HEADER MEMBRANE PROTEIN 28-SEP-13 4MZ3 TITLE CRYSTAL STRUCTURE OF THE VOLTAGE-GATED SODIUM CHANNEL BETA 4 SUBUNIT TITLE 2 EXTRACELLULAR DOMAIN, C131W MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM CHANNEL SUBUNIT BETA-4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 32-157; COMPND 5 ENGINEERED: YES; COMPND 6 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: SCN4B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ION CONDUCTANCE, EXTRACELLULAR, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.DAS,F.VAN PETEGEM REVDAT 3 20-SEP-23 4MZ3 1 SEQADV LINK REVDAT 2 15-JAN-14 4MZ3 1 JRNL REVDAT 1 04-DEC-13 4MZ3 0 JRNL AUTH J.GILCHRIST,S.DAS,F.VAN PETEGEM,F.BOSMANS JRNL TITL CRYSTALLOGRAPHIC INSIGHTS INTO SODIUM-CHANNEL MODULATION BY JRNL TITL 2 THE BETA 4 SUBUNIT. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 E5016 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 24297919 JRNL DOI 10.1073/PNAS.1314557110 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 24173 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1232 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 26.0848 - 3.6192 0.97 2583 132 0.1570 0.2005 REMARK 3 2 3.6192 - 2.8738 0.99 2548 139 0.1644 0.1961 REMARK 3 3 2.8738 - 2.5109 0.99 2585 127 0.1849 0.2212 REMARK 3 4 2.5109 - 2.2815 1.00 2575 130 0.1756 0.2229 REMARK 3 5 2.2815 - 2.1180 0.99 2509 156 0.1717 0.2432 REMARK 3 6 2.1180 - 1.9932 1.00 2578 140 0.1833 0.2217 REMARK 3 7 1.9932 - 1.8934 1.00 2559 136 0.1946 0.2573 REMARK 3 8 1.8934 - 1.8110 1.00 2562 139 0.2086 0.2543 REMARK 3 9 1.8110 - 1.7410 0.96 2442 133 0.2453 0.3022 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.740 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 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 : 0.007 2010 REMARK 3 ANGLE : 1.172 2736 REMARK 3 CHIRALITY : 0.078 315 REMARK 3 PLANARITY : 0.004 348 REMARK 3 DIHEDRAL : 14.245 734 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 4MZ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082546. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9749 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24173 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 29.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 ENTRY 4MZ2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG FORMATE, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.26050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 SER A 29 REMARK 465 ASN A 30 REMARK 465 ALA A 31 REMARK 465 GLU A 32 REMARK 465 VAL A 33 REMARK 465 SER A 34 REMARK 465 VAL A 35 REMARK 465 GLU A 156 REMARK 465 GLU A 157 REMARK 465 SER B 29 REMARK 465 ASN B 30 REMARK 465 ALA B 31 REMARK 465 GLU B 32 REMARK 465 VAL B 33 REMARK 465 SER B 34 REMARK 465 VAL B 35 REMARK 465 GLU B 156 REMARK 465 GLU B 157 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 LYS A 37 CG CD CE NZ REMARK 470 ARG A 154 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 155 CG CD1 CD2 REMARK 470 LYS B 37 CG CD CE NZ REMARK 470 LEU B 155 CG CD1 CD2 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 O HOH A 335 O HOH A 336 2.17 REMARK 500 O HOH A 218 O HOH A 232 2.18 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 THR A 47 -158.03 -96.59 REMARK 500 LYS A 108 119.57 -160.10 REMARK 500 GLU A 109 -118.87 52.