PDB Short entry for 2K4A HEADER PROTEIN TRANSPORT 02-JUN-08 2K4A TITLE FGF-1-C2A BINARY COMPLEX STRUCTURE: A KEY COMPONENT IN THE FIBROBLAST TITLE 2 GROWTHFACTOR NON-CLASSICAL PATHWAY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2 DOMAIN, UNP RESIDUES 141-268; COMPND 5 SYNONYM: SYNAPTOTAGMIN I, SYTI, P65, C2A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HEPARIN-BINDING GROWTH FACTOR 1; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 23-155; COMPND 11 SYNONYM: HBGF-1, ACIDIC FIBROBLAST GROWTH FACTOR, AFGF, BETA- COMPND 12 ENDOTHELIAL CELL GROWTH FACTOR, ECGF-BETA; COMPND 13 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: SYT1, SVP65, SYT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PGEX; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: FGF1, FGFA; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 20 EXPRESSION_SYSTEM_VECTOR: PET20 KEYWDS BETA BARREL, FGF1-C2A BINARY COMPLEX, CALCIUM, CELL JUNCTION, KEYWDS 2 CYTOPLASMIC VESICLE, GLYCOPROTEIN, LIPOPROTEIN, MEMBRANE, METAL- KEYWDS 3 BINDING, PALMITATE, PHOSPHOPROTEIN, SYNAPSE, TRANSMEMBRANE, KEYWDS 4 ACETYLATION, ANGIOGENESIS, DEVELOPMENTAL PROTEIN, DIFFERENTIATION, KEYWDS 5 GROWTH FACTOR, HEPARIN-BINDING, MITOGEN, POLYMORPHISM, PROTEIN KEYWDS 6 TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.YU,S.K.MOHAN REVDAT 2 16-MAR-22 2K4A 1 REMARK REVDAT 1 09-JUN-09 2K4A 0 JRNL AUTH S.K.MOHAN,C.YU JRNL TITL FGF-1-C2A BINARY COMPLEX STRUCTURE: KEY COMPONENT IN THE JRNL TITL 2 ACIDIC FIBROBLAST GROWTH FACTOR RELEASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, HADDOCK 2.0, ARIA/CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE, NILGES (ARIA), ALEXANDRE BONVIN REMARK 3 (HADDOCK), BRUNGER, ADAMS, CLORE, DELANO, GROS, REMARK 3 GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, REMARK 3 READ, RICE, SIMONSON,WARREN (ARIA/CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HADDOCK REMARK 4 REMARK 4 2K4A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000100657. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50MM (NH4)2SO4 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2MM FGF-1-C2A; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C(W2)-EDITED 12C(W2) REMARK 210 -FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AV800 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK 2.0, SPARKY, TOPSPIN REMARK 210 1.3, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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 HG CYS B 9 O LEU B 124 1.42 REMARK 500 OE1 GLU A 103 HZ3 LYS A 105 1.42 REMARK 500 O TYR B 8 H LEU B 126 1.46 REMARK 500 HD1 HIS B 14 O GLY B 26 1.46 REMARK 500 H ASN B 88 O PHE B 125 1.46 REMARK 500 OE2 GLU A 103 HZ3 LYS A 128 1.48 REMARK 500 HZ1 LYS B 5 OE1 GLN B 38 1.48 REMARK 500 O LEU A 10 H THR A 117 1.48 REMARK 500 HH11 ARG B 17 OG1 THR B 27 1.49 REMARK 500 OE2 GLU B 75 HZ2 LYS B 94 1.50 REMARK 500 OG SER B 10 HZ2 LYS B 106 1.50 REMARK 500 OD1 ASN B 85 HZ1 LYS B 121 1.51 REMARK 500 O PRO A 40 HD1 HIS A 59 1.51 REMARK 500 OE1 GLU A 79 HZ3 LYS A 83 1.52 REMARK 500 OE2 GLU B 46 HZ1 LYS B 93 1.53 REMARK 500 