HEADER SIGNALING PROTEIN/METAL BINDING PROTEIN 19-JAN-14 2MJW TITLE STRUCTURAL INSIGHTS INTO CALCIUM BOUND S100P - V DOMAIN OF THE TITLE 2 RECEPTOR FOR ADVANCED GLYCATION END PRODUCTS (RAGE) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 23-121; COMPND 5 SYNONYM: RECEPTOR FOR ADVANCED GLYCOSYLATION END PRODUCTS; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN S100-P; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: UNP RESIDUES 1-94; COMPND 11 SYNONYM: MIGRATION-INDUCING GENE 9 PROTEIN, MIG9, PROTEIN S100-E, COMPND 12 S100 CALCIUM-BINDING PROTEIN P; 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: AGER, RAGE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-15B(+); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: S100P, S100E; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: (PET20B+) KEYWDS S100P V DOMAIN OF RAGE, SIGNALING PROTEIN-METAL BINDING PROTEIN KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR P.S.RAO REVDAT 2 14-JUN-23 2MJW 1 REMARK SEQADV REVDAT 1 05-NOV-14 2MJW 0 JRNL AUTH S.R.PENUMUTCHU,R.H.CHOU,C.YU JRNL TITL STRUCTURAL INSIGHTS INTO CALCIUM-BOUND S100P AND THE V JRNL TITL 2 DOMAIN OF THE RAGE COMPLEX. JRNL REF PLOS ONE V. 9 03947 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 25084534 JRNL DOI 10.1371/JOURNAL.PONE.0103947 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY, HADDOCK REMARK 3 AUTHORS : GODDARD (SPARKY) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MJW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000103701. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-100% 13C; U-100% 15N] REMARK 210 ENTITY_1-1, 0.6 MM [U-100% 13C; REMARK 210 U-100% 15N] ENTITY_2-2, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCACB; REMARK 210 3D CBCA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HBHA(CO)NH; 3D 1H-13C NOESY; 3D REMARK 210 HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, C 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 OD2 ASP D 107 HH21 ARG D 111 1.55 REMARK 500 OXT LEU D 188 HZ1 LYS C 110 1.56 REMARK 500 HZ1 LYS B 30 OD1 ASP B 55 1.57 REMARK 500 HZ1 LYS D 124 OD1 ASP D 149 1.58 REMARK 500 OD2 ASP D 149 HZ2 LYS D 153 1.59 REMARK 500 HZ1 LYS B 34 OE1 GLU B 38 1.59 REMARK 500 HG1 THR D 96 OE1 GLU D 99 1.59 REMARK 500 OD2 ASP B 13 HH21 ARG B 17 1.60 REMARK 500 OE1 GLU A 94 HH21 ARG A 114 1.60 REMARK 500 HH12 ARG B 17 OE2 GLU D 97 1.60 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 THR A 58 96.81 67.33 REMARK 500 1 ALA A 60 44.91 -101.46 REMARK 500 1 LYS A 62 121.07 -170.18 REMARK 500 1 PRO A 71 76.77 -67.67 REMARK 500 1 TRP A 72 -32.98 177.93 REMARK 500 1 ARG A 104 40.29 -76.93 REMARK 500 1 LYS A 110 62.92 -102.48 REMARK 500 1 LYS B 39 -55.13 -136.23 REMARK 500 1 LYS D 133 -56.85 -135.18 REMARK 500 1 LYS D 143 13.40 -146.88 REMARK 500 1 LYS D 145 -106.51 -82.67 REMARK 500 1 ASP D 146 -85.91 45.80 REMARK 500 1 ASP D 156 108.49 -59.70 REMARK 500 1 PRO C 42 -165.92 -77.68 REMARK 500 1 LYS C 43 48.71 -85.87 REMARK 500 1 THR C 58 95.62 68.31 REMARK 500 1 LYS C 62 123.58 -170.68 REMARK 500 1 PRO C 71 84.37 -66.59 REMARK 500 1 TRP C 72 -38.49 176.73 REMARK 500 1 LYS C 110 58.01 -103.70 REMARK 500 2 LYS A 62 123.56 -173.03 REMARK 500 2 LYS B 39 -54.61 -133.53 REMARK 500 2 LYS B 49 24.53 -140.84 REMARK 500 2 LYS D 133 -55.27 -131.90 REMARK 500 2 ASP D 144 -163.69 -114.71 REMARK 500 2 LYS D 145 -107.43 -84.76 REMARK 500 2 ASP D 146 -85.28 54.27 REMARK 500 2 LYS C 62 118.74 -173.54 REMARK 500 3 PRO A 42 -157.77 -80.18 REMARK 500 3 LYS A 43 35.66 -86.42 REMARK 500 3 LYS A 62 129.04 -174.19 REMARK 500 3 GLU A 108 -164.05 -123.85 REMARK 500 3 LYS B 39 -52.70 -132.91 REMARK 500 3 LYS B 49 17.88 -153.98 REMARK 500 3 THR D 96 -174.73 -69.91 REMARK 500 3 LYS D 133 -55.53 -125.02 REMARK 500 3 LYS D 145 -127.64 -78.30 REMARK 500 3 ASP D 146 -77.21 64.96 REMARK 500 3 PRO C 42 -163.76 -79.87 REMARK 500 3 LYS C 43 47.19 -82.23 REMARK 500 3 LYS C 62 129.70 -177.82 REMARK 500 3 GLN C 67 14.74 -145.04 REMARK 500 3 ALA C 88 114.23 -163.21 REMARK 500 3 GLU C 108 -163.77 -121.00 REMARK 500 4 ALA A 60 40.16 -82.29 REMARK 500 4 LYS A 62 130.12 -178.14 REMARK 500 4 GLN A 67 32.18 -140.86 REMARK 500 4 ARG A 104 1.73 -68.52 REMARK 500 4 LYS B 39 -50.37 -127.37 REMARK 500 4 LYS B 49 17.39 -157.60 REMARK 500 REMARK 500 THIS ENTRY HAS 156 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19739 RELATED DB: BMRB REMARK 900 RELATED ID: 1J55 RELATED DB: PDB REMARK 900 USED FOR MODEL BUILDING REMARK 900 RELATED ID: 2E5E RELATED DB: PDB REMARK 900 USED FOR MODEL BUILDING DBREF 2MJW A 23 121 UNP Q15109 RAGE_HUMAN 23 121 DBREF 2MJW B 1 94 UNP P25815 S100P_HUMAN 1 94 DBREF 2MJW D 95 188 UNP P25815 S100P_HUMAN 1 94 DBREF 2MJW C 23 121 UNP Q15109 RAGE_HUMAN 23 121 SEQADV 2MJW ALA A 21 UNP Q15109 EXPRESSION TAG SEQADV 2MJW MET A 22 UNP Q15109 EXPRESSION TAG SEQADV 2MJW ALA C 21 UNP Q15109 EXPRESSION TAG SEQADV 2MJW MET C 22 UNP Q15109 EXPRESSION TAG SEQRES 1 A 101 ALA MET ALA GLN ASN ILE THR ALA ARG ILE GLY GLU PRO SEQRES 2 A 101 LEU VAL LEU LYS CYS LYS GLY ALA PRO LYS LYS PRO PRO SEQRES 3 A 101 GLN ARG LEU GLU TRP LYS LEU ASN THR GLY ARG THR GLU SEQRES 4 A 101 ALA TRP LYS VAL LEU SER PRO GLN GLY GLY GLY PRO TRP SEQRES 5 A 101 ASP SER VAL ALA ARG VAL LEU PRO ASN GLY SER LEU PHE SEQRES 6 A 101 LEU PRO ALA VAL GLY ILE GLN ASP GLU GLY ILE PHE ARG SEQRES 7 A 101 CYS GLN ALA MET ASN ARG ASN GLY LYS GLU THR LYS SER SEQRES 8 A 101 ASN TYR ARG VAL