HEADER RECEPTOR/GLYCOPROTEIN COMPLEX 03-OCT-08 2V5E TITLE THE STRUCTURE OF THE GDNF:CORECEPTOR COMPLEX: INSIGHTS INTO RET TITLE 2 SIGNALLING AND HEPARIN BINDING. COMPND MOL_ID: 1; COMPND 2 MOLECULE: GDNF FAMILY RECEPTOR ALPHA-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 150-349; COMPND 5 SYNONYM: GFR-ALPHA-1, GDNF RECEPTOR ALPHA, GDNFR-ALPHA, TGF-BETA- COMPND 6 RELATED NEUROTROPHIC FACTOR RECEPTOR 1, RET LIGAND 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: RESIDUES 111-211; COMPND 12 SYNONYM: ASTROCYTE-DERIVED TROPHIC FACTOR, HGDNF, ATF; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON_FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFASTBAC; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 16 EXPRESSION_SYSTEM_COMMON_FALL ARMYWORM; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS RECEPTOR-GLYCOPROTEIN COMPLEX, ALTERNATIVE SPLICING, CELL MEMBRANE, KEYWDS 2 GROWTH FACTOR, LIGAND-CORECEPTOR, GPI-ANCHOR, LIPOPROTEIN, KEYWDS 3 POLYMORPHISM, GLYCOPROTEIN, MEMBRANE, RECEPTOR, SECRETED, GFRALPHA1, KEYWDS 4 CLEAVAGE ON PAIR OF BASIC RESIDUES, RECEPTOR-GLYCOPROTEIN COMPLEX KEYWDS 5 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.PARKASH,V.-M.LEPPANEN,H.VIRTANEN,J.-M.JURVANSUU,M.M.BESPALOV, AUTHOR 2 Y.A.SIDOROVA,P.RUNEBERG-ROOS,M.SAARMA,A.GOLDMAN REVDAT 5 13-DEC-23 2V5E 1 HETSYN REVDAT 4 29-JUL-20 2V5E 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 FORMUL SSBOND LINK SITE REVDAT 4 3 1 ATOM REVDAT 3 05-FEB-14 2V5E 1 TITLE SOURCE KEYWDS REMARK REVDAT 3 2 1 VERSN FORMUL SSBOND SITE REVDAT 2 16-DEC-08 2V5E 1 VERSN JRNL REVDAT 1 21-OCT-08 2V5E 0 JRNL AUTH V.PARKASH,V.-M.LEPPANEN,H.VIRTANEN,J.-M.JURVANSUU, JRNL AUTH 2 M.M.BESPALOV,Y.A.SIDOROVA,P.RUNEBERG-ROOS,M.SAARMA,A.GOLDMAN JRNL TITL THE STRUCTURE OF THE GLIAL CELL LINE-DERIVED NEUROTROPHIC JRNL TITL 2 FACTOR-CORECEPTOR COMPLEX: INSIGHTS INTO RET SIGNALING AND JRNL TITL 3 HEPARIN BINDING. JRNL REF J.BIOL.CHEM. V. 283 35164 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18845535 JRNL DOI 10.1074/JBC.M802543200 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0066 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 18089 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 981 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1108 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2348 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.265 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.219 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.822 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2490 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3374 ; 1.206 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 5.496 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;34.563 ;23.565 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 425 ;13.813 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;14.883 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 378 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1822 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1501 ; 2.127 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2412 ; 3.484 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 989 ; 2.314 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 961 ; 3.415 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. BECAUSE OF POOR ELECTRON DENSITY, FOLLOWING RESIDUES REMARK 3 ATOMS WERE MISSING: ARG A 238 CG CD NE CZ NH1 NH2 LYS B 96 CG CD REMARK 3 CE NZ REMARK 4 REMARK 4 2V5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1290035222. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 190 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19071 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.290 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRIES 1AGQ CHAIN A, 2GH0 CHAIN A REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH7.5, 10% PEG-8K, 8% REMARK 280 ETHYLENE GLYCOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.45000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.45000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.85000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 238 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 96 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 ND2 ASN B 49 C1 NAG B 1135 1.45 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 TYR A 235 -60.09 -125.52 REMARK 500 ASN A 276 11.47 80.59 REMARK 500 THR A 298 114.59 -39.85 REMARK 500 SER A 304 -13.22 -49.52 REMARK 500 VAL B 93 76.09 -65.77 REMARK 500 SER B 94 165.09 165.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2060 DISTANCE = 6.34 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 N-ACETYLGLUCOSAMINE (NAG): THE N-GLYCAN IS LINKED TO GDNF REMARK 600 CHAIN B RESIDUE N 49. REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG B 1135 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AGQ RELATED DB: PDB REMARK 900 GLIAL CELL-DERIVED NEUROTROPHIC FACTOR FROM RAT REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE NUMBERING OF THE MATURE GDNF EXCLUDES THE 77 REMARK 999 RESIDUES OF THE PREPRO REGION FROM THE SEQUENCE. DBREF 2V5E A 150 349 UNP Q62997 GFRA1_RAT 150 349 DBREF 2V5E B 34 134 UNP P39905 GDNF_HUMAN 111 211 SEQRES 1 A 200 LYS GLY ASN ASN CYS LEU ASP ALA ALA LYS ALA CYS ASN SEQRES 2 A 200 LEU ASP ASP THR CYS LYS LYS TYR ARG SER ALA TYR ILE SEQRES 3 A 200 THR PRO CYS THR THR SER MET SER ASN GLU VAL CYS ASN SEQRES 4 A 200 ARG ARG LYS CYS HIS LYS ALA LEU ARG GLN PHE PHE ASP SEQRES 5 A 200 LYS VAL PRO ALA LYS HIS SER TYR GLY MET LEU PHE CYS SEQRES 6 A 200 SER CYS ARG ASP ILE ALA CYS THR GLU ARG ARG ARG GLN SEQRES 7 A 200 THR ILE VAL PRO VAL CYS SER TYR GLU GLU ARG GLU ARG SEQRES 8 A 200 PRO ASN CYS LEU SER LEU GLN ASP SER CYS LYS THR ASN SEQRES 9 A 200 TYR ILE CYS ARG SER ARG LEU ALA ASP PHE PHE THR ASN SEQRES 10 A 200 CYS GLN PRO GLU SER ARG SER VAL SER ASN CYS LEU LYS SEQRES 11 A 200 GLU ASN TYR ALA ASP CYS LEU LEU ALA TYR SER GLY LEU SEQRES 12 A 200 ILE GLY THR VAL MET THR PRO ASN TYR VAL ASP SER SER SEQRES 13 A 200 SER LEU SER VAL ALA PRO TRP CYS ASP CYS SER ASN SER SEQRES 14 