HEADER CELL INVASION 08-MAY-25 9R4V TITLE SOLUTION STRUCTURE OF N-WASP GBD IN COMPLEX WITH ESPF COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACTIN NUCLEATION-PROMOTING FACTOR WASL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN,N-WASP; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: LEE-ENCODED EFFECTOR ESPF; 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: WASL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562; SOURCE 11 GENE: ESPF, NCTC8621_00139; 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 9R4V 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 9R4V 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_1292147598. 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 : 0.1 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-13C; U-15N] N-WASP REMARK 210 GBD, 0.6 MM ESPF, 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 93% H2O/7% D2O; 0.7 MM GBD, 0.5 REMARK 210 MM [U-13C; U-15N] ESPF, 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 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; 4D HACACON; REMARK 210 3D HA(CA)CON; 3D HA(CA)NCO 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: 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 273 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 273 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 273 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 273 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 7 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 10 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 10 ARG B 122 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 10 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG A 273 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 11 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 12 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 12 ARG A 273 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 12 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 13 ARG A 273 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 4.3 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 14 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 15 ARG A 273 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG B 138 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 17 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 18 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 18 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 58 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 PHE A 209 13.40 -69.10 REMARK 500 1 ILE A 212 -129.64 -128.96 REMARK 500 1 THR A 221 -8.72 -143.48 REMARK 500 1 LYS B 119 71.87 56.13 REMARK 500 1 THR B 129 4.08 54.40 REMARK 500 1 SER B 137 42.19 -74.25 REMARK 500 2 MET A 206 -7.90 -154.40 REMARK 500 2 ALA B 133 39.38 -144.11 REMARK 500 3 HIS A 205 -0.68 59.71 REMARK 500 3 THR A 221 -5.84 -141.54 REMARK 500 3 THR B 129 -9.78 -57.88 REMARK 500 4 SER A 207 41.12 -74.05 REMARK 500 4 ASN A 208 49.24 -70.21 REMARK 500 4 THR A 221 -10.13 -141.95 REMARK 500 4 THR B 115 23.33 48.81 REMARK 500 5 SER A 207 39.10 -70.96 REMARK 500 6 SER B 137 33.99 -78.53 REMARK 500 7 THR A 221 -5.90 -140.90 REMARK 500 7 ASN A 227 12.10 -140.27 REMARK 500 8 THR A 221 -7.80 -141.58 REMARK 500 8 ASN B 117 49.03 -76.19 REMARK 500 8 THR B 129 54.55 -144.58 REMARK 500 8 SER B 137 22.55 -143.86 REMARK 500 9 MET A 206 16.72 56.51 REMARK 500 9 PHE A 209 42.49 -104.13 REMARK 500 10 MET A 206 54.45 -118.02 REMARK 500 10 THR A 221 -9.10 -145.75 REMARK 500 10 SER B 121 40.30 -68.22 REMARK 500 10 THR B 129 80.65 -150.29 REMARK 500 11 SER A 204 -21.72 -151.51 REMARK 500 11 MET A 206 -8.32 59.68 REMARK 500 11 THR A 221 -16.46 -144.62 REMARK 500 11 ASP A 224 98.67 -69.98 REMARK 500 12 SER A 207 -2.17 -141.63 REMARK 500 12 ASN A 208 12.93 -67.11 REMARK 500 12 THR A 221 -11.35 -145.51 REMARK 500 13 THR A 221 -3.02 -141.15 REMARK 500 13 THR B 129 48.07 -73.44 REMARK 500 13 SER B 137 64.72 -117.23 REMARK 500 14 HIS A 205 -49.66 -165.72 REMARK 500 14 GLN A 210 -30.57 -134.75 REMARK 500 14 THR A 221 -5.33 -142.46 REMARK 500 14 SER B 137 49.32 -79.10 REMARK 500 15 THR A 221 -8.33 -140.99 REMARK 500 15 LYS B 119 64.34 -119.19 REMARK 500 15 THR B 129 107.49 -58.84 REMARK 500 15 PRO B 139 158.41 -49.72 REMARK 500 15 ALA B 159 33.14 -83.58 REMARK 500 16 HIS A 205 -14.29 -143.53 REMARK 500 16 ALA B 136 -140.05 -104.22 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 13 ARG B 138 0.10 SIDE CHAIN REMARK 500 19 ARG A 249 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34993 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF N-WASP GBD IN COMPLEX WITH ESPF DBREF 9R4V A 207 275 UNP O00401 WASL_HUMAN 207 275 DBREF1 9R4V B 115 161 UNP A0A376PNR8_ECOLX DBREF2 9R4V B A0A376PNR8 115 161 SEQADV 9R4V GLY A 203 UNP O00401 EXPRESSION TAG SEQADV 9R4V SER A 204 UNP O00401 EXPRESSION TAG SEQADV 9R4V HIS A 205 UNP O00401 EXPRESSION TAG SEQADV 9R4V MET A 206 UNP O00401 EXPRESSION TAG SEQADV 9R4V GLY B 114 UNP A0A376PNR EXPRESSION TAG SEQADV 9R4V SER B 121 UNP A0A376PNR THR 121 CONFLICT SEQRES 1 A 73 GLY SER HIS MET SER ASN PHE GLN HIS ILE GLY HIS VAL SEQRES 2 A 73 GLY TRP ASP PRO ASN THR GLY PHE ASP LEU ASN ASN LEU SEQRES 3 A 73 ASP PRO GLU LEU LYS ASN LEU PHE ASP MET CYS GLY ILE SEQRES 4 A 73 SER GLU ALA GLN LEU LYS ASP ARG GLU THR SER LYS VAL SEQRES 5 A 73 ILE TYR ASP PHE ILE GLU LYS THR GLY GLY VAL GLU ALA SEQRES 6 A 73 VAL LYS ASN GLU LEU ARG ARG GLN SEQRES 1 B 48 GLY THR VAL ASN PHE LYS PRO SER 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 HELIX 1 AA1 MET A 206 ILE A 212 5 7 HELIX 2 AA2 ASP A 229 GLY A 240 1 12 HELIX 3 AA3 SER A 242 LYS A 247 1 6 HELIX 4 AA4 ASP A 248 GLY A 263 1 16 HELIX 5 AA5 GLY A 264 ARG A 273 1 10 HELIX 6 AA6 PRO B 141 ALA B 159 1 19 SHEET 1 AA1 2 TRP A 217 ASP A 218 0 SHEET 2 AA1 2 GLY A 222 PHE A 223 -1 O GLY A 222 N ASP A 218 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 252 0 0 6 2 0 0 6 930 2 0 10 END