PDB Short entry for 6VSV HEADER MEMBRANE PROTEIN 12-FEB-20 6VSV TITLE CRYSTAL STRUCTURE OF A DISEASE MUTANT OF THE VOLTAGE-GATED SODIUM TITLE 2 CHANNEL BETA 4 SUBUNIT EXTRACELLULAR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM CHANNEL SUBUNIT BETA-4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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 SODIUM CHANNEL, BETA4 SUBUNIT, DISEASE MUTANT, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.DAS,F.VAN PETEGEM REVDAT 3 11-OCT-23 6VSV 1 REMARK REVDAT 2 15-SEP-21 6VSV 1 JRNL REVDAT 1 26-AUG-20 6VSV 0 JRNL AUTH J.P.LLONGUERAS,S.DAS,J.DE WAELE,L.CAPULZINI,A.SORGENTE, JRNL AUTH 2 F.VAN PETEGEM,F.BOSMANS JRNL TITL BIOPHYSICAL INVESTIGATION OF SODIUM CHANNEL INTERACTION WITH JRNL TITL 2