HEADER CELL ADHESION 15-JAN-24 8VOH TITLE HADDOCK MODELS OF HUMAN ALPHAM I-DOMAIN BOUND TO THE THE N-TERMINAL TITLE 2 DOMAIN OF THE CYTOKINE PLEIOTROPHIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRIN ALPHA-M; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: I-DOMAIN, RESIDUES 147-340; COMPND 5 SYNONYM: CD11 ANTIGEN-LIKE FAMILY MEMBER B,CR-3 ALPHA CHAIN,CELL COMPND 6 SURFACE GLYCOPROTEIN MAC-1 SUBUNIT ALPHA,LEUKOCYTE ADHESION RECEPTOR COMPND 7 MO1,NEUTROPHIL ADHERENCE RECEPTOR; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PLEIOTROPHIN; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 33-90; COMPND 13 SYNONYM: PTN,HEPARIN-BINDING BRAIN MITOGEN,HBBM,HEPARIN-BINDING COMPND 14 GROWTH FACTOR 8,HBGF-8,HEPARIN-BINDING GROWTH-ASSOCIATED MOLECULE,HB- COMPND 15 GAM,HEPARIN-BINDING NEURITE OUTGROWTH-PROMOTING FACTOR,HBNF,HEPARIN- COMPND 16 BINDING NEURITE OUTGROWTH-PROMOTING FACTOR 1,HBNF-1,OSTEOBLAST- COMPND 17 SPECIFIC FACTOR 1,OSF-1; COMPND 18 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: ITGAM, CD11B, CR3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: PTN, HBNF1, NEGF1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTEGRIN, MAC-1, PLEIOTROPHIN, CELL ADHESION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR X.WANG,H.NGUYEN REVDAT 1 15-MAY-24 8VOH 0 JRNL AUTH X.WANG,H.NGUYEN JRNL TITL NMR STRUCTURE OF ALPHAM I-DOMAIN OF INTEGRIN MAC-1 IN JRNL TITL 2 COMPLEX WITH THE CYTOKINE PLEIOTROPHIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE INTEGRIN ALPHA-M STARTING STRUCTURE REMARK 3 IS 1JLM. THE PLEIOTROPHIN STARTING STRUCTURE IS 2N6F. REMARK 4 REMARK 4 8VOH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000280405. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.2 MM [U-13C; U-15N] HUMAN REMARK 210 ALPHAM I-DOMAIN, 1 MM THE N- REMARK 210 TERMINAL DOMAIN OF PLEIOTROPHIN, REMARK 210 90% H2O/10% D2O; 0.5 MM [U-13C; REMARK 210 U-15N] HUMAN ALPHAM I-DOMAIN, 90% REMARK 210 H2O/10% D2O; 0.5 MM [U-13C; U- REMARK 210 15N] THE N-TERMINAL DOMAIN OF REMARK 210 PLEIOTROPHIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D F1-13C-EDITED/F3-13C,15N REMARK 210 -FILTERED HSQCNOESY; 3D HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEWJ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 HH22 ARG A 216 OD2 ASP A 254 1.50 REMARK 500 HZ1 LYS B 3 OE1 GLU B 4 1.51 REMARK 500 HH22 ARG A 152 OE1 GLU A 303 1.53 REMARK 500 OD1 ASP A 294 HZ1 LYS A 315 1.53 REMARK 500 OD2 ASP A 260 HH22 ARG A 266 1.54 REMARK 500 OD1 ASP A 273 HH11 ARG A 276 1.56 REMARK 500 OE1 