HEADER TRANSPORT PROTEIN 08-AUG-23 8KCQ TITLE SOLUTION STRUCTURES OF THE N-TERMINAL DIVERGENT CAPLONIN HOMOLOGY (NN- TITLE 2 CH) DOMAINS OF HUMAN INTRAFLAGELLAR TRANSPORT PROTEIN 54 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRAF3-INTERACTING PROTEIN 1; COMPND 3 CHAIN: A; 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: TRAF3IP1; SOURCE 6 EXPRESSION_SYSTEM: CELL-FREE GATEWAY CLONING VECTOR N-TERM 8XHIS SOURCE 7 MCHERRY PCELLFREE_G05; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1508208; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS NN-CH DOMAIN, INTRAFLAGELLAR TRANSPORT (IFT) MACHINERY, IFT54, KEYWDS 2 CILIOPATHY, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.DANG,K.KUWASAKO,F.HE,M.TAKAHASHI,K.TSUDA,T.NAGATA,A.TANAKA, AUTHOR 2 N.KOBAYASHI,T.KIGAWA,P.GUENTERT,M.SHIROUZU,S.YOKOYAMA,Y.MUTO,RIKEN AUTHOR 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 1 22-MAY-24 8KCQ 0 JRNL AUTH K.KUWASAKO,W.DANG,F.HE,M.TAKAHASHI,K.TSUDA,T.NAGATA, JRNL AUTH 2 A.TANAKA,N.KOBAYASHI,T.KIGAWA,P.GUNTERT,M.SHIROUZU, JRNL AUTH 3 S.YOKOYAMA,Y.MUTO JRNL TITL 1 H, 13 C, AND 15 N RESONANCE ASSIGNMENTS AND SOLUTION JRNL TITL 2 STRUCTURE OF THE N-TERMINAL DIVERGENT CALPONIN HOMOLOGY JRNL TITL 3 (NN-CH) DOMAIN OF HUMAN INTRAFLAGELLAR TRANSPORT PROTEIN 54. JRNL REF BIOMOL.NMR ASSIGN. V. 18 71 2024 JRNL REFN ESSN 1874-270X JRNL PMID 38551798 JRNL DOI 10.1007/S12104-024-10170-W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 12 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8KCQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300040075. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] NN REMARK 210 -CH DOMAIN OF HUMAN IFT54, 100 REMARK 210 MM NONE NACL, 1 MM [U-99% 2H] D- REMARK 210 DTT, 20 MM [U-99% 2H] D-TRIS HCL, REMARK 210 0.02 % NONE NAN3, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C,15N-SEPARATED_NOESY REMARK 210 SPECTRA; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HCCH-COSY; 3D HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : KUJIRA 0.863, CYANA 2.2, MAGRO REMARK 210 -NMRVIEW 1.2.38, TALOS, TOPSPIN REMARK 210 METHOD USED : SUMILATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON REMARK 210 -BOND ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 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 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A 51 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG A 101 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 14 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 101 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 11 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 13 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 15 ARG A 110 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 17 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 17 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 18 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 18 ARG A 110 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 19 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 19 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 19 ARG A 101 NE - CZ - NH1 ANGL. DEV. = 3.1 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 SER A 6 119.49 61.77 REMARK 500 1 ARG A 26 -75.68 -73.44 REMARK 500 1 LYS A 36 91.31 -163.59 REMARK 500 1 VAL A 70 41.16 -76.17 REMARK 500 1 SER A 128 6.42 59.10 REMARK 500 2 MET A 8 126.64 64.27 REMARK 500 2 LYS A 36 85.69 -156.55 REMARK 500 2 VAL A 70 