A 200 GLY ASN ASP LEU GLU ASP CYS LEU LYS PHE LEU ASN PHE SEQRES 15 A 200 PHE LYS ASP ASN THR CYS LEU LYS ASN ALA ILE GLN ALA SEQRES 16 A 200 PHE GLY ASN GLY SER SEQRES 1 B 101 GLN ARG GLY LYS ASN ARG GLY CYS VAL LEU THR ALA ILE SEQRES 2 B 101 HIS LEU ASN VAL THR ASP LEU GLY LEU GLY TYR GLU THR SEQRES 3 B 101 LYS GLU GLU LEU ILE PHE ARG TYR CYS SER GLY SER CYS SEQRES 4 B 101 ASP ALA ALA GLU THR THR TYR ASP LYS ILE LEU LYS ASN SEQRES 5 B 101 LEU SER ARG ASN ARG ARG LEU VAL SER ASP LYS VAL GLY SEQRES 6 B 101 GLN ALA CYS CYS ARG PRO ILE ALA PHE ASP ASP ASP LEU SEQRES 7 B 101 SER PHE LEU ASP ASP ASN LEU VAL TYR HIS ILE LEU ARG SEQRES 8 B 101 LYS HIS SER ALA LYS ARG CYS GLY CYS ILE HET GU4 C 1 27 HET YYJ C 2 28 HET EDO A1351 4 HET EDO A1352 4 HET EDO A1353 4 HET EDO A1354 4 HET NAG B1135 14 HETNAM GU4 2,3,4,6-TETRA-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE HETNAM YYJ 1,3,4,6-TETRA-O-SULFO-BETA-D-FRUCTOFURANOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN GU4 2,3,4,6-TETRA-O-SULFONATO-ALPHA-D-GLUCOSE; 2,3,4,6- HETSYN 2 GU4 TETRA-O-SULFONATO-D-GLUCOSE; 2,3,4,6-TETRA-O- HETSYN 3 GU4 SULFONATO-GLUCOSE HETSYN EDO ETHYLENE GLYCOL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 GU4 C6 H12 O18 S4 FORMUL 3 YYJ C6 H12 O18 S4 FORMUL 4 EDO 4(C2 H6 O2) FORMUL 8 NAG C8 H15 N O6 FORMUL 9 HOH *223(H2 O) HELIX 1 1 ASN A 152 LEU A 163 1 12 HELIX 2 2 ASP A 164 THR A 180 1 17 HELIX 3 3 ASN A 188 VAL A 203 1 16 HELIX 4 4 PRO A 204 CYS A 214 1 11 HELIX 5 5 ASP A 218 GLN A 227 1 10 HELIX 6 6 VAL A 230 TYR A 235 1 6 HELIX 7 7 ASN A 242 THR A 252 1 11 HELIX 8 8 ASN A 253 CYS A 267 1 15 HELIX 9 9 ASN A 281 LEU A 292 1 12 HELIX 10 10 SER A 318 ASN A 320 5 3 HELIX 11 11 ASP A 321 ASP A 334 1 14 HELIX 12 12 ASN A 335 GLY A 348 1 14 HELIX 13 13 THR B 51 GLY B 54 5 4 HELIX 14 14 THR B 77 ASN B 89 1 13 SHEET 1 AA 2 PRO A 299 TYR A 301 0 SHEET 2 AA 2 VAL A 309 PRO A 311 -1 O ALA A 310 N ASN A 300 SHEET 1 BA 2 VAL B 42 ASN B 49 0 SHEET 2 BA 2 GLU B 62 SER B 69 -1 O LEU B 63 N LEU B 48 SHEET 1 BB 2 CYS B 101 PHE B 107 0 SHEET 2 BB 2 ALA B 128 ILE B 134 -1 N LYS B 129 O ALA B 106 SHEET 1 BC 2 LEU B 111 LEU B 114 0 SHEET 2 BC 2 TYR B 120 LEU B 123 -1 O HIS B 121 N PHE B 113 SSBOND 1 CYS A 154 CYS A 214 1555 1555 2.02 SSBOND 2 CYS A 161 CYS A 167 1555 1555 2.04 SSBOND 3 CYS A 178 CYS A 192 1555 1555 2.03 SSBOND 4 CYS A 187 CYS A 233 1555 1555 2.02 SSBOND 5 CYS A 216 CYS A 221 1555 1555 2.05 SSBOND 6 CYS A 243 CYS A 313 1555 1555 2.06 SSBOND 7 CYS A 250 CYS A 256 1555 1555 2.05 SSBOND 8 CYS A 267 CYS A 285 1555 1555 2.05 SSBOND 9 CYS A 277 CYS A 337 1555 1555 2.03 SSBOND 10 CYS A 315 CYS A 325 1555 1555 2.06 SSBOND 11 CYS B 41 CYS B 102 1555 1555 2.03 SSBOND 12 CYS B 68 CYS B 131 1555 1555 2.04 SSBOND 13 CYS B 72 CYS B 133 1555 1555 2.03 LINK C1 GU4 C 1 O2 YYJ C 2 1555 1555 1.46 CRYST1 58.900 75.700 105.500 90.00 91.90 90.00 C 1 2 1 4 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 0.016978 0.000000 0.000563 0.00000 SCALE2 0.000000 0.013210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009484 0.00000