HEADER PROTEIN FIBRIL 17-DEC-24 9HR9 TITLE SSNMR STRUCTURE OF AMYLOID FIBRILS FORMED BY HUMAN RIPK1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL DEATH PROTEIN RIP,RECEPTOR-INTERACTING PROTEIN 1,RIP-1; COMPND 5 EC: 2.7.11.1; 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: RIPK1, RIP, RIP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS AMYLOID, KINASE, PROTEIN FIBRIL EXPDTA SOLID-STATE NMR NUMMDL 10 AUTHOR P.POLONIO,F.C.ESCOBEDO-GONZALES,G.A.TITAUX-DELGADO,M.MOMPEAN REVDAT 3 22-OCT-25 9HR9 1 JRNL REVDAT 2 01-OCT-25 9HR9 1 JRNL REVDAT 1 17-SEP-25 9HR9 0 JRNL AUTH P.POLONIO,M.MOMPEAN JRNL TITL RESONANCE ASSIGNMENTS OF THE HUMAN RECEPTOR INTERACTING JRNL TITL 2 PROTEIN KINASE 1 (RIPK1) IN ITS FIBRILLAR CONFORMATION. JRNL REF BIOMOL.NMR ASSIGN. V. 19 299 2025 JRNL REFN ESSN 1874-270X JRNL PMID 40952585 JRNL DOI 10.1007/S12104-025-10249-Y REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS REMARK 3 AUTHORS : HTTPS://DOI.ORG/10.5281/ZENODO.11148638 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 100 STRUCTURES CALCULATED WITH CYANA REMARK 3 AND 10 LOWEST-ENERGY CONFORMERS REFINED USING GROMACS REMARK 4 REMARK 4 9HR9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1292143994. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 25 % W/W [U-100% 13C; U-100% REMARK 210 15N] PROTEIN, 75 % W/W NONE REMARK 210 PROTEIN, 100% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NCACX; NCOCX; CANCOCX; CORD 20 REMARK 210 MS; CORD 50 MS; CORD 100 MS; REMARK 210 CORD 500 MS REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, CCPNMR ANALYSIS REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: 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 1 TYR A 531 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 TYR A 531 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 TYR A 534 CB - CG - CD2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 TYR A 534 CB - CG - CD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 TYR A 531 CB - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 TYR A 531 CB - CG - CD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 TYR A 534 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 TYR A 534 CB - CG - CD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 4 TYR A 534 CB - CG - CD2 ANGL. DEV. = -5.3 DEGREES REMARK 500 4 TYR A 534 CB - CG - CD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 6 TYR A 531 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 6 TYR A 531 CB - CG - CD1 ANGL. DEV. = 4.1 DEGREES REMARK 500 6 TYR A 534 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 6 TYR A 534 CB - CG - CD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 7 TYR A 531 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 7 TYR A 531 CB - CG - CD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 7 TYR A 534 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 7 TYR A 534 CB - CG - CD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 8 TYR A 531 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 8 TYR A 531 CB - CG - CD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 8 