O GLN A 7 H ILE A 24 1.53 REMARK 500 OD2 ASP A 33 HZ3 LYS A 61 1.53 REMARK 500 O VAL B 24 HG SER B 109 1.53 REMARK 500 H LYS A 43 O ALA A 88 1.54 REMARK 500 H TYR A 41 O TYR A 90 1.54 REMARK 500 O GLU B 53 HG1 THR B 54 1.55 REMARK 500 OE1 GLU A 1 HZ3 LYS B 105 1.55 REMARK 500 HH TYR A 90 O HIS A 98 1.55 REMARK 500 OD1 ASP B 25 HG1 THR B 27 1.55 REMARK 500 HG1 THR A 84 OD2 ASP B 25 1.55 REMARK 500 OD1 ASP B 29 HG SER B 31 1.55 REMARK 500 OH TYR B 1 HZ1 LYS B 3 1.55 REMARK 500 H ALA B 59 O TYR B 67 1.55 REMARK 500 OD2 ASP A 93 H SER A 96 1.56 REMARK 500 O ASN B 11 HZ3 LYS B 106 1.57 REMARK 500 OD1 ASP B 21 HG1 THR B 23 1.57 REMARK 500 O LEU B 6 H LEU B 128 1.57 REMARK 500 OD2 ASP A 39 HH11 ARG A 94 1.57 REMARK 500 H2 TYR B 1 OG SER B 132 1.57 REMARK 500 OH TYR A 8 HE ARG A 121 1.57 REMARK 500 OE2 GLU A 119 HH21 ARG A 121 1.57 REMARK 500 O ASP A 11 H LEU A 20 1.58 REMARK 500 O ILE B 18 HD1 HIS B 34 1.58 REMARK 500 O PRO B 20 HG SER B 69 1.58 REMARK 500 H ASP B 61 O LEU B 65 1.58 REMARK 500 O LYS A 5 H ALA A 27 1.58 REMARK 500 OD1 ASP A 49 HZ2 LYS A 83 1.59 REMARK 500 HE21 GLN A 7 OE1 GLN A 25 1.59 REMARK 500 OG SER B 109 HZ1 LYS B 111 1.59 REMARK 500 O VAL A 42 HG1 THR A 56 1.59 REMARK 500 OE2 GLU A 127 HH21 ARG B 115 1.59 REMARK 500 HH TYR A 41 OE1 GLU A 55 1.59 REMARK 500 O CYS B 110 HZ2 LYS B 111 1.60 REMARK 500 O SER B 92 H HIS B 95 1.60 REMARK 500 H LEU A 6 O ARG A 121 1.60 REMARK 500 REMARK 500 THIS ENTRY HAS 1056 CLOSE CONTACTS 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 ASN A 17 64.16 74.68 REMARK 500 1 LEU A 32 -51.24 -153.09 REMARK 500 1 ASP A 39 64.41 -113.79 REMARK 500 1 LEU A 47 -173.41 -61.30 REMARK 500 1 PRO A 48 -44.72 -24.45 REMARK 500 1 LYS A 50 28.70 44.23 REMARK 500 1 LYS A 51 57.32 -96.73 REMARK 500 1 LYS A 52 137.10 169.80 REMARK 500 1 LYS A 61 76.65 37.53 REMARK 500 1 ASN A 64 55.48 -150.97 REMARK 500 1 PHE A 67 -49.08 -165.21 REMARK 500 1 ASN A 68 71.82 68.72 REMARK 500 1 LYS A 74 92.06 -62.40 REMARK 500 1 VAL A 75 130.15 -179.70 REMARK 500 1 ARG A 94 20.26 81.88 REMARK 500 1 PHE A 95 -59.59 -137.32 REMARK 500 1 ASP A 112 97.80 -63.42 REMARK 500 1 PHE A 113 66.27 -69.54 REMARK 500 1 HIS A 115 -78.74 -150.35 REMARK 500 1 LYS B 2 108.49 -50.63 REMARK 500 1 PRO B 4 105.04 -18.76 REMARK 500 1 SER B 10 120.10 75.89 REMARK 500 1 GLN B 33 76.16 -68.59 REMARK 500 1 HIS B 34 16.56 -144.30 REMARK 500 1 VAL B 44 93.83 -53.39 REMARK 500 1 THR B 52 -70.14 -54.24 REMARK 500 1 THR B 54 -41.17 175.12 REMARK 500 1 ALA B 59 84.29 -159.89 REMARK 500 1 ASP B 63 -52.51 68.77 REMARK 500 1 SER B 69 -62.68 171.08 REMARK 500 1 GLN B 70 -71.42 -62.57 REMARK 500 1 ASN B 85 21.38 -143.89 REMARK 500 1 SER B 92 79.99 -69.09 REMARK 500 1 VAL B 102 121.85 -16.53 REMARK 500 1 SER B 109 175.55 138.95 REMARK 500 1 LYS B 111 81.36 -179.44 REMARK 500 1 ARG B 112 27.09 -143.72 REMARK 500 1 TYR B 118 75.25 -62.77 REMARK 500 1 SER B 132 65.49 -110.21 REMARK 500 2 ASN A 17 65.25 67.06 REMARK 500 2 ILE A 24 -63.90 -98.99 REMARK 500 2 ASP A 39 62.77 -115.28 REMARK 500 2 LEU A 47 -174.51 -60.08 REMARK 500 2 PRO A 48 -43.46 -25.50 REMARK 500 2 LYS