HEADER SIGNALING PROTEIN 11-JUN-18 6DRF TITLE STRUCTURE OF HUMAN RETINAL DEGENERATION 3(RD3) PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN RD3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 19-153; COMPND 5 SYNONYM: RETINAL DEGENERATION PROTEIN 3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RD3, C1ORF36; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SENSORY TRANSDUCTION, VISION, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Q.YU,S.LIM,I.PESHENKO,D.CUDIA,A.M.DIZHOOR,J.B.AMES REVDAT 5 15-MAY-24 6DRF 1 REMARK REVDAT 4 14-JUN-23 6DRF 1 REMARK REVDAT 3 11-DEC-19 6DRF 1 REMARK REVDAT 2 27-FEB-19 6DRF 1 JRNL REMARK DBREF SEQADV REVDAT 2 2 1 HELIX ATOM REVDAT 1 06-FEB-19 6DRF 0 JRNL AUTH I.V.PESHENKO,Q.YU,S.LIM,D.CUDIA,A.M.DIZHOOR,J.B.AMES JRNL TITL RETINAL DEGENERATION 3 (RD3) PROTEIN, A RETINAL GUANYLYL JRNL TITL 2 CYCLASE REGULATOR, FORMS A MONOMERIC AND ELONGATED JRNL TITL 3 FOUR-HELIX BUNDLE. JRNL REF J. BIOL. CHEM. V. 294 2318 2019 JRNL REFN ESSN 1083-351X JRNL PMID 30559291 JRNL DOI 10.1074/JBC.RA118.006106 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.47 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DRF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234992. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-15N] HUMAN RD3, 20 MM REMARK 210 D11 TRIS, 3 MM D10 DTT, 50 UM REMARK 210 D12 EDTA, 0.04 % W/V SODIUM REMARK 210 AZIDE, 93% H2O/7% D2O; 0.9 MM [U- REMARK 210 13C; U-15N] HUMAN RD3, 20 MM D11 REMARK 210 TRIS, 3 MM D10 DTT, 50 UM D12 REMARK 210 EDTA, 0.04 % W/V SODIUM AZIDE, REMARK 210 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HNCO; REMARK 210 3D HCCH-TOCSY; 3D CCCONH; 3D REMARK 210 HCCCONH; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; 3D 1H-15N TOCSY; 2D REMARK 210 1H-13C HSQC 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 : NMRPIPE 8.9, SPARKY 3.134, X REMARK 210 -PLOR NIH 2.47 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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 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 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 ARG A 52 -152.71 64.80 REMARK 500 1 LYS A 53 -22.03 78.20 REMARK 500 1 THR A 56 -67.70 72.98 REMARK 500 1 SER A 61 15.28 -178.47 REMARK 500 1 ALA A 64 -8.26 -144.17 REMARK 500 1 PRO A 67 -82.95 -84.09 REMARK 500 1 ASP A 68 -61.69 69.84 REMARK 500 1 GLU A 108 149.68 75.53 REMARK 500 1 GLU A 110 124.11 175.83 REMARK 500 1 ARG A 145 97.89 -163.53 REMARK 500 1 GLU A 158 -177.50 63.90 REMARK 500 2 ARG A 52 -155.90 67.79 REMARK 500 2 ALA A 64 -14.69 69.59 REMARK 500 2 SER A 65 127.87 62.24 REMARK 500 2 ASP A 68 67.85 61.52 REMARK 500 2 LEU A 73 73.62 -105.65 REMARK 500 2 GLU A 108 145.90 75.04 REMARK 500 2 GLU A 110 108.62 -175.84 REMARK 500 2 ARG A 140 -87.57 -94.43 REMARK 500 2 GLN A 141 -92.82 73.44 REMARK 500 2 TRP A 142 -82.80 57.83 REMARK 500 2 SER A 149 -44.64 70.79 REMARK 500 2 ALA A 157 111.26 -160.56 REMARK 500 3 THR A 56 -44.55 66.76 REMARK 500 3 LEU A 63 -65.43 -132.52 REMARK 500 3 ASP A 68 -67.83 -90.72 REMARK 500 3 GLU A 108 129.93 77.62 REMARK 500 3 GLU A 110 102.50 -168.58 REMARK 500 3 ARG A 140 140.10 81.80 REMARK 500 3 TRP A 142 -63.85 70.81 REMARK 500 3 ARG A 145 104.75 -164.73 REMARK 500 3 ARG A 147 -150.73 -122.58 REMARK 500 3 THR A 152 10.26 -152.62 REMARK 500 3 GLU A 156 103.20 60.52 REMARK 500 4 ARG A 52 -66.33 69.71 REMARK 500 4 VAL A 58 126.17 71.87 REMARK 500 4 ALA A 64 -40.22 82.44 REMARK 500 4 PRO A 67 -72.91 -62.97 REMARK 500 4 GLU A 108 161.10 72.91 REMARK 500 4 GLU A 110 95.78 -163.69 REMARK 500 4 ARG A 140 36.75 -97.26 REMARK 500 4 TRP A 142 -56.85 -125.23 REMARK 500 4 ARG A 147 -59.01 -174.92 REMARK 500 4 LEU A 150 107.96 69.25 REMARK 500 4 THR A 152 -60.15 74.81 REMARK 500 4 GLU A 158 151.61 72.70 REMARK 500 5 ARG A 52 177.88 74.21 REMARK 500 5 LYS A 53 69.89 63.90 REMARK 500 5 TYR A 60 -34.22 -174.98 REMARK 500 5 ASP A 68 -55.17 74.34 REMARK 500 REMARK 500 THIS ENTRY HAS 110 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27305 RELATED DB: BMRB DBREF 6DRF A 19 153 UNP Q7Z3Z2 RD3_HUMAN 19 153 SEQADV 6DRF ALA A 18 UNP Q7Z3Z2 EXPRESSION TAG SEQADV 6DRF ASP A 68 UNP Q7Z3Z2 ARG 68 ENGINEERED MUTATION SEQADV 6DRF GLU A 154 UNP Q7Z3Z2 EXPRESSION TAG SEQADV 6DRF THR A 155 UNP Q7Z3Z2 EXPRESSION TAG SEQADV 6DRF GLU A 156 UNP Q7Z3Z2 EXPRESSION TAG SEQADV 6DRF ALA A 157 UNP Q7Z3Z2 EXPRESSION TAG SEQADV 6DRF GLU A 158 UNP Q7Z3Z2 EXPRESSION TAG SEQADV 6DRF ILE A 159 UNP Q7Z3Z2 EXPRESSION TAG SEQADV 6DRF ASP A 160 UNP Q7Z3Z2 EXPRESSION TAG SEQRES 1 A 143 ALA ARG SER PRO ALA GLU MET VAL LEU GLU THR LEU MET SEQRES 2 A 143 MET GLU LEU THR GLY GLN MET ARG GLU ALA GLU ARG GLN SEQRES 3 A 143 GLN ARG GLU ARG SER ASN ALA VAL ARG LYS VAL CYS THR SEQRES 4 A 143 GLY VAL ASP TYR SER TRP LEU ALA SER THR PRO ASP SER SEQRES 5 A 143 THR TYR ASP LEU SER PRO ILE GLU ARG LEU GLN LEU GLU SEQRES 6 A 143 ASP VAL CYS VAL LYS ILE HIS PRO SER TYR CYS GLY PRO SEQRES 7 A 143 ALA ILE LEU ARG PHE ARG GLN LEU LEU ALA GLU GLN GLU SEQRES 8 A 143 PRO GLU VAL GLN GLU VAL SER GLN LEU PHE ARG SER VAL SEQRES 9 A 143 LEU GLN GLU VAL LEU GLU ARG MET LYS GLN GLU GLU GLU SEQRES 10 A 143 ALA HIS LYS LEU THR ARG GLN TRP SER LEU ARG PRO ARG SEQRES 11 A 143 GLY SER LEU ALA THR PHE GLU THR GLU ALA GLU ILE ASP HELIX 1 AA1 SER A 20 ARG A 52 1 33 HELIX 2 AA2 SER A 74 LYS A 87 1 14 HELIX 3 AA3 HIS A 89 SER A 91 5 3 HELIX 4 AA4 TYR A 92 GLU A 108 1 17 HELIX 5 AA5 GLU A 110 ARG A 140 1 31 HELIX 6 AA6 GLN A 141 LEU A 144 5 4 HELIX 7 AA7 ALA A 151 THR A 155 5 5 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