HEADER SIGNALING PROTEIN/INHIBITOR 21-FEB-20 6VXG TITLE STRUCTURE OF THE C-TERMINAL DOMAIN OF RAGE AND ITS INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL RESIDUES 363-404; COMPND 5 SYNONYM: RECEPTOR FOR ADVANCED GLYCOSYLATION END PRODUCTS; COMPND 6 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS INHIBITOR, COMPLEX, DIABETES, RECEPTOR FOR ADVANCED GLYCATED END KEYWDS 2 PRODUCTS, INFLAMMATION, SIGNALING PROTEIN, SIGNALING PROTEIN- KEYWDS 3 INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.RAMIREZ,A.SHEKHTMAN REVDAT 3 15-MAY-24 6VXG 1 REMARK REVDAT 2 09-MAR-22 6VXG 1 JRNL REVDAT 1 24-FEB-21 6VXG 0 JRNL AUTH M.B.MANIGRASSO,P.RABBANI,L.EGANA-GORRONO,N.QUADRI,L.FRYE, JRNL AUTH 2 B.ZHOU,S.REVERDATTO,L.S.RAMIREZ,S.DANSEREAU,J.PAN,H.LI, JRNL AUTH 3 V.D.D'AGATI,R.RAMASAMY,R.J.DEVITA,A.SHEKHTMAN,A.M.SCHMIDT JRNL TITL SMALL-MOLECULE ANTAGONISM OF THE INTERACTION OF THE RAGE JRNL TITL 2 CYTOPLASMIC DOMAIN WITH DIAPH1 REDUCES DIABETIC JRNL TITL 3 COMPLICATIONS IN MICE. JRNL REF SCI TRANSL MED V. 13 F7084 2021 JRNL REFN ESSN 1946-6242 JRNL PMID 34818060 JRNL DOI 10.1126/SCITRANSLMED.ABF7084 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.RAI,A.Y.MALDONADO,D.S.BURZ,S.REVERDATTO,S.F.YAN, REMARK 1 AUTH 2 A.M.SCHMIDT,A.SHEKHTMAN REMARK 1 TITL SIGNAL TRANSDUCTION IN RECEPTOR FOR ADVANCED GLYCATION END REMARK 1 TITL 2 PRODUCTS (RAGE): SOLUTION STRUCTURE OF C-TERMINAL RAGE REMARK 1 TITL 3 (CTRAGE) AND ITS BINDING TO MDIA1. REMARK 1 REF J. BIOL. CHEM. V. 287 5133 2012 REMARK 1 REFN ESSN 1083-351X REMARK 1 PMID 22194616 REMARK 1 DOI 10.1074/JBC.M111.277731 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.5 REMARK 3 AUTHORS : GUNTERT P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VXG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000246866. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 300 UM [U-100% 13C; U-100% 15N] REMARK 210 C-TERMINAL RAGE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D 1H-15N NOESY; 3D 1H REMARK 210 -13C NOESY ALIPHATIC; 3D HNCACB; REMARK 210 3D HN(CO)CA; 3D 1H-15N TOCSY; 3D REMARK 210 1H-13C NOESY AROMATIC; 3D REMARK 210 CBCA(CO)NH; 3D HCCCONH; 3D HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.9.1.7, CYANA 3.98.5 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 ASN A 17 REMARK 465 GLN A 18 REMARK 465 GLU A 19 REMARK 465 GLU A 20 REMARK 465 GLU A 21 REMARK 465 GLU A 22 REMARK 465 GLU A 23 REMARK 465 ARG A 24 REMARK 465 ALA A 25 REMARK 465 GLU A 26 REMARK 465 LEU A 27 REMARK 465 ASN A 28 REMARK 465 GLN A 29 REMARK 465 SER A 30 REMARK 465 GLU A 31 REMARK 465 GLU A 32 REMARK 465 PRO A 33 REMARK 465 GLU A 34 REMARK 465 ALA A 35 REMARK 465 GLY A 36 REMARK 465 GLU A 37 REMARK 465 SER A 38 REMARK 465 SER A 39 REMARK 465 THR A 40 REMARK 465 GLY