A 50 26.89 44.06 REMARK 500 2 LYS A 52 141.41 173.02 REMARK 500 2 ASN A 64 53.31 -142.02 REMARK 500 2 PHE A 67 -48.18 -172.95 REMARK 500 2 ASN A 68 66.96 69.18 REMARK 500 2 LYS A 74 98.15 -64.22 REMARK 500 REMARK 500 THIS ENTRY HAS 836 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K43 RELATED DB: PDB REMARK 900 FGF-1 REMARK 900 RELATED ID: 2K45 RELATED DB: PDB REMARK 900 C2A REMARK 900 RELATED ID: 15794 RELATED DB: BMRB DBREF 2K4A A 1 128 UNP P21579 SYT1_HUMAN 141 268 DBREF 2K4A B 1 133 UNP P05230 FGF1_HUMAN 23 155 SEQRES 1 A 128 GLU LYS LEU GLY LYS LEU GLN TYR SER LEU ASP TYR ASP SEQRES 2 A 128 PHE GLN ASN ASN GLN LEU LEU VAL GLY ILE ILE GLN ALA SEQRES 3 A 128 ALA GLU LEU PRO ALA LEU ASP MET GLY GLY THR SER ASP SEQRES 4 A 128 PRO TYR VAL LYS VAL PHE LEU LEU PRO ASP LYS LYS LYS SEQRES 5 A 128 LYS PHE GLU THR LYS VAL HIS ARG LYS THR LEU ASN PRO SEQRES 6 A 128 VAL PHE ASN GLU GLN PHE THR PHE LYS VAL PRO TYR SER SEQRES 7 A 128 GLU LEU GLY GLY LYS THR LEU VAL MET ALA VAL TYR ASP SEQRES 8 A 128 PHE ASP ARG PHE SER LYS HIS ASP ILE ILE GLY GLU PHE SEQRES 9 A 128 LYS VAL PRO MET ASN THR VAL ASP PHE GLY HIS VAL THR SEQRES 10 A 128 GLU GLU TRP ARG ASP LEU GLN SER ALA GLU LYS SEQRES 1 B 133 TYR LYS LYS PRO LYS LEU LEU TYR CYS SER ASN GLY GLY SEQRES 2 B 133 HIS PHE LEU ARG ILE LEU PRO ASP GLY THR VAL ASP GLY SEQRES 3 B 133 THR ARG ASP ARG SER ASP GLN HIS ILE GLN LEU GLN LEU SEQRES 4 B 133 SER ALA GLU SER VAL GLY GLU VAL TYR ILE LYS SER THR SEQRES 5 B 133 GLU THR GLY GLN TYR LEU ALA MET ASP THR ASP GLY LEU SEQRES 6 B 133 LEU TYR GLY SER GLN THR PRO ASN GLU GLU CYS LEU PHE SEQRES 7 B 133 LEU GLU ARG LEU GLU GLU ASN HIS TYR ASN THR TYR ILE SEQRES 8 B 133 SER LYS LYS HIS ALA GLU LYS ASN TRP PHE VAL GLY LEU SEQRES 9 B 133 LYS LYS ASN GLY SER CYS LYS ARG GLY PRO ARG THR HIS SEQRES 10 B 133 TYR GLY GLN LYS ALA ILE LEU PHE LEU PRO LEU PRO VAL SEQRES 11 B 133 SER SER ASP HELIX 1 1 PRO A 76 GLY A 81 1 6 HELIX 2 2 ASN A 109 VAL A 111 5 3 HELIX 3 3 ASN B 73 GLU B 75 5 3 HELIX 4 4 SER B 92 GLU B 97 1 6 HELIX 5 5 ARG B 112 THR B 116 5 5 HELIX 6 6 GLN B 120 ILE B 123 5 4 SHEET 1 A 4 GLN A 70 LYS A 74 0 SHEET 2 A 4 GLN A 18 ALA A 27 -1 N LEU A 19 O PHE A 73 SHEET 3 A 4 GLY A 4 ASP A 13 -1 N LYS A 5 O ALA A 27 SHEET 4 A 4 VAL A 116 LEU A 123 -1 O THR A 117 N LEU A 10 SHEET 1 B 4 PHE A 54 GLU A 55 0 SHEET 2 B 4 TYR A 41 LEU A 46 -1 N VAL A 44 O PHE A 54 SHEET 3 B 4 THR A 84 TYR A 90 -1 O ALA A 88 N LYS A 43 SHEET 4 B 4 ILE A 100 PRO A 107 -1 O PHE A 104 N MET A 87 SHEET 1 C 2 LEU B 7 CYS B 9 0 SHEET 2 C 2 PHE B 125 PRO B 127 -1 O LEU B 126 N TYR B 8 SHEET 1 D 2 PHE B 15 ARG B 17 0 SHEET 2 D 2 ASP B 25 THR B 27 -1 O ASP B 25 N ARG B 17 SHEET 1 E 4 SER B 40 SER B 43 0 SHEET 2 E 4 GLU B 46 TYR B 48 -1 O TYR B 48 N SER B 40 SHEET 3 E 4 LEU B 77 GLU B 83 -1 O PHE B 78 N VAL B 47 SHEET 4 E 4 TYR B 87 ILE B 91 -1 O THR B 89 N ARG B 81 SHEET 1 F 2 TYR B 57 LEU B 58 0 SHEET 2 F 2 GLY B 68 SER B 69 -1 O SER B 69 N TYR B 57 SHEET 1 G 2 LEU B 104 LYS B 105 0 SHEET 2 G 2 SER B 109 CYS B 110 -1 O SER B 109 N LYS B 105 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