HEADER SIGNALING PROTEIN 28-NOV-23 8X8T TITLE NMR STRUCTURE OF P75NTR JUXTAMEMBRANE DOMAIN IN COMPLEX WITH RHOGDI N- TITLE 2 TERMINAL DOMAIN CONTAINING A PHOSPHORYLATION-MIMICKING S34D MUTATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO GDP-DISSOCIATION INHIBITOR 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 16; COMPND 8 CHAIN: B; COMPND 9 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: ARHGDIA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: NGFR; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS INHIBITOR, COMPLEX, SIGNALING, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Z.LIN,Z.LI REVDAT 2 15-MAY-24 8X8T 1 REMARK REVDAT 1 03-APR-24 8X8T 0 JRNL AUTH A.RAMANUJAN,Z.LI,Y.MA,Z.LIN,C.F.IBANEZ JRNL TITL RHOGDI PHOSPHORYLATION BY PKC PROMOTES ITS INTERACTION WITH JRNL TITL 2 DEATH RECEPTOR P75 NTR TO GATE AXON GROWTH AND NEURON JRNL TITL 3 SURVIVAL. JRNL REF EMBO REP. V. 25 1490 2024 JRNL REFN ESSN 1469-3178 JRNL PMID 38253689 JRNL DOI 10.1038/S44319-024-00064-2 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 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 8X8T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300042532. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 PA REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-13C; U-15N] RHOGDI REMARK 210 -NTD, 2.4 MM NA P75NTR-JMD, 90% REMARK 210 H2O/10% D2O; 0.8 MM [U-13C; U- REMARK 210 15N] P75NTR-JMD, 2.4 MM NA REMARK 210 RHOGDI-NTD, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 H(CCCO)NH; 3D CC(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 13C,13C-NOESY; 3D 15N, REMARK 210 13C-NOESY; 3D 13C,15N-FILTERED REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRVIEW, NMRPIPE REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 B 274 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.5 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 ALA A 2 82.62 -155.21 REMARK 500 1 ASP A 21 -71.00 -114.85 REMARK 500 1 SER A 24 -37.42 -139.70 REMARK 500 1 PRO A 30 88.66 -68.25 REMARK 500 1 ALA A 31 -26.11 -140.35 REMARK 500 1 LYS A 43 -142.61 -81.06 REMARK 500 1 ASP A 45 -67.25 -145.45 REMARK 500 1 GLU A 46 74.41 -162.71 REMARK 500 1 SER A 47 28.45 -64.37 REMARK 500 1 LEU A 48 -33.66 -149.83 REMARK 500 1 ARG A 58 -39.79 -37.62 REMARK 500 1 SER B 272 21.21 -70.10 REMARK 500 1 GLN B 280 -65.98 49.02 REMARK 500 1 ASN B 281 -25.27 -167.25 REMARK 500 1 ALA B 285 105.47 -57.17 REMARK 500 1 SER B 287 -135.41 -142.55 REMARK 500 1 VAL B 290 -87.10 -138.14 REMARK 500 1 GLN B 292 91.92 -67.67 REMARK 500 1 VAL B 309 -27.82 -154.69 REMARK 500 1 SER B 311 51.39 -149.56 REMARK 500 1 ASP B 316 -36.67 -168.25 REMARK 500 1 PRO B 319 37.77 -78.61 REMARK 500 1 ALA B 324 80.25 49.54 REMARK 500 1 SER B 325 36.60 -67.10 REMARK 500 1 ALA B 328 -5.31 58.34 REMARK 500 1 LEU B 329 -62.87 -147.86 REMARK 500 2 GLN A 4 84.58 -66.23 REMARK 500 2 GLU A 5 -53.22 -150.27 REMARK 500 2 GLN A 13 1.74 -69.50 REMARK 500 2 ASN A 18 -34.06 -131.51 REMARK 500 2 ASP A 21 -69.11 -120.28 REMARK 500 2 SER A 24 -43.48 -132.32 REMARK 500 2 TYR A 27 -38.68 -133.14 REMARK 500 2 PRO A 30 84.33 -68.57 REMARK 500 2 LYS A 43 -147.01 -82.97 REMARK 500 2 ASP A 44 50.13 -69.94 REMARK 500 2 ASP A 45 -70.97 -141.11 REMARK 500 2 SER A 47 20.78 -60.44 REMARK 500 2 LEU A 48 -46.21 -149.62 REMARK 500 2 ASN B 281 -56.91 -154.62 REMARK 500 2 GLN B 283 32.63 -68.63 REMARK 500 2 ASN B 286 24.25 49.37 REMARK 500 2 VAL B 290 -92.26 -142.29 REMARK 500 2 ASN B 291 70.61 -150.36 REMARK 500 2 GLN B 292 99.57 -65.06 REMARK 500 2 LYS B 300 -1.92 -146.02 REMARK 500 2 LEU B 301 69.37 -153.86 REMARK 500 2 HIS B 302 -42.50 -144.54 REMARK 500 2 VAL B 309 -12.86 -146.08 REMARK 500 2 SER B 311 48.08 -157.64 REMARK 500 REMARK 500 THIS ENTRY HAS 293 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36619 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF THE N-TERMINAL DOMAIN OF RHOGDI CONTAINING THE REMARK 900 S34D MUTATION WITH THE JUXTAMEMBRANE DOMAIN OF P75NTR DBREF 8X8T A 2 60 UNP P52565 GDIR1_HUMAN 2 60 DBREF 8X8T B 273 332 UNP P08138 TNR16_HUMAN 273 332 SEQADV 8X8T GLY A 0 UNP P52565 EXPRESSION TAG SEQADV 8X8T SER A 1 UNP P52565 EXPRESSION TAG SEQADV 8X8T ASP A 34 UNP P52565 SER 34 ENGINEERED MUTATION SEQADV 8X8T GLY B 271 UNP P08138 EXPRESSION TAG SEQADV 8X8T SER B 272 UNP P08138 EXPRESSION TAG SEQRES 1 A 61 GLY SER ALA GLU GLN GLU PRO THR ALA GLU GLN LEU ALA SEQRES 2 A 61 GLN ILE ALA ALA GLU ASN GLU GLU ASP GLU HIS SER VAL SEQRES 3 A 61 ASN TYR LYS PRO PRO ALA GLN LYS ASP ILE GLN GLU ILE SEQRES 4 A 61 GLN GLU LEU ASP LYS ASP ASP GLU SER LEU ARG LYS TYR SEQRES 5 A 61 LYS GLU ALA LEU LEU GLY ARG VAL ALA SEQRES 1 B 62 GLY SER LYS ARG TRP ASN SER CYS LYS GLN ASN LYS GLN SEQRES 2 B 62 GLY ALA ASN SER ARG PRO VAL ASN GLN THR PRO PRO PRO SEQRES 3 B 62 GLU GLY GLU LYS LEU HIS SER ASP SER GLY ILE SER VAL SEQRES 4 B 62 ASP SER GLN SER LEU HIS ASP GLN GLN PRO HIS THR GLN SEQRES 5 B 62 THR ALA SER GLY GLN ALA LEU LYS GLY ASP HELIX 1 AA1 THR A 7 ALA A 12 1 6 HELIX 2 AA2 GLN A 13 HIS A 23 1 11 HELIX 3 AA3 GLN A 36 LEU A 41 1 6 HELIX 4 AA4 LEU A 48 GLY A 57 1 10 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