41.31 -89.02 REMARK 500 2 ALA A 97 95.44 -69.14 REMARK 500 3 MET A 8 72.71 -156.90 REMARK 500 3 ARG A 25 -7.83 -140.70 REMARK 500 3 LYS A 36 79.81 -161.66 REMARK 500 3 VAL A 70 39.86 -76.83 REMARK 500 4 LYS A 36 84.32 -156.34 REMARK 500 4 VAL A 70 39.44 -77.50 REMARK 500 5 SER A 5 -27.66 62.62 REMARK 500 5 ARG A 26 -71.04 -59.08 REMARK 500 5 LYS A 36 82.05 -164.04 REMARK 500 5 VAL A 70 42.49 -77.15 REMARK 500 6 ARG A 26 -71.52 -70.63 REMARK 500 6 LYS A 36 80.02 -152.35 REMARK 500 6 ALA A 97 99.69 -62.06 REMARK 500 7 LYS A 36 80.89 -150.61 REMARK 500 7 VAL A 70 40.78 -77.66 REMARK 500 7 GLU A 139 -170.70 55.86 REMARK 500 8 LYS A 36 71.48 -157.79 REMARK 500 8 VAL A 70 39.60 -78.33 REMARK 500 9 LYS A 36 77.72 -153.54 REMARK 500 9 VAL A 70 47.37 -76.80 REMARK 500 10 MET A 8 136.35 68.87 REMARK 500 10 LYS A 36 82.02 -152.23 REMARK 500 10 VAL A 70 44.49 -77.86 REMARK 500 11 SER A 3 165.03 63.23 REMARK 500 11 LYS A 36 78.38 -159.48 REMARK 500 11 VAL A 70 48.37 -74.23 REMARK 500 11 GLU A 139 172.34 58.42 REMARK 500 12 SER A 2 173.76 61.17 REMARK 500 12 ARG A 26 -73.85 -70.07 REMARK 500 12 LYS A 36 77.70 -159.88 REMARK 500 13 ARG A 26 -71.68 -74.60 REMARK 500 13 LYS A 36 82.81 -163.53 REMARK 500 13 VAL A 70 37.22 -76.89 REMARK 500 14 LYS A 36 85.44 -162.25 REMARK 500 14 VAL A 70 43.06 -76.36 REMARK 500 14 ALA A 97 93.89 -67.90 REMARK 500 15 SER A 2 37.77 -75.51 REMARK 500 15 SER A 5 -38.06 63.41 REMARK 500 15 ARG A 26 -74.93 -98.65 REMARK 500 15 LYS A 36 79.71 -158.37 REMARK 500 15 VAL A 70 41.22 -77.21 REMARK 500 REMARK 500 THIS ENTRY HAS 67 RAMACHANDRAN OUTLIERS. 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 4 ARG A 40 0.12 SIDE CHAIN REMARK 500 8 ARG A 40 0.17 SIDE CHAIN REMARK 500 11 ARG A 110 0.23 SIDE CHAIN REMARK 500 15 ARG A 110 0.08 SIDE CHAIN REMARK 500 18 ARG A 110 0.10 SIDE CHAIN REMARK 500 20 ARG A 51 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36589 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURES OF THE N-TERMINAL DIVERGENT CAPLONIN HOMOLOGY REMARK 900 (NN-CH) DOMAINS OF HUMAN INTRAFLAGELLAR TRANSPORT PROTEIN 54 DBREF 8KCQ A 8 140 UNP Q8TDR0 MIPT3_HUMAN 1 133 SEQADV 8KCQ GLY A 1 UNP Q8TDR0 EXPRESSION TAG SEQADV 8KCQ SER A 2 UNP Q8TDR0 EXPRESSION TAG SEQADV 8KCQ SER A 3 UNP Q8TDR0 EXPRESSION TAG SEQADV 8KCQ GLY A 4 UNP Q8TDR0 EXPRESSION TAG SEQADV 8KCQ SER A 5 UNP Q8TDR0 EXPRESSION TAG SEQADV 8KCQ SER A 6 UNP Q8TDR0 EXPRESSION TAG SEQADV 8KCQ GLY A 7 UNP Q8TDR0 EXPRESSION TAG SEQRES 1 A 140 GLY SER SER GLY SER SER GLY MET ASN ALA ALA VAL VAL SEQRES 2 A 140 ARG ARG THR GLN GLU ALA LEU GLY LYS VAL ILE ARG ARG SEQRES 3 A 140 PRO PRO LEU THR GLU LYS LEU LEU SER LYS PRO PRO PHE SEQRES 4 A 140 ARG TYR LEU HIS ASP ILE ILE THR GLU VAL ILE ARG MET SEQRES 5 A 140 THR GLY PHE MET LYS GLY LEU TYR THR ASP ALA GLU MET SEQRES 6 A 140 LYS SER ASP ASN VAL LYS ASP LYS ASP ALA LYS ILE SER SEQRES 7 A 140 PHE LEU GLN LYS ALA ILE ASP VAL VAL VAL MET VAL SER SEQRES 8 A 140 GLY GLU PRO LEU LEU ALA LYS PRO ALA ARG ILE VAL ALA SEQRES 9 A 140 GLY HIS GLU PRO GLU ARG THR ASN GLU LEU LEU GLN ILE SEQRES 10 A 140 ILE GLY LYS CYS CYS LEU ASN LYS LEU SER SER ASP ASP SEQRES 11 A 140 ALA VAL ARG ARG VAL LEU ALA GLY GLU LYS HELIX 1 AA1 ASN A 9 GLY A 21 1 13 HELIX 2 AA2 THR A 30 LYS A 36 1 7 HELIX 3 AA3 PRO A 38 THR A 53 1 16 HELIX 4 AA4 ASP A 72 GLY A 92 1 21 HELIX 5 AA5 LYS A 98 GLY A 105 1 8 HELIX 6 AA6 GLU A 107 ASN A 124 1 18 HELIX 7 AA7 SER A 128 GLY A 138 1 11 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