GLU A 155 HZ2 LYS A 306 1.57 REMARK 500 OE1 GLU A 162 HH22 ARG A 196 1.57 REMARK 500 HG1 THR A 185 OE1 GLU A 188 1.58 REMARK 500 OD1 ASP A 260 H LEU B 32 1.59 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 ASP A 132 -74.96 -75.65 REMARK 500 1 SER A 177 -83.78 -148.50 REMARK 500 1 LEU A 206 124.39 77.28 REMARK 500 1 ARG A 208 -157.75 -101.36 REMARK 500 1 ASN A 232 -2.03 76.18 REMARK 500 1 LYS B 2 -67.13 -124.45 REMARK 500 1 LYS B 3 132.54 -178.76 REMARK 500 1 PRO B 6 -152.56 -89.69 REMARK 500 1 LYS B 9 145.83 -170.33 REMARK 500 1 LYS B 12 -110.11 -85.87 REMARK 500 1 SER B 13 -157.21 67.03 REMARK 500 1 CYS B 30 131.43 74.52 REMARK 500 1 GLN B 46 93.10 -65.95 REMARK 500 2 ASP A 132 -75.15 -76.85 REMARK 500 2 SER A 177 -87.41 -148.93 REMARK 500 2 LEU A 206 126.89 78.38 REMARK 500 2 ARG A 208 -159.11 -101.46 REMARK 500 2 ASN A 232 -3.04 77.00 REMARK 500 2 LYS A 245 107.46 -59.26 REMARK 500 2 VAL A 255 -52.19 -125.07 REMARK 500 2 THR A 322 164.50 163.77 REMARK 500 2 GLN A 323 -72.26 -100.62 REMARK 500 2 LYS B 2 -66.12 -121.05 REMARK 500 2 LYS B 3 132.73 -179.18 REMARK 500 2 PRO B 6 -151.68 -90.10 REMARK 500 2 LYS B 12 -108.42 -85.39 REMARK 500 2 SER B 13 -157.04 66.43 REMARK 500 2 CYS B 30 134.82 70.74 REMARK 500 2 GLN B 46 89.40 -67.09 REMARK 500 3 ASP A 132 -73.35 -71.67 REMARK 500 3 SER A 177 -78.50 -147.61 REMARK 500 3 PHE A 184 138.91 -170.87 REMARK 500 3 PRO A 193 32.08 -80.64 REMARK 500 3 LEU A 206 118.26 78.63 REMARK 500 3 ARG A 208 -154.88 -101.02 REMARK 500 3 HIS A 210 54.20 -143.37 REMARK 500 3 ASN A 232 -5.73 75.88 REMARK 500 3 LYS A 245 108.12 -59.06 REMARK 500 3 VAL A 255 -52.55 -129.56 REMARK 500 3 ARG A 293 33.47 -77.33 REMARK 500 3 ASP A 294 -20.45 -154.88 REMARK 500 3 ALA A 304 2.91 -68.69 REMARK 500 3 GLU A 320 -60.57 -133.75 REMARK 500 3 LYS B 2 -67.76 -129.22 REMARK 500 3 LYS B 3 130.62 -179.35 REMARK 500 3 PRO B 6 -157.93 -89.76 REMARK 500 3 GLU B 7 92.32 -68.62 REMARK 500 3 LYS B 9 142.19 -174.06 REMARK 500 3 LYS B 12 -114.22 -85.74 REMARK 500 3 SER B 13 -156.40 69.84 REMARK 500 REMARK 500 THIS ENTRY HAS 176 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31138 RELATED DB: BMRB REMARK 900 HADDOCK MODELS OF HUMAN ALPHAM I-DOMAIN BOUND TO THE THE N-TERMINAL REMARK 900 DOMAIN OF THE CYTOKINE PLEIOTROPHIN DBREF 8VOH A 131 324 UNP P11215 ITAM_HUMAN 147 340 DBREF 8VOH B 1 58 UNP P21246 PTN_HUMAN 33 90 SEQRES 1 A 194 GLU ASP SER ASP ILE ALA PHE LEU ILE ASP GLY SER GLY SEQRES 2 A 194 SER ILE ILE PRO HIS ASP PHE ARG ARG MET LYS GLU PHE SEQRES 3 A 194 VAL SER THR VAL MET GLU