TYR A 534 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 8 TYR A 534 CB - CG - CD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 9 TYR A 534 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 9 TYR A 534 CB - CG - CD1 ANGL. DEV. = 5.7 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 1 LYS A 530 -92.21 -69.99 REMARK 500 1 TYR A 531 158.39 48.51 REMARK 500 1 ASN A 535 80.56 -41.98 REMARK 500 1 TYR A 544 85.11 -47.65 REMARK 500 2 LYS A 530 -86.82 -71.61 REMARK 500 2 TYR A 531 152.68 55.78 REMARK 500 2 ASN A 535 78.98 -36.92 REMARK 500 2 TYR A 544 81.30 -49.03 REMARK 500 3 LYS A 530 -81.36 -77.52 REMARK 500 3 TYR A 531 162.00 48.10 REMARK 500 3 ASN A 535 103.90 -55.04 REMARK 500 3 TYR A 544 81.15 -44.31 REMARK 500 4 LYS A 530 -72.87 -87.90 REMARK 500 4 TYR A 531 92.04 71.19 REMARK 500 4 ASN A 535 90.53 -37.00 REMARK 500 4 TYR A 544 84.35 -49.39 REMARK 500 4 GLU A 548 88.19 -152.03 REMARK 500 5 TYR A 531 111.97 67.61 REMARK 500 5 SER A 536 157.17 178.98 REMARK 500 5 TYR A 544 83.02 -53.07 REMARK 500 5 GLU A 548 82.43 -152.47 REMARK 500 6 LYS A 530 -78.68 -74.65 REMARK 500 6 TYR A 531 160.63 48.16 REMARK 500 6 ASN A 535 84.42 -29.42 REMARK 500 6 TYR A 544 81.41 -42.59 REMARK 500 7 LYS A 530 -85.26 54.51 REMARK 500 7 TYR A 531 162.82 52.27 REMARK 500 7 TYR A 544 84.43 -52.67 REMARK 500 7 GLU A 548 80.38 -152.97 REMARK 500 8 LYS A 530 -74.86 -70.66 REMARK 500 8 TYR A 531 165.38 53.68 REMARK 500 8 ASN A 535 73.20 -39.11 REMARK 500 8 TYR A 544 88.81 -57.95 REMARK 500 9 LYS A 530 -64.28 -90.20 REMARK 500 9 TYR A 531 167.13 46.78 REMARK 500 9 ASN A 535 77.90 -46.67 REMARK 500 9 TYR A 544 79.93 -45.53 REMARK 500 10 LYS A 530 -103.50 57.34 REMARK 500 10 TYR A 531 97.87 72.96 REMARK 500 10 ASN A 535 83.75 -45.11 REMARK 500 10 TYR A 544 96.15 -54.51 REMARK 500 10 GLU A 548 87.44 -156.50 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 LYS A 530 TYR A 531 1 -148.53 REMARK 500 LYS A 530 TYR A 531 3 -148.01 REMARK 500 ASN A 535 SER A 536 5 -149.28 REMARK 500 LYS A 530 TYR A 531 6 -146.83 REMARK 500 LYS A 530 TYR A 531 7 -143.18 REMARK 500 LYS A 530 TYR A 531 8 -147.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR A 534 0.09 SIDE CHAIN REMARK 500 5 TYR A 544 0.08 SIDE CHAIN REMARK 500 6 TYR A 534 0.08 SIDE CHAIN REMARK 500 7 TYR A 544 0.08 SIDE CHAIN REMARK 500 10 TYR A 531 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9HR6 RELATED DB: PDB REMARK 900 CRYO-EM REMARK 900 RELATED ID: 34971 RELATED DB: BMRB REMARK 900 SSNMR STRUCTURE OF AMYLOID FIBRILS FORMED BY HUMAN RIPK1 DBREF 9HR9 A 529 550 UNP Q13546 RIPK1_HUMAN 529 550 SEQRES 1 A 22 ILE LYS TYR THR ILE TYR ASN SER THR GLY ILE GLN ILE SEQRES 2 A 22 GLY ALA TYR ASN TYR MET GLU ILE GLY 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 TER 349 GLY A 550 ENDMDL MODEL 2 TER 349 GLY A 550 ENDMDL MODEL 3 TER 349 GLY A 550 ENDMDL MODEL 4 TER 349 GLY A 550 ENDMDL MODEL 5 TER 349 GLY A 550 ENDMDL MODEL 6 TER 349 GLY A 550 ENDMDL MODEL 7 TER 349 GLY A 550 ENDMDL MODEL 8 TER 349 GLY A 550 ENDMDL MODEL 9 TER 349 GLY A 550 ENDMDL MODEL 10 TER 349 GLY A 550 ENDMDL MASTER 214 0 0 0 0 0 0 6 176 1 0 2 END