PDB Short entry for 2JXC HEADER ENDOCYTOSIS/PROTEIN BINDING 12-NOV-07 2JXC TITLE STRUCTURE OF THE EPS15-EH2 STONIN2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EH 2 DOMAIN; COMPND 5 SYNONYM: PROTEIN EPS15, AF-1P PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: STONIN-2; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: STONED B; COMPND 11 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: EPS15, AF1P; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE 3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: STON2, STN2, STNB; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE 3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX6P1 KEYWDS ENDOCYTOSIS, MEMBRANE, PHOSPHORYLATION, PROTO-ONCOGENE, SH3-BINDING, KEYWDS 2 ENDOCYTOSIS-PROTEIN BINDING COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.RUMPF,B.SIMON,N.JUNG,T.MARITZEN,V.HAUCKE,M.SATTLER,Y.GROEMPING REVDAT 4 01-MAY-24 2JXC 1 REMARK SEQADV REVDAT 3 19-JUN-13 2JXC 1 JRNL VERSN REVDAT 2 24-FEB-09 2JXC 1 VERSN REVDAT 1 08-JAN-08 2JXC 0 JRNL AUTH J.RUMPF,B.SIMON,N.JUNG,T.MARITZEN,V.HAUCKE,M.SATTLER, JRNL AUTH 2 Y.GROEMPING JRNL TITL STRUCTURE OF THE EPS15-STONIN2 COMPLEX PROVIDES A MOLECULAR JRNL TITL 2 EXPLANATION FOR EH-DOMAIN LIGAND SPECIFICITY. JRNL REF EMBO J. V. 27 558 2008 JRNL REFN ISSN 0261-4189 JRNL PMID 18200045 JRNL DOI 10.1038/SJ.EMBOJ.7601980 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.RUMPF,B.SIMON,Y.GROEMPING,M.SATTLER REMARK 1 TITL 1H, 13C, AND 15N CHEMICAL SHIFT ASSIGNMENTS FOR THE REMARK 1 TITL 2 EPS15-STONIN2 COMPLEX REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRVIEW 5.0.4, CNS 1.1 REMARK 3 AUTHORS : JOHNSON, B.A. ET AL. (NMRVIEW), BRUNGER, A.T. ET REMARK 3 AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JXC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000100408. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-1 MM [U-99% 13C; U-99% 15N] REMARK 210 EH2, 0.5-1 MM STONIN PEPTIDE, 2 REMARK 210 MM CA, 93% H2O/7% D2O; 0.5-1 MM REMARK 210 EH2, 0.5-1 MM [U-99% 13C; U-99% REMARK 210 15N] STONIN PEPTIDE, 2 MM CA, 93% REMARK 210 H2O/7% D2O; 0.5-1 MM [U-99% 13C; REMARK 210 U-99% 15N] EH2, 0.5-1 MM STONIN REMARK 210 PEPTIDE, 2 MM CA, 100% D2O; 0.5- REMARK 210 1 MM EH2, 0.5-1 MM [U-99% 13C; U- REMARK 210 99% 15N] STONIN PEPTIDE, 2 MM CA, REMARK 210 100% D2O; 0.6 MM EH2, 0.6 MM REMARK 210 STONIN PEPTIDE, 2 MM CA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HNCACB; 3D C(CO)NH; REMARK 210 3D CBCA(CO)NH; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 3D HCCH-TOCSY; REMARK 210 3D H(CCO)NH; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, NMRPIPE, ARIA 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 116 REMARK 465 PRO A 117 REMARK 465 LEU A 118 REMARK 465 GLY A 119 REMARK 465 SER A 120 REMARK 465 GLY B 296 REMARK 465 PRO B 297 REMARK 465 LEU B 298 REMARK 465 GLY B 299 REMARK 465 SER B 300 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 HB3 ASN B 317 HD11 LEU B 320 1.