GLN LEU LYS LYS SER LYS THR SEQRES 4 A 194 LEU PHE SER LEU MET GLN TYR SER GLU GLU PHE ARG ILE SEQRES 5 A 194 HIS PHE THR PHE LYS GLU PHE GLN ASN ASN PRO ASN PRO SEQRES 6 A 194 ARG SER LEU VAL LYS PRO ILE THR GLN LEU LEU GLY ARG SEQRES 7 A 194 THR HIS THR ALA THR GLY ILE ARG LYS VAL VAL ARG GLU SEQRES 8 A 194 LEU PHE ASN ILE THR ASN GLY ALA ARG LYS ASN ALA PHE SEQRES 9 A 194 LYS ILE LEU VAL VAL ILE THR ASP GLY GLU LYS PHE GLY SEQRES 10 A 194 ASP PRO LEU GLY TYR GLU ASP VAL ILE PRO GLU ALA ASP SEQRES 11 A 194 ARG GLU GLY VAL ILE ARG TYR VAL ILE GLY VAL GLY ASP SEQRES 12 A 194 ALA PHE ARG SER GLU LYS SER ARG GLN GLU LEU ASN THR SEQRES 13 A 194 ILE ALA SER LYS PRO PRO ARG ASP HIS VAL PHE GLN VAL SEQRES 14 A 194 ASN ASN PHE GLU ALA LEU LYS THR ILE GLN ASN GLN LEU SEQRES 15 A 194 ARG GLU LYS ILE PHE ALA ILE GLU GLY THR GLN THR SEQRES 1 B 58 GLY LYS LYS GLU LYS PRO GLU LYS LYS VAL LYS LYS SER SEQRES 2 B 58 ASP CYS GLY GLU TRP GLN TRP SER VAL CYS VAL PRO THR SEQRES 3 B 58 SER GLY ASP CYS GLY LEU GLY THR ARG GLU GLY THR ARG SEQRES 4 B 58 THR GLY ALA GLU CYS LYS GLN THR MET LYS THR GLN ARG SEQRES 5 B 58 CYS LYS ILE PRO CYS ASN HELIX 1 AA1 ILE A 146 LEU A 164 1 19 HELIX 2 AA2 THR A 185 ASN A 192 1 8 HELIX 3 AA3 ASN A 194 LYS A 200 1 7 HELIX 4 AA4 HIS A 210 GLU A 221 1 12 HELIX 5 AA5 ASN A 224 GLY A 228 5 5 HELIX 6 AA6 VAL A 255 GLU A 262 1 8 HELIX 7 AA7 ASP A 273 ARG A 276 5 4 HELIX 8 AA8 SER A 277 ALA A 288 1 12 HELIX 9 AA9 PRO A 291 HIS A 295 1 5 HELIX 10 AB1 ALA A 304 ALA A 318 1 15 SHEET 1 AA1 6 PHE A 180 PHE A 184 0 SHEET 2 AA1 6 THR A 169 TYR A 176 -1 N LEU A 173 O HIS A 183 SHEET 3 AA1 6 SER A 133 ASP A 140 1 N PHE A 137 O SER A 172 SHEET 4 AA1 6 PHE A 234 THR A 241 1 O PHE A 234 N ASP A 134 SHEET 5 AA1 6 ILE A 265 VAL A 271 1 O ILE A 265 N LEU A 237 SHEET 6 AA1 6 VAL A 296 VAL A 299 1 O VAL A 299 N GLY A 270 SHEET 1 AA2 3 VAL B 24 PRO B 25 0 SHEET 2 AA2 3 LEU B 32 ARG B 39 -1 O THR B 34 N VAL B 24 SHEET 3 AA2 3 THR B 47 LYS B 54 -1 O LYS B 49 N GLY B 37 SSBOND 1 CYS B 15 CYS B 44 1555 1555 2.03 SSBOND 2 CYS B 23 CYS B 53 1555 1555 2.03 SSBOND 3 CYS B 30 CYS B 57 1555 1555 2.03 CISPEP 1 LYS A 290 PRO A 291 1 -1.51 CISPEP 2 LYS A 290 PRO A 291 2 -1.63 CISPEP 3 LYS A 290 PRO A 291 3 -0.96 CISPEP 4 LYS A 290 PRO A 291 4 -1.28 CISPEP 5 LYS A 290 PRO A 291 5 -1.39 CISPEP 6 LYS A 290 PRO A 291 6 -1.35 CISPEP 7 LYS A 290 PRO A 291 7 -1.55 CISPEP 8 LYS A 290 PRO A 291 8 -1.38 CISPEP 9 LYS A 290 PRO A 291 9 -1.17 CISPEP 10 LYS A 290 PRO A 291 10 -1.48 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