HEADER TRANSPORT PROTEIN 08-AUG-12 4GIF
TITLE C-TERMINAL COILED-COIL DOMAIN OF TRANSIENT RECEPTOR POTENTIAL CHANNEL
TITLE 2 TRPP3 (PKD2L1, POLYCYSTIN-L)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: POLYCYSTIC KIDNEY DISEASE 2-LIKE 1 PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 699-743;
COMPND 5 SYNONYM: POLYCYSTIN-2 HOMOLOG, POLYCYSTIN-2L1, POLYCYSTIN-L,
COMPND 6 POLYCYSTIN-L1;
COMPND 7 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: PKD2L1, PKD2L, PKDL;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS COILED-COIL, TRIMER, TRP CHANNEL, TRANSIENT RECEPTOR POTENTIAL
KEYWDS 2 CHANNEL, POLYCYSTIC KIDNEY DISEASE (PKD), MEMBRANE, TRANSPORT
KEYWDS 3 PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.YU,M.H.ULBRICH,M.-H.LI,S.DOBBINS,W.K.ZHANG,L.TONG,E.Y.ISACOFF,
AUTHOR 2 J.YANG
REVDAT 2 26-DEC-12 4GIF 1 JRNL
REVDAT 1 05-DEC-12 4GIF 0
JRNL AUTH Y.YU,M.H.ULBRICH,M.H.LI,S.DOBBINS,W.K.ZHANG,L.TONG,
JRNL AUTH 2 E.Y.ISACOFF,J.YANG
JRNL TITL MOLECULAR MECHANISM OF THE ASSEMBLY OF AN ACID-SENSING
JRNL TITL 2 RECEPTOR ION CHANNEL COMPLEX.
JRNL REF NAT COMMUN V. 3 1252 2012
JRNL REFN ESSN 2041-1723
JRNL PMID 23212381
JRNL DOI 10.1038/NCOMMS2257
REMARK 2
REMARK 2 RESOLUTION. 2.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.4
REMARK 3 NUMBER OF REFLECTIONS : 1896
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 SET) : 0.235
REMARK 3 FREE R VALUE : 0.286
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 177
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.90
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2670
REMARK 3 BIN FREE R VALUE : 0.3070
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 14
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 357
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 44
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.013
REMARK 3 BOND ANGLES (DEGREES) : 1.60
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4GIF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-12.
REMARK 100 THE RCSB ID CODE IS RCSB074222.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-FEB-05
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X4C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
REMARK 200 MONOCHROMATOR : SI 111 CHANNEL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1928
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800
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 (%) : 99.1
REMARK 200 DATA REDUNDANCY : 9.000
REMARK 200 R MERGE (I) : 0.05500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 9.20
REMARK 200 R MERGE FOR SHELL (I) : 0.10300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 25.200
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: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 64.80
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 18-20% PEG 8000, 100 MM HEPES, PH 7.5,
REMARK 280 3.9 MM HEGA-9, EVAPORATION, TEMPERATURE 293.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1
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 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z
REMARK 290 6555 -X,-X+Y,-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 -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 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3830 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 10040 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 44.52700
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 22.26350
REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 38.56151
REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
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 A 823 DISTANCE = 6.34 ANGSTROMS
REMARK 525 HOH A 832 DISTANCE = 5.40 ANGSTROMS
REMARK 525 HOH A 833 DISTANCE = 5.71 ANGSTROMS
REMARK 525 HOH A 836 DISTANCE = 6.10 ANGSTROMS
REMARK 525 HOH A 837 DISTANCE = 7.02 ANGSTROMS
REMARK 525 HOH A 839 DISTANCE = 6.35 ANGSTROMS
REMARK 525 HOH A 844 DISTANCE = 5.91 ANGSTROMS
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE CRYSTALLIZED SEQUENCE IS:
REMARK 999 MGSSHHHHHHSQDPKEELAGQKDELQLSDLLKQGYNKTLLRLRLRKERVSDVQKVLQGGEQEIQFEDF
REMARK 999 TNTLRELGHAEHEITELTATFTKFDRDGNRILDEKEQEKMRQDLEEERVALNTEIEKLGRSIVSSPQ
REMARK 999 GKSGPEAARA(GGWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKLKMLERKGW)
REMARK 999 LAPSPGVKEQAIWKHPQPAPAVTPDPWGVQGGQESEVPYKREEEALEERRLSRGEIPTLQRS OF
REMARK 999 WHICH THE SEGMENT LISTED IN SEQRES RECORD WAS OBSERVED IN THE
REMARK 999 ELECTRON DENSITY. THE AUTHORS BELIEVE THAT THE PROTEIN WAS DEGRADED
REMARK 999 DURING THE PROCESS OF CRYSTALLIZATION AND ONLY THE COILED COIL
REMARK 999 DOMAIN WAS CRYSTALLIZATION. TO TEST THIS POSSIBILITY, THE AUTHORS
REMARK 999 COLLECTED SOME CRYSTALS AND RAN IT ON SDS-PAGE. ONLY A DEGRADED
REMARK 999 BAND WITH A MOLECULAR WEIGHT MATCH THE COILED COIL DOMAIN WAS SHOWN
REMARK 999 ON THE GEL. HOWEVER THE AUTHORS DO NOT KNOW HOW MANY AMINO ACIDS
REMARK 999 ARE MISSING FROM THE N- AND C-TERMINUS DUE TO DISORDER.
DBREF 4GIF A 699 743 UNP Q9P0L9 PK2L1_HUMAN 699 743
SEQRES 1 A 45 GLY GLY TRP VAL SER GLY GLU GLU PHE TYR MET LEU THR
SEQRES 2 A 45 ARG ARG VAL LEU GLN LEU GLU THR VAL LEU GLU GLY VAL
SEQRES 3 A 45 VAL SER GLN ILE ASP ALA VAL GLY SER LYS LEU LYS MET
SEQRES 4 A 45 LEU GLU ARG LYS GLY TRP
FORMUL 2 HOH *44(H2 O)
HELIX 1 1 SER A 703 SER A 733 1 31
HELIX 2 2 SER A 733 GLY A 742 1 10
CRYST1 44.527 44.527 62.306 90.00 90.00 120.00 P 3 2 1 6
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 0.022458 0.012966 0.000000 0.00000
SCALE2 0.000000 0.025933 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016050 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