ARG VAL TYR GLN ILE PRO SEQRES 1 B 94 MET THR GLU LEU GLU THR ALA MET GLY MET ILE ILE ASP SEQRES 2 B 94 VAL PHE SER ARG TYR SER GLY SER GLU GLY SER THR GLN SEQRES 3 B 94 THR LEU THR LYS GLY GLU LEU LYS VAL LEU MET GLU LYS SEQRES 4 B 94 GLU LEU PRO GLY PHE LEU GLN SER GLY LYS ASP LYS ASP SEQRES 5 B 94 ALA VAL ASP LYS LEU LEU LYS ASP LEU ASP ALA ASN GLY SEQRES 6 B 94 ASP ALA GLN VAL ASP PHE SER GLU PHE ILE VAL PHE VAL SEQRES 7 B 94 ALA ALA ILE THR SER ALA CYS HIS LYS TYR PHE GLU LYS SEQRES 8 B 94 ALA GLY LEU SEQRES 1 D 94 MET THR GLU LEU GLU THR ALA MET GLY MET ILE ILE ASP SEQRES 2 D 94 VAL PHE SER ARG TYR SER GLY SER GLU GLY SER THR GLN SEQRES 3 D 94 THR LEU THR LYS GLY GLU LEU LYS VAL LEU MET GLU LYS SEQRES 4 D 94 GLU LEU PRO GLY PHE LEU GLN SER GLY LYS ASP LYS ASP SEQRES 5 D 94 ALA VAL ASP LYS LEU LEU LYS ASP LEU ASP ALA ASN GLY SEQRES 6 D 94 ASP ALA GLN VAL ASP PHE SER GLU PHE ILE VAL PHE VAL SEQRES 7 D 94 ALA ALA ILE THR SER ALA CYS HIS LYS TYR PHE GLU LYS SEQRES 8 D 94 ALA GLY LEU SEQRES 1 C 101 ALA MET ALA GLN ASN ILE THR ALA ARG ILE GLY GLU PRO SEQRES 2 C 101 LEU VAL LEU LYS CYS LYS GLY ALA PRO LYS LYS PRO PRO SEQRES 3 C 101 GLN ARG LEU GLU TRP LYS LEU ASN THR GLY ARG THR GLU SEQRES 4 C 101 ALA TRP LYS VAL LEU SER PRO GLN GLY GLY GLY PRO TRP SEQRES 5 C 101 ASP SER VAL ALA ARG VAL LEU PRO ASN GLY SER LEU PHE SEQRES 6 C 101 LEU PRO ALA VAL GLY ILE GLN ASP GLU GLY ILE PHE ARG SEQRES 7 C 101 CYS GLN ALA MET ASN ARG ASN GLY LYS GLU THR LYS SER SEQRES 8 C 101 ASN TYR ARG VAL ARG VAL TYR GLN ILE PRO HELIX 1 1 THR B 2 SER B 19 1 18 HELIX 2 2 THR B 29 GLU B 38 1 10 HELIX 3 3 LYS B 51 ASP B 62 1 12 HELIX 4 4 ASP B 70 GLY B 93 1 24 HELIX 5 5 THR D 96 ARG D 111 1 16 HELIX 6 6 THR D 123 GLU D 132 1 10 HELIX 7 7 ASP D 146 ASP D 156 1 11 HELIX 8 8 PHE D 165 LYS D 185 1 21 SHEET 1 A 4 GLN A 24 ALA A 28 0 SHEET 2 A 4 TYR A 113 VAL A 117 1 O ARG A 116 N ALA A 28 SHEET 3 A 4 ILE A 96 ARG A 98 -1 N PHE A 97 O TYR A 113 SHEET 4 A 4 LYS A 52 ASN A 54 -1 N ASN A 54 O ILE A 96 SHEET 1 B 3 GLU A 32 LYS A 37 0 SHEET 2 B 3 SER A 83 VAL A 89 -1 O LEU A 84 N LEU A 36 SHEET 3 B 3 ARG A 77 LEU A 79 -1 N LEU A 79 O SER A 83 SHEET 1 C 2 THR D 121 LEU D 122 0 SHEET 2 C 2 VAL D 163 ASP D 164 -1 O VAL D 163 N LEU D 122 SHEET 1 D 4 GLN C 24 ALA C 28 0 SHEET 2 D 4 TYR C 113 VAL C 117 1 O ARG C 116 N ALA C 28 SHEET 3 D 4 ILE C 96 ARG C 98 -1 N PHE C 97 O TYR C 113 SHEET 4 D 4 LYS C 52 ASN C 54 -1 N ASN C 54 O ILE C 96 SHEET 1 E 3 GLU C 32 LYS C 37 0 SHEET 2 E 3 SER C 83 VAL C 89 -1 O LEU C 84 N LEU C 36 SHEET 3 E 3 ARG C 77 LEU C 79 -1 N LEU C 79 O SER C 83 SSBOND 1 CYS A 38 CYS A 99 1555 1555 2.04 SSBOND 2 CYS C 38 CYS C 99 1555 1555 2.03 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