HEADER CELL INVASION 08-MAY-25 9R4W TITLE SOLUTION NMR STRUCTURE OF SNX9 SH3 IN COMPLEX WITH ESPF COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEE-ENCODED EFFECTOR ESPF; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SORTING NEXIN-9; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: SH3 AND PX DOMAIN-CONTAINING PROTEIN 1,PROTEIN SDP1,SH3 AND COMPND 9 PX DOMAIN-CONTAINING PROTEIN 3A; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ESPF, NCTC8621_00139; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: SNX9, SH3PX1, SH3PXD3A; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, CELL INVASION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.TOSSAVAINEN,P.PERMI REVDAT 1 22-OCT-25 9R4W 0 JRNL AUTH H.TOSSAVAINEN,M.KARJALAINEN,L.ANTENUCCI,M.HELLMAN,P.PERMI JRNL TITL INTRINSICALLY DISORDERED ENTEROPATHOGENIC E. COLI ESPF JRNL TITL 2 EXPLOITS MOTIF MIMICRY IN HIGH-AFFINITY BINDING TO NEURAL JRNL TITL 3 WISKOTT-ALDRICH SYNDROME PROTEIN AND SORTING NEXIN 9. JRNL REF INT.J.BIOL.MACROMOL. V. 330 48227 2025 JRNL REFN ISSN 0141-8130 JRNL PMID 41075884 JRNL DOI 10.1016/J.IJBIOMAC.2025.148227 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 9R4W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1292147588. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1.3 MM [U-13C; U-15N] SNX9 SH3, REMARK 210 1.5 MM ESPF, 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 93% H2O/7% D2O; 1.9 MM SNX9 SH3, REMARK 210 1.5 MM [U-13C; U-15N] ESPF, 20 REMARK 210 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCACB; 3D HN(COCA) REMARK 210 CB; 3D HNCO; 3D IHNCO; 3D H(CCO) REMARK 210 NH; 3D C(CO)NH; 3D HBHA(CO)NH; REMARK 210 3D HCCH-COSY; 3D HCCMHM-TOCSY; REMARK 210 2D (HB)CB(CGCD)HD; 2D (HB) REMARK 210 CB(CGCDCE)HE; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CCPNMR ANALYSIS, CYANA REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 APPLY THE FOLLOWING TO CHAINS: B, 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 6 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 5 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 8 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 9 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 11 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 11 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 11 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 11 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 12 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 13 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 13 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 13 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 14 TYR B 154 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 14 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 14 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 15 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 15 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 15 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 16 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 64 ANGLE DEVIATIONS. 