILE D 4 82.61 64.17 REMARK 500 8 ASN D 10 82.05 61.30 REMARK 500 8 SER D 12 -76.19 -77.85 REMARK 500 8 ILE E 4 81.67 63.99 REMARK 500 9 ILE A 4 91.52 66.82 REMARK 500 9 ILE B 4 110.05 71.81 REMARK 500 9 LEU C 3 67.80 64.07 REMARK 500 9 ILE C 4 108.22 71.87 REMARK 500 9 LEU D 3 73.42 65.36 REMARK 500 9 ILE D 4 101.09 70.31 REMARK 500 9 LEU E 3 77.42 63.11 REMARK 500 9 ILE E 4 95.93 71.22 REMARK 500 10 SER A 12 -158.87 -92.50 REMARK 500 10 ASN C 10 72.06 59.56 REMARK 500 10 LEU E 3 61.76 61.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36734 RELATED DB: BMRB REMARK 900 THE FORMATION MECHANISM OF HIGH-ORDER STRUCTURES OF RIPK1 NETWORK REMARK 900 FIBRIL DBREF 9M6M A 1 25 UNP Q60855 RIPK1_MOUSE 515 539 DBREF 9M6M B 1 25 UNP Q60855 RIPK1_MOUSE 515 539 DBREF 9M6M C 1 25 UNP Q60855 RIPK1_MOUSE 515 539 DBREF 9M6M D 1 25 UNP Q60855 RIPK1_MOUSE 515 539 DBREF 9M6M E 1 25 UNP Q60855 RIPK1_MOUSE 515 539 SEQRES 1 A 25 ASP ASP LEU ILE LYS TYR THR ILE PHE ASN SER SER GLY SEQRES 2 A 25 ILE GLN ILE GLY ASN HIS ASN TYR MET ASP VAL GLY SEQRES 1 B 25 ASP ASP LEU ILE LYS TYR THR ILE PHE ASN SER SER GLY SEQRES 2 B 25 ILE GLN ILE GLY ASN HIS ASN TYR MET ASP VAL GLY SEQRES 1 C 25 ASP ASP LEU ILE LYS TYR THR ILE PHE ASN SER SER GLY SEQRES 2 C 25 ILE GLN ILE GLY ASN HIS ASN TYR MET ASP VAL GLY SEQRES 1 D 25 ASP ASP LEU ILE LYS TYR THR ILE PHE ASN SER SER GLY SEQRES 2 D 25 ILE GLN ILE GLY ASN HIS ASN TYR MET ASP VAL GLY SEQRES 1 E 25 ASP ASP LEU ILE LYS TYR THR ILE PHE ASN SER SER GLY SEQRES 2 E 25 ILE GLN ILE GLY ASN HIS ASN TYR MET ASP VAL GLY SHEET 1 AA1 5 ILE A 4 THR A 7 0 SHEET 2 AA1 5 ILE B 4 PHE B 9 1 O TYR B 6 N THR A 7 SHEET 3 AA1 5 ILE C 4 PHE C 9 1 O TYR C 6 N THR B 7 SHEET 4 AA1 5 ILE D 4 PHE D 9 1 O TYR D 6 N THR C 7 SHEET 5 AA1 5 ILE E 4 PHE E 9 1 O ILE E 4 N LYS D 5 SHEET 1 AA2 2 GLN A 15 ILE A 16 0 SHEET 2 AA2 2 GLN B 15 ILE B 16 1 O ILE B 16 N GLN A 15 SHEET 1 AA3 5 TYR A 21 VAL A 24 0 SHEET 2 AA3 5 TYR B 21 VAL B 24 1 O ASP B 23 N VAL A 24 SHEET 3 AA3 5 MET C 22 ASP C 23 1 O ASP C 23 N VAL B 24 SHEET 4 AA3 5 TYR D 21 VAL D 24 1 O TYR D 21 N MET C 22 SHEET 5 AA3 5 TYR E 21 VAL E 24 1 O ASP E 23 N VAL D 24 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 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MASTER 132 0 0 0 12 0 0 6 990 5 0 10 END