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 TYR A 132 CE1 TYR A 132 CZ -0.125 REMARK 500 2 TYR A 132 CZ TYR A 132 CE2 0.130 REMARK 500 3 TYR A 132 CE1 TYR A 132 CZ -0.124 REMARK 500 3 TYR A 132 CZ TYR A 132 CE2 0.129 REMARK 500 3 PHE B 334 CE1 PHE B 334 CZ 0.149 REMARK 500 3 PHE B 334 CZ PHE B 334 CE2 -0.117 REMARK 500 4 TYR A 193 CE1 TYR A 193 CZ 0.086 REMARK 500 4 TYR A 193 CZ TYR A 193 CE2 -0.078 REMARK 500 4 PHE B 334 CE1 PHE B 334 CZ 0.229 REMARK 500 4 PHE B 334 CZ PHE B 334 CE2 -0.203 REMARK 500 6 TYR A 132 CE1 TYR A 132 CZ -0.126 REMARK 500 6 TYR A 132 CZ TYR A 132 CE2 0.135 REMARK 500 6 PHE B 334 CE1 PHE B 334 CZ 0.237 REMARK 500 6 PHE B 334 CZ PHE B 334 CE2 -0.208 REMARK 500 7 PHE B 334 CE1 PHE B 334 CZ 0.193 REMARK 500 7 PHE B 334 CZ PHE B 334 CE2 -0.153 REMARK 500 8 TYR A 132 CE1 TYR A 132 CZ -0.130 REMARK 500 8 TYR A 132 CZ TYR A 132 CE2 0.135 REMARK 500 8 PHE B 334 CE1 PHE B 334 CZ 0.129 REMARK 500 9 TYR A 193 CE1 TYR A 193 CZ -0.086 REMARK 500 9 TYR A 193 CZ TYR A 193 CE2 0.086 REMARK 500 9 PHE B 334 CE1 PHE B 334 CZ 0.209 REMARK 500 9 PHE B 334 CZ PHE B 334 CE2 -0.184 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 A 126 -31.76 -33.46 REMARK 500 1 VAL B 303 30.78 -160.80 REMARK 500 1 SER B 307 109.60 -49.29 REMARK 500 1 ALA B 311 -32.37 73.31 REMARK 500 1 LEU B 320 -38.71 -163.29 REMARK 500 1 GLN B 321 41.57 -165.54 REMARK 500 1 VAL B 323 84.04 -67.84 REMARK 500 1 PRO B 327 41.50 -74.55 REMARK 500 1 GLU B 337 -65.90 -97.52 REMARK 500 1 GLN B 338 -70.69 69.24 REMARK 500 2 PRO A 126 -31.27 -34.31 REMARK 500 2 SER A 140 71.15 60.49 REMARK 500 2 THR B 304 41.87 -75.71 REMARK 500 2 GLU B 305 116.75 -166.62 REMARK 500 2 PRO B 308 56.68 -62.19 REMARK 500 2 ALA B 311 -43.24 69.96 REMARK 500 2 VAL B 323 -45.75 -141.96 REMARK 500 2 GLN B 324 72.11 49.44 REMARK 500 2 PRO B 327 39.17 -71.07 REMARK 500 2 GLN B 338 -38.95 69.98 REMARK 500 3 PRO A 126 -35.36 -32.89 REMARK 500 3 SER A 140 72.69 58.38 REMARK 500 3 LEU A 156 7.98 -68.18 REMARK 500 3 SER B 302 70.23 -110.94 REMARK 500 3 THR B 304 -94.81 33.77 REMARK 500 3 PRO B 308 44.82 -82.75 REMARK 500 3 ARG B 310 33.01 -84.70 REMARK 500 3 ALA B 311 -48.40 69.39 REMARK 500 3 ASN B 317 8.95 -65.72 REMARK 500 3 GLN B 321 80.84 56.51 REMARK 500 3 ILE B 328 32.85 -81.26 REMARK 500 3 GLU B 339 31.63 -93.28 REMARK 500 4 VAL A 124 98.97 -68.63 REMARK 500 4 PRO A 126 -27.05 -33.97 REMARK 500 4 PRO A 141 172.73 -59.61 REMARK 500 4 SER B 302 63.81 60.85 REMARK 500 4 THR B 304 45.00 37.80 REMARK 500 4 GLU B 305 130.54 178.20 REMARK 500 4 ALA B 306 17.64 -140.60 REMARK 500 4 SER B 307 105.48 52.26 REMARK 500 4 PRO B 308 24.08 -69.00 REMARK 500 4 ALA B 311 -177.38 60.67 REMARK 500 4 THR B 312 11.02 55.88 REMARK 500 4 ASN B 317 35.86 -94.01 REMARK 500 4 GLN B 321 148.23 73.16 REMARK 500 4 PRO B 327 30.76 -73.84 REMARK 500 4 GLU B 337 21.19 -142.64 REMARK 500 4 GLN B 338 -50.74 72.85 REMARK 500 5 SER A 140 73.03 59.81 REMARK 500 5 LEU A 156 20.59 -76.17 REMARK 500 REMARK 500 THIS ENTRY HAS 124 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 TYR A 193 0.06 SIDE CHAIN REMARK 500 6 TYR A 132 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1000 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 175 OD2 REMARK 620 2 MET A 179 O 139.8 REMARK 620 3 GLU A 184 OE2 68.2 126.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EH2 RELATED DB: PDB REMARK 900 APO EH DOMAIN REMARK 900 RELATED ID: 1FF1 RELATED DB: PDB REMARK 900 LOW AFFINITY COMPLEX DBREF 2JXC A 121 215 UNP P42566 EP15_HUMAN 121 215 DBREF 2JXC B 301 340 UNP Q8WXE9 STON2_HUMAN 301 340 SEQADV 2JXC GLY A 116 UNP P42566 EXPRESSION TAG SEQADV 2JXC PRO A 117 UNP P42566 EXPRESSION TAG SEQADV 2JXC LEU A 118 UNP P42566 EXPRESSION TAG SEQADV 2JXC GLY A 119 UNP P42566 EXPRESSION TAG SEQADV 2JXC SER A 120 UNP P42566 EXPRESSION TAG SEQADV 2JXC GLY B 296 UNP Q8WXE9 EXPRESSION TAG SEQADV 2JXC PRO B 297 UNP Q8WXE9 EXPRESSION TAG SEQADV 2JXC LEU B 298 UNP Q8WXE9 EXPRESSION TAG SEQADV 2JXC GLY B 299 UNP Q8WXE9 EXPRESSION TAG SEQADV 2JXC SER B 300 UNP Q8WXE9 EXPRESSION TAG SEQRES 1 A 100 GLY PRO LEU GLY SER PRO TRP ALA VAL LYS PRO GLU ASP SEQRES 2 A 100 LYS ALA LYS TYR ASP ALA ILE PHE ASP SER LEU SER PRO SEQRES 3 A 100 VAL ASN GLY PHE LEU SER GLY ASP LYS VAL LYS PRO VAL SEQRES 4 A 100 LEU LEU ASN SER LYS LEU PRO VAL ASP ILE LEU GLY ARG SEQRES 5 A 100 VAL TRP GLU LEU SER ASP ILE ASP HIS ASP GLY MET LEU SEQRES 6 A 100 ASP ARG ASP GLU PHE ALA VAL ALA MET PHE LEU VAL TYR SEQRES 7 A 100 CYS ALA LEU GLU LYS GLU PRO VAL PRO MET SER LEU PRO SEQRES 8 A 100 PRO ALA LEU VAL PRO PRO SER LYS ARG SEQRES 1 B 45 GLY PRO LEU GLY SER PRO SER VAL THR GLU ALA SER PRO SEQRES 2 B 45 TRP ARG ALA THR ASN PRO PHE LEU ASN GLU THR LEU GLN SEQRES 3 B 45 ASP VAL GLN PRO SER PRO ILE ASN PRO PHE SER ALA PHE SEQRES 4 B 45 PHE GLU GLU GLN GLU ARG HET CA A1000 1 HETNAM CA CALCIUM ION FORMUL 3 CA CA 2+ HELIX 1 1 LYS A 125 LEU A 139 1 15 HELIX 2 2 GLY A 148 LEU A 156 1 9 HELIX 3 3 PRO A 161 ASP A 173 1 13 HELIX 4 4 ARG A 182 GLU A 197 1 16 HELIX 5 5 PRO A 211 ARG A 215 5 5 HELIX 6 6 ALA B 333 GLN B 338 1 6 SHEET 1 A 2 PHE A 145 SER A 147 0 SHEET 2 A 2 MET A 179 ASP A 181 -1 O LEU A 180 N LEU A 146 LINK OD2 ASP A 175 CA CA A1000 1555 1555 2.95 LINK O MET A 179 CA CA A1000 1555 1555 2.25 LINK OE2 GLU A 184 CA CA A1000 1555 1555 2.83 SITE 1 AC1 5 ASP A 173 ASP A 175 ASP A 177 MET A 179 SITE 2 AC1 5 GLU A 184 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