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 THR B 129 -18.08 61.94 REMARK 500 1 ALA B 146 152.22 64.28 REMARK 500 1 LEU B 147 -170.48 -172.42 REMARK 500 1 LYS B 148 64.79 -68.17 REMARK 500 1 HIS A 0 17.77 56.83 REMARK 500 1 PRO A 61 -168.86 -72.58 REMARK 500 2 THR B 129 28.70 47.92 REMARK 500 2 ALA B 133 -21.62 -146.72 REMARK 500 2 LEU B 156 99.87 -51.30 REMARK 500 2 ASN A 32 89.67 -154.68 REMARK 500 3 ARG B 138 147.50 55.40 REMARK 500 3 ASP A 63 10.58 59.49 REMARK 500 4 THR B 129 24.95 48.62 REMARK 500 4 ALA B 136 -9.56 -147.55 REMARK 500 4 SER B 160 -3.37 -160.82 REMARK 500 4 VAL A 35 -16.17 -140.24 REMARK 500 5 SER B 137 69.39 35.17 REMARK 500 5 LYS B 148 68.93 -67.36 REMARK 500 5 LEU B 151 -19.84 60.67 REMARK 500 5 ALA B 159 43.46 -95.47 REMARK 500 5 HIS A 0 18.91 59.45 REMARK 500 5 VAL A 35 -19.36 -140.32 REMARK 500 6 THR B 129 8.72 52.95 REMARK 500 6 ASP B 149 -145.97 -80.90 REMARK 500 6 LEU B 151 8.72 58.43 REMARK 500 6 LEU B 156 108.77 -43.07 REMARK 500 6 SER B 157 11.33 55.12 REMARK 500 6 VAL A 35 -14.78 -143.31 REMARK 500 7 LYS B 148 40.66 -63.61 REMARK 500 7 SER B 160 27.78 -69.80 REMARK 500 7 ASN A 32 84.85 -152.47 REMARK 500 8 THR B 129 9.80 57.61 REMARK 500 8 LYS B 148 52.18 -69.69 REMARK 500 8 LEU B 151 15.21 57.27 REMARK 500 8 VAL A 35 -16.48 -145.62 REMARK 500 8 ASP A 63 1.64 -68.74 REMARK 500 9 GLN B 145 -41.82 64.49 REMARK 500 9 PRO A 33 0.09 -68.66 REMARK 500 9 VAL A 35 -16.92 -144.02 REMARK 500 10 THR B 129 16.34 51.17 REMARK 500 10 SER B 134 6.30 -157.53 REMARK 500 10 ARG B 138 148.99 60.66 REMARK 500 10 LYS B 148 72.70 -69.76 REMARK 500 10 ASN A 17 13.86 -140.78 REMARK 500 10 ASN A 18 41.76 38.75 REMARK 500 10 ASP A 63 37.21 -79.50 REMARK 500 11 THR B 129 -11.08 66.62 REMARK 500 11 SER B 137 33.01 -84.03 REMARK 500 11 ARG B 138 160.99 61.88 REMARK 500 11 LEU B 151 6.88 54.20 REMARK 500 REMARK 500 THIS ENTRY HAS 96 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 6 ARG A 6 0.08 SIDE CHAIN REMARK 500 16 ARG A 43 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34994 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF SNX9 SH3 IN COMPLEX WITH ESPF DBREF1 9R4W B 115 161 UNP A0A376PNR8_ECOLX DBREF2 9R4W B A0A376PNR8 115 161 DBREF 9R4W A 1 64 UNP Q9Y5X1 SNX9_HUMAN 1 64 SEQADV 9R4W GLY B 114 UNP A0A376PNR EXPRESSION TAG SEQADV 9R4W GLY A -2 UNP Q9Y5X1 EXPRESSION TAG SEQADV 9R4W SER A -1 UNP Q9Y5X1 EXPRESSION TAG SEQADV 9R4W HIS A 0 UNP Q9Y5X1 EXPRESSION TAG SEQRES 1 B 48 GLY THR VAL ASN PHE LYS PRO THR ARG PRO ALA PRO PRO SEQRES 2 B 48 PRO PRO THR SER GLY GLN ALA SER GLY ALA SER ARG PRO SEQRES 3 B 48 LEU PRO PRO ILE ALA GLN ALA LEU LYS ASP HIS LEU ALA SEQRES 4 B 48 ALA TYR GLU LEU SER LYS ALA SER GLU SEQRES 1 A 67 GLY SER HIS MET ALA THR LYS ALA ARG VAL MET TYR ASP SEQRES 2 A 67 PHE ALA ALA GLU PRO GLY ASN ASN GLU LEU THR VAL ASN SEQRES 3 A 67 GLU GLY GLU ILE ILE THR ILE THR ASN PRO ASP VAL GLY SEQRES 4 A 67 GLY GLY TRP LEU GLU GLY ARG ASN ILE LYS GLY GLU ARG SEQRES 5 A 67 GLY LEU VAL PRO THR ASP TYR VAL GLU ILE LEU PRO SER SEQRES 6 A 67 ASP GLY HELIX 1 AA1 LEU B 151 LEU B 156 1 6 SHEET 1 AA1 5 ARG A 49 PRO A 53 0 SHEET 2 AA1 5 TRP A 39 ARG A 43 -1 N LEU A 40 O VAL A 52 SHEET 3 AA1 5 ILE A 27 ASN A 32 -1 N THR A 29 O ARG A 43 SHEET 4 AA1 5 LYS A 4 VAL A 7 -1 N ALA A 5 O ILE A 28 SHEET 5 AA1 5 VAL A 57 ILE A 59 -1 O GLU A 58 N ARG A 6 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 MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MASTER 242 0 0 1 5 0 0 6 852 2 0 10 END