A 41 REMARK 465 GLY A 42 REMARK 465 PRO A 43 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 GLU A 11 -72.87 72.37 REMARK 500 1 ARG A 12 74.30 -152.63 REMARK 500 1 ALA A 14 163.37 -46.26 REMARK 500 1 PRO A 15 98.33 -69.78 REMARK 500 2 GLU A 11 -67.26 72.97 REMARK 500 2 ARG A 12 91.98 -164.49 REMARK 500 2 ALA A 14 165.48 -49.03 REMARK 500 2 PRO A 15 97.10 -69.62 REMARK 500 3 GLU A 11 -70.99 72.55 REMARK 500 3 ARG A 12 77.46 -164.56 REMARK 500 3 ALA A 14 163.88 -47.06 REMARK 500 3 PRO A 15 95.51 -69.70 REMARK 500 4 TRP A 2 141.75 -173.80 REMARK 500 4 GLN A 3 62.22 61.65 REMARK 500 4 GLU A 11 -66.50 75.61 REMARK 500 4 ARG A 12 31.65 -161.30 REMARK 500 4 ALA A 14 159.86 -49.32 REMARK 500 4 PRO A 15 83.10 -69.80 REMARK 500 5 GLU A 11 -66.55 72.77 REMARK 500 5 ARG A 12 68.52 -171.70 REMARK 500 5 PRO A 15 99.32 -69.84 REMARK 500 6 GLU A 11 -70.02 73.92 REMARK 500 6 ARG A 12 87.22 -160.75 REMARK 500 6 PRO A 15 94.89 -69.73 REMARK 500 7 GLU A 10 -3.37 -142.79 REMARK 500 7 GLU A 11 -74.74 69.24 REMARK 500 7 ARG A 12 -164.71 -111.95 REMARK 500 7 ALA A 14 81.85 -163.97 REMARK 500 7 PRO A 15 66.12 -69.78 REMARK 500 8 GLU A 11 -75.82 69.66 REMARK 500 8 PRO A 15 90.64 -69.80 REMARK 500 9 GLU A 11 -69.48 73.94 REMARK 500 9 ARG A 12 81.98 -153.82 REMARK 500 9 PRO A 15 99.78 -69.78 REMARK 500 10 GLU A 11 -74.88 70.99 REMARK 500 10 PRO A 15 89.21 -69.69 REMARK 500 11 GLU A 11 -75.47 67.37 REMARK 500 11 ARG A 12 70.44 -168.92 REMARK 500 11 PRO A 15 98.87 -69.68 REMARK 500 12 GLU A 11 -66.85 72.32 REMARK 500 12 ARG A 12 69.12 -163.26 REMARK 500 12 ALA A 14 165.72 -48.79 REMARK 500 13 GLU A 11 -70.44 72.32 REMARK 500 13 ALA A 14 164.69 -49.04 REMARK 500 14 GLU A 11 -70.71 73.33 REMARK 500 14 ARG A 12 88.43 -153.36 REMARK 500 14 PRO A 15 86.31 -69.75 REMARK 500 15 GLU A 10 -32.68 -164.35 REMARK 500 15 GLU A 11 -71.71 77.89 REMARK 500 15 ALA A 14 126.54 179.67 REMARK 500 REMARK 500 THIS ENTRY HAS 67 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RQV A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LMB RELATED DB: PDB REMARK 900 RELATED ID: 30726 RELATED DB: BMRB REMARK 900 STRUCTURE OF THE C-TERMINAL DOMAIN OF RAGE AND ITS INHIBITOR DBREF 6VXG A 2 43 UNP Q15109 RAGE_HUMAN 363 404 SEQADV 6VXG MET A 1 UNP Q15109 INITIATING METHIONINE SEQRES 1 A 43 MET TRP GLN ARG ARG GLN ARG ARG GLY GLU GLU ARG LYS SEQRES 2 A 43 ALA PRO GLU ASN GLN GLU GLU GLU GLU GLU ARG ALA GLU SEQRES 3 A 43 LEU ASN GLN SER GLU GLU PRO GLU ALA GLY GLU SER SER SEQRES 4 A 43 THR GLY GLY PRO HET RQV A 101 51 HETNAM RQV N-(4-{7-CYANO-4-[(MORPHOLIN-4-YL)METHYL]QUINOLIN-2- HETNAM 2 RQV YL}PHENYL)ACETAMIDE FORMUL 2 RQV C23 H22 N4 O2 SITE 1 AC1 5 ARG A 4 ARG A 5 ARG A 8 LYS A 13 SITE 2 AC1 5 GLU A 16 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