HEADER SIGNALING PROTEIN 09-MAY-12 4F3J TITLE CRYSTAL STRUCTURE OF TRIMERIC GC1Q DOMAIN OF HUMAN C1QTNF5 ASSOCIATED TITLE 2 WITH LATE-ONSET RETINAL MACULAR DEGENERATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT C1Q TUMOR NECROSIS FACTOR-RELATED PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C1QTNF5 GC1Q DOMAIN, UNP RESIDUES 103-243; COMPND 5 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: C1QTNF5, CTRP5, UNQ303/PRO344; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LATE-ONSET RETINAL MACULAR DEGENERATION, L-ORMD, L-ORD, AMD, AGE- KEYWDS 2 RELATED MACULAR DEGENERATION, C1QTNF5, CTRP5, S163R, SER163ARG, KEYWDS 3 DRUSEN, RETINAL DEPOSITES, 10-STRAND JELLY-ROLL FOLD, MFRP, RPE, KEYWDS 4 CILIARY BODY, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.TU,K.PALCZEWSKI REVDAT 3 28-FEB-24 4F3J 1 SEQADV REVDAT 2 12-DEC-12 4F3J 1 JRNL REVDAT 1 07-NOV-12 4F3J 0 JRNL AUTH X.TU,K.PALCZEWSKI JRNL TITL CRYSTAL STRUCTURE OF THE GLOBULAR DOMAIN OF C1QTNF5: JRNL TITL 2 IMPLICATIONS FOR LATE-ONSET RETINAL MACULAR DEGENERATION. JRNL REF J.STRUCT.BIOL. V. 180 439 2012 JRNL REFN ISSN 1047-8477 JRNL PMID 22892318 JRNL DOI 10.1016/J.JSB.2012.07.011 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 24801 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1268 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 46.2770 - 2.7807 0.99 2671 158 0.1434 0.1528 REMARK 3 2 2.7807 - 2.2071 0.99 2637 153 0.1361 0.1586 REMARK 3 3 2.2071 - 1.9281 0.99 2655 154 0.1179 0.1585 REMARK 3 4 1.9281 - 1.7518 1.00 2677 150 0.1059 0.1588 REMARK 3 5 1.7518 - 1.6262 0.99 2684 117 0.1001 0.1595 REMARK 3 6 1.6262 - 1.5304 1.00 2680 144 0.1236 0.1845 REMARK 3 7 1.5304 - 1.4537 0.99 2644 141 0.1452 0.2127 REMARK 3 8 1.4537 - 1.3904 0.98 2662 133 0.2092 0.2573 REMARK 3 9 1.3904 - 1.3370 0.84 2223 118 0.2740 0.3397 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 54.03 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.19140 REMARK 3 B22 (A**2) : 4.19140 REMARK 3 B33 (A**2) : -8.38270 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 1154 REMARK 3 ANGLE : 1.373 1573 REMARK 3 CHIRALITY : 0.095 163 REMARK 3 PLANARITY : 0.007 205 REMARK 3 DIHEDRAL : 13.046 397 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4F3J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072409. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25129 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.337 REMARK 200 RESOLUTION RANGE LOW (A) : 46.277 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.32400 REMARK 200 R SYM FOR SHELL (I) : 0.32400 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 5.0, 2 M NACL, REMARK 280 10% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.31050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.45832 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.27667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 23.31050 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 13.45832 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 46.27667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 23.31050 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 13.45832 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 46.27667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.91665 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 92.55333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 26.91665 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 92.55333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 26.91665 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 92.55333 REMARK 290 REMARK 290 REMARK: NULL 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -46.62100 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -23.31050 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -40.37497 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 301 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 304 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 326 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 346 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 380 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 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 ARG A 161 -9.58 75.63 REMARK 500 ALA A 189 -169.58 -109.42 REMARK 500 GLU A 202 -8.81 81.95 REMARK 500 ALA A 243 -165.98 -118.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 4F3J A 103 243 UNP Q9BXJ0 C1QT5_HUMAN 103 243 SEQADV 4F3J ALA A 102 UNP Q9BXJ0 EXPRESSION TAG SEQADV 4F3J HIS A 244 UNP Q9BXJ0 EXPRESSION TAG SEQADV 4F3J HIS A 245 UNP Q9BXJ0 EXPRESSION TAG SEQADV 4F3J HIS A 246 UNP Q9BXJ0 EXPRESSION TAG SEQADV 4F3J HIS A 247 UNP Q9BXJ0 EXPRESSION TAG SEQADV 4F3J HIS A 248 UNP Q9BXJ0 EXPRESSION TAG SEQADV 4F3J HIS A 249 UNP Q9BXJ0 EXPRESSION TAG SEQRES 1 A 148 ALA ARG SER ALA PHE SER ALA LYS ARG SER GLU SER ARG SEQRES 2 A 148 VAL PRO PRO PRO SER ASP ALA PRO LEU PRO PHE ASP ARG SEQRES 3 A 148 VAL LEU VAL ASN GLU GLN GLY HIS TYR ASP ALA VAL THR SEQRES 4 A 148 GLY LYS PHE THR CYS GLN VAL PRO GLY VAL TYR TYR PHE SEQRES 5 A 148 ALA VAL HIS ALA THR VAL TYR ARG ALA SER LEU GLN PHE SEQRES 6 A 148 ASP LEU VAL LYS ASN GLY GLU SER ILE ALA SER PHE PHE SEQRES 7 A 148 GLN PHE PHE GLY GLY TRP PRO LYS PRO ALA SER LEU SER SEQRES 8 A 148 GLY GLY ALA MET VAL ARG LEU GLU PRO GLU ASP GLN VAL SEQRES 9 A 148 TRP VAL GLN VAL GLY VAL GLY ASP TYR ILE GLY ILE TYR SEQRES 10 A 148 ALA SER ILE LYS THR ASP SER THR PHE SER GLY PHE LEU SEQRES 11 A 148 VAL TYR SER ASP TRP HIS SER SER PRO VAL PHE ALA HIS SEQRES 12 A 148 HIS HIS HIS HIS HIS FORMUL 2 HOH *90(H2 O) CRYST1 46.621 46.621 138.830 90.00 90.00 120.00 H 3 9 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 0.021450 0.012384 0.000000 0.00000 SCALE2 0.000000 0.024768 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007203 0.00000