PDB Short entry for 1GQ5 HEADER SIGNALING PROTEIN 20-NOV-01 1GQ5 TITLE STRUCTURAL DETERMINANTS OF THE NHERF INTERACTION WITH BETA2-AR AND TITLE 2 PDGFR COMPND MOL_ID: 1; COMPND 2 MOLECULE: EZRIN-RADIXIN-MOESIN BINDING PHOSPHOPROTEIN-50; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ1 DOMAIN, RESIDUES 11-94; COMPND 5 SYNONYM: NA+/H+ EXCHANGER REGULATORY FACTOR; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS SIGNALING PROTEIN, PDZ, BETA2-ADRENERGIC RECEPTOR, PDGFR, NHERF, KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.KARTHIKEYAN,T.LEUNG,J.A.A.LADIAS REVDAT 3 13-DEC-23 1GQ5 1 REMARK REVDAT 2 24-FEB-09 1GQ5 1 VERSN REVDAT 1 14-NOV-02 1GQ5 0 JRNL AUTH S.KARTHIKEYAN,T.LEUNG,J.A.A.LADIAS JRNL TITL STRUCTURAL DETERMINANTS OF THE NA+/H+ EXCHANGER REGULATORY JRNL TITL 2 FACTOR INTERACTION WITH THE BETA 2 ADRENERGIC AND JRNL TITL 3 PLATELET-DERIVED GROWTH FACTOR RECEPTORS JRNL REF J.BIOL.CHEM. V. 277 18973 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11882663 JRNL DOI 10.1074/JBC.M201507200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.KARTHIKEYAN,T.LEUNG,J.A.A.LADIAS REMARK 1 TITL STRUCTURAL BASIS OF THE NA+/H+ EXCHANGER REGULATORY FACTOR REMARK 1 TITL 2 PDZ1 INTERACTION WITH THE CARBOXYL-TERMINAL REGION OF THE REMARK 1 TITL 3 CYSTIC FIBROSIS TRANSMEMBRABE CONDUCTANCE REGULATOR REMARK 1 REF J.BIOL.CHEM. V. 276 19683 2001 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 11304524 REMARK 1 DOI 10.1074/JBC.C100154200 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.KARTHIKEYAN,T.LEUNG,G.BIRRANE,G.WEBSTER,J.A.A.LADIAS REMARK 1 TITL CRYSTAL STRUCTURE OF THE PDZ1 DOMAIN OF HUMAN NA+/ H+ REMARK 1 TITL 2 EXCHANGER REGULATORY FACTOR PROVIDES INSIGHTS INTO THE REMARK 1 TITL 3 MECHANISM OF CARBOXYL-TERMINAL LEUCINE RECOGNITION BY CLASS REMARK 1 TITL 4 I PDZ DOMAINS REMARK 1 REF J.MOL.BIOL. V. 308 963 2001 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11352585 REMARK 1 DOI 10.1006/JMBI.2001.4634 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4690 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 268 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 682 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.37000 REMARK 3 B22 (A**2) : 1.37000 REMARK 3 B33 (A**2) : -2.05000 REMARK 3 B12 (A**2) : 0.68000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.325 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.234 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.203 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.267 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GQ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1290009025. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-01 REMARK 200 TEMPERATURE (KELVIN) : 115.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4966 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 26.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1I92 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, SODIUM CHLORIDE, PH REMARK 280 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 22.22667 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 44.45333 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 44.45333 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 22.22667 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 GLU A 31 CG CD OE1 OE2 REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 LYS A 69 CG CD CE NZ 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 ASN A 22 37.67 -96.22 REMARK 500 LYS A 32 132.23 -39.88 REMARK 500 LEU A 41 70.09 51.37 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 CL A1100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I92 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF THE NHERF PDZ1-CFTR INTERACTION REMARK 900 RELATED ID: 1GQ5 RELATED DB: PDB REMARK 900 STRUCTURAL DETERMINANTS OF THE NHERF INTERACTION WITH BETA2AR AND REMARK 900 PDGFR REMARK 900 RELATED ID: 1G9O RELATED DB: PDB REMARK 900 FIRST PDZ DOMAIN OF THE HUMAN NA+/H+ EXCHANGER REGULATORY FACTOR REMARK 900 RELATED ID: 1LWP RELATED DB: PDB REMARK 900 BETA PLATELET-DERIVED GROWTH FACTOR RECEPTOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 9-10 ARE CLONING ARTIFACTS. THE AMINO ACID RESIDUES REMARK 999 95-99 OF PDZ1 CORRESPOND TO THE CARBOXYL-TERMINAL REGION REMARK 999 1102-1106 OF PDGFR AND SERVE AS A LIGAND FOR A NEIGHBOURING REMARK 999 PDZ1 MOLECULE IN THE CRYSTAL. DBREF 1GQ5 A 9 10 PDB 1GQ5 1GQ5 9 10 DBREF 1GQ5 A 11 94 UNP O14745 O14745 11 94 DBREF 1GQ5 A 95 99 UNP P09619 P09619 1102 1106 SEQRES 1 A 91 GLY MET LEU PRO ARG LEU CYS CYS LEU GLU LYS GLY PRO SEQRES 2 A 91 ASN GLY TYR GLY PHE HIS LEU HIS GLY GLU LYS GLY LYS SEQRES 3 A 91 LEU GLY GLN TYR ILE ARG LEU VAL GLU PRO GLY SER PRO SEQRES 4 A 91 ALA GLU LYS ALA GLY LEU LEU ALA GLY ASP ARG LEU VAL SEQRES 5 A 91 GLU VAL ASN GLY GLU ASN VAL GLU LYS GLU THR HIS GLN SEQRES 6 A 91 GLN VAL VAL SER ARG ILE ARG ALA ALA LEU ASN ALA VAL SEQRES 7 A 91 ARG LEU LEU VAL VAL ASP PRO GLU GLU ASP SER PHE LEU HET CL A1100 1 HET CL A1101 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 2(CL 1-) FORMUL 4 HOH *55(H2 O) HELIX 1 1 SER A 46 GLY A 52 1 7 HELIX 2 2 THR A 71 ALA A 82 1 12 SHEET 1 AA 4 ARG A 13 GLU A 18 0 SHEET 2 AA 4 ALA A 85 VAL A 91 -1 O VAL A 86 N LEU A 17 SHEET 3 AA 4 ARG A 58 VAL A 62 -1 O ARG A 58 N VAL A 91 SHEET 4 AA 4 GLU A 65 ASN A 66 -1 O GLU A 65 N VAL A 62 SHEET 1 AB 2 HIS A 27 HIS A 29 0 SHEET 2 AB 2 TYR A 38 ARG A 40 -1 O TYR A 38 N HIS A 29 SITE 1 AC1 4 LEU A 41 ALA A 55 HOH A2014 HOH A2031 SITE 1 AC2 4 ARG A 40 VAL A 91 ASP A 92 HOH A2003 CRYST1 50.073 50.073 66.680 90.00 90.00 120.00 P 31 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 0.019971 0.011530 0.000000 0.00000 SCALE2 0.000000 0.023060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014997 0.00000