HEADER ENDOCYTOSIS 14-MAY-21 7OJ9 TITLE NMR SOLUTION STRUCTURE OF SNX9 SH3 - EEEV NSP3 PEPTIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: EEEV NSP3 PEPTIDE; 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 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: EASTERN EQUINE ENCEPHALITIS VIRUS; SOURCE 4 ORGANISM_TAXID: 11021; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: SNX9, SH3PX1, SH3PXD3A; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, ENDOCYTOSIS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.TOSSAVAINEN,P.PERMI REVDAT 3 15-JUN-22 7OJ9 1 JRNL REVDAT 2 20-APR-22 7OJ9 1 JRNL REVDAT 1 13-APR-22 7OJ9 0 JRNL AUTH H.TOSSAVAINEN,H.UGURLU,M.KARJALAINEN,M.HELLMAN,L.ANTENUCCI, JRNL AUTH 2 R.FAGERLUND,K.SAKSELA,P.PERMI JRNL TITL STRUCTURE OF SNX9 SH3 IN COMPLEX WITH A VIRAL LIGAND REVEALS JRNL TITL 2 THE MOLECULAR BASIS OF ITS UNIQUE SPECIFICITY FOR JRNL TITL 3 ALANINE-CONTAINING CLASS I SH3 MOTIFS. JRNL REF STRUCTURE V. 30 828 2022 JRNL REFN ISSN 0969-2126 JRNL PMID 35390274 JRNL DOI 10.1016/J.STR.2022.03.006 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 7OJ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292115870. 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 : 0.15 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] SNX9 SH3, 1 REMARK 210 MM EEEV NSP3 PEPTIDE, 20 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 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 CBCA(CO) REMARK 210 NH; 3D HNCO; 3D IHNCO; 3D H(CCO) REMARK 210 NH; 3D (H)CC(CO)NH; 3D HBHA(CO) REMARK 210 NH; 3D HCCH-COSY; 3D HCCMHM- REMARK 210 TOCSY; 2D (HB)CB(CGCD)HD; 2D (HB) REMARK 210 CB(CGCDCE)HE; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; X- REMARK 210 FILTERED-, 13C-EDITED NOESY; F1, REMARK 210 F2, 15N, 13C-FILTERED NOESY; X- REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CCPNMR ANALYSIS, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING - MOLECULAR REMARK 210 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 TOTAL BURIED SURFACE AREA: 1320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 B1669 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 ARG B1670 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 ARG B1680 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 ARG B1685 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 ARG B1669 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG B1680 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG B1685 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 ARG B1665 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 ARG B1669 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG B1670 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG B1680 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG B1669 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG B1685 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG B1665 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG B1669 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG B1680 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG B1685 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG B1665 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 ARG B1669 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG B1685 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 6 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 ARG B1669 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG B1670 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 7 ARG B1680 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 7 ARG B1685 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG B1685 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 ARG B1680 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 9 ARG B1685 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG B1665 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG B1669 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 10 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 ARG B1670 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 86 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 PRO B1676 45.75 -83.42 REMARK 500 2 PRO B1676 42.00 -82.00 REMARK 500 3 PRO B1676 48.13 -80.51 REMARK 500 3 ASN A 18 34.61 73.71 REMARK 500 4 PRO B1676 48.13 -83.21 REMARK 500 4 ASP A 63 38.39 -75.66 REMARK 500 5 PRO B1676 41.94 -79.74 REMARK 500 6 PRO B1676 43.23 -83.03 REMARK 500 6 PRO B1682 20.11 -77.28 REMARK 500 7 ARG B1665 46.01 -85.90 REMARK 500 7 PRO B1676 41.26 -81.22 REMARK 500 7 ILE B1681 88.22 45.94 REMARK 500 7 SER B1683 95.55 62.32 REMARK 500 7 SER A -1 -18.88 59.62 REMARK 500 7 MET A 1 155.21 64.69 REMARK 500 8 SER A -1 42.66 -72.16 REMARK 500 8 SER A 62 36.57 -97.92 REMARK 500 9 PRO B1676 44.65 -83.83 REMARK 500 9 ALA B1679 19.89 -149.06 REMARK 500 9 HIS A 0 -1.94 61.67 REMARK 500 9 ASN A 18 37.80 72.79 REMARK 500 9 SER A 62 41.48 -74.42 REMARK 500 10 PRO B1676 48.63 -87.17 REMARK 500 10 ARG B1680 9.00 54.57 REMARK 500 11 PRO B1676 45.33 -83.41 REMARK 500 11 ALA B1679 18.53 -155.29 REMARK 500 11 SER B1683 69.45 33.96 REMARK 500 12 PRO B1676 41.52 -80.79 REMARK 500 13 PRO B1676 47.91 -82.19 REMARK 500 13 SER A 62 49.06 -74.61 REMARK 500 14 PRO B1676 49.28 -79.45 REMARK 500 14 ALA B1679 143.45 -170.44 REMARK 500 14 ASN A 18 30.54 74.37 REMARK 500 14 SER A 62 37.91 -71.22 REMARK 500 16 PRO B1678 35.72 -81.42 REMARK 500 16 ASP A 34 76.37 -153.70 REMARK 500 17 PRO B1676 42.59 -82.04 REMARK 500 17 SER B1683 75.42 -119.14 REMARK 500 17 ASN A 18 40.40 74.71 REMARK 500 18 PRO B1676 44.33 -81.18 REMARK 500 18 PRO B1678 36.53 -75.95 REMARK 500 18 ASP A 63 15.77 -144.70 REMARK 500 19 PRO B1676 44.25 -84.29 REMARK 500 20 ASN A 18 34.48 71.52 REMARK 500 20 ASP A 63 -1.21 58.48 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 2 ARG B1685 0.09 SIDE CHAIN REMARK 500 8 ARG B1665 0.14 SIDE CHAIN REMARK 500 10 ARG B1670 0.08 SIDE CHAIN REMARK 500 15 TYR A 9 0.07 SIDE CHAIN REMARK 500 16 ARG B1670 0.09 SIDE CHAIN REMARK 500 18 ARG B1665 0.12 SIDE CHAIN REMARK 500 19 TYR A 9 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34628 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF SNX9 SH3 - EEEV NSP3 PEPTIDE COMPLEX DBREF 7OJ9 B 1663 1685 PDB 7OJ9 7OJ9 1663 1685 DBREF 7OJ9 A 1 64 UNP Q9Y5X1 SNX9_HUMAN 1 64 SEQADV 7OJ9 GLY A -2 UNP Q9Y5X1 EXPRESSION TAG SEQADV 7OJ9 SER A -1 UNP Q9Y5X1 EXPRESSION TAG SEQADV 7OJ9 HIS A 0 UNP Q9Y5X1 EXPRESSION TAG SEQRES 1 B 23 ALA GLU ARG LEU ILE PRO ARG ARG PRO ALA PRO PRO VAL SEQRES 2 B 23 PRO VAL PRO ALA ARG ILE PRO SER PRO ARG 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 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 ASN A 32 O GLU A 41 SHEET 4 AA1 5 THR A 3 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