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MZ2 RELATED DB: PDB DBREF 4MZ3 A 32 157 UNP Q8IWT1 SCN4B_HUMAN 32 157 DBREF 4MZ3 B 32 157 UNP Q8IWT1 SCN4B_HUMAN 32 157 SEQADV 4MZ3 SER A 29 UNP Q8IWT1 EXPRESSION TAG SEQADV 4MZ3 ASN A 30 UNP Q8IWT1 EXPRESSION TAG SEQADV 4MZ3 ALA A 31 UNP Q8IWT1 EXPRESSION TAG SEQADV 4MZ3 TRP A 131 UNP Q8IWT1 CYS 131 ENGINEERED MUTATION SEQADV 4MZ3 SER B 29 UNP Q8IWT1 EXPRESSION TAG SEQADV 4MZ3 ASN B 30 UNP Q8IWT1 EXPRESSION TAG SEQADV 4MZ3 ALA B 31 UNP Q8IWT1 EXPRESSION TAG SEQADV 4MZ3 TRP B 131 UNP Q8IWT1 CYS 131 ENGINEERED MUTATION SEQRES 1 A 129 SER ASN ALA GLU VAL SER VAL GLY LYS ALA THR ASP ILE SEQRES 2 A 129 TYR ALA VAL ASN GLY THR GLU ILE LEU LEU PRO CYS THR SEQRES 3 A 129 PHE SER SER CME PHE GLY PHE GLU ASP LEU HIS PHE ARG SEQRES 4 A 129 TRP THR TYR ASN SER SER ASP ALA PHE LYS ILE LEU ILE SEQRES 5 A 129 GLU GLY THR VAL LYS ASN GLU LYS SER ASP PRO LYS VAL SEQRES 6 A 129 THR LEU LYS ASP ASP ASP ARG ILE THR LEU VAL GLY SER SEQRES 7 A 129 THR LYS GLU LYS MET ASN ASN ILE SER ILE VAL LEU ARG SEQRES 8 A 129 ASP LEU GLU PHE SER ASP THR GLY LYS TYR THR TRP HIS SEQRES 9 A 129 VAL LYS ASN PRO LYS GLU ASN ASN LEU GLN HIS HIS ALA SEQRES 10 A 129 THR ILE PHE LEU GLN VAL VAL ASP ARG LEU GLU GLU SEQRES 1 B 129 SER ASN ALA GLU VAL SER VAL GLY LYS ALA THR ASP ILE SEQRES 2 B 129 TYR ALA VAL ASN GLY THR GLU ILE LEU LEU PRO CYS THR SEQRES 3 B 129 PHE SER SER CME PHE GLY PHE GLU ASP LEU HIS PHE ARG SEQRES 4 B 129 TRP THR TYR ASN SER SER ASP ALA PHE LYS ILE LEU ILE SEQRES 5 B 129 GLU GLY THR VAL LYS ASN GLU LYS SER ASP PRO LYS VAL SEQRES 6 B 129 THR LEU LYS ASP ASP ASP ARG ILE THR LEU VAL GLY SER SEQRES 7 B 129 THR LYS GLU LYS MET ASN ASN ILE SER ILE VAL LEU ARG SEQRES 8 B 129 ASP LEU GLU PHE SER ASP THR GLY LYS TYR THR TRP HIS SEQRES 9 B 129 VAL LYS ASN PRO LYS GLU ASN ASN LEU GLN HIS HIS ALA SEQRES 10 B 129 THR ILE PHE LEU GLN VAL VAL ASP ARG LEU GLU GLU MODRES 4MZ3 CME A 58 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 4MZ3 CME B 58 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET CME A 58 10 HET CME B 58 10 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 3 HOH *272(H2 O) HELIX 1 1 GLU A 122 THR A 126 5 5 HELIX 2 2 GLU B 122 THR B 126 5 5 SHEET 1 A 6 THR A 39 VAL A 44 0 SHEET 2 A 6 HIS A 143 VAL A 152 1 O PHE A 148 N THR A 39 SHEET 3 A 6 GLY A 127 LYS A 134 -1 N TYR A 129 O ILE A 147 SHEET 4 A 6 LEU A 64 SER A 72 -1 N HIS A 65 O LYS A 134 SHEET 5 A 6 ALA A 75 VAL A 84 -1 O LYS A 77 N TYR A 70 SHEET 6 A 6 LYS A 92 LYS A 96 -1 O LYS A 92 N THR A 83 SHEET 1 B 3 ILE A 49 LEU A 51 0 SHEET 2 B 3 ILE A 116 LEU A 118 -1 O ILE A 116 N LEU A 51 SHEET 3 B 3 ILE A 101 LEU A 103 -1 N THR A 102 O VAL A 117 SHEET 1 C 6 ILE B 41 VAL B 44 0 SHEET 2 C 6 GLN B 142 VAL B 152 1 O GLN B 150 N ILE B 41 SHEET 3 C 6 GLY B 127 LYS B 134 -1 N GLY B 127 O LEU B 149 SHEET 4 C 6 GLU B 62 ASN B 71 -1 N ASN B 71 O LYS B 128 SHEET 5 C 6 PHE B 76 ASN B 86 -1 O LYS B 77 N TYR B 70 SHEET 6 C 6 LYS B 92 LYS B 96 -1 O LYS B 92 N THR B 83 SHEET 1 D 3 ILE B 49 LEU B 51 0 SHEET 2 D 3 ILE B 116 LEU B 118 -1 O ILE B 116 N LEU B 51 SHEET 3 D 3 ILE B 101 LEU B 103 -1 N THR B 102 O VAL B 117 LINK C SER A 57 N CME A 58 1555 1555 1.33 LINK C CME A 58 N PHE A 59 1555 1555 1.33 LINK C SER B 57 N CME B 58 1555 1555 1.33 LINK C CME B 58 N PHE B 59 1555 1555 1.33 CRYST1 31.574 42.521 89.142 90.00 91.51 90.00 P 1 21 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 0.031672 0.000000 0.000835 0.00000 SCALE2 0.000000 0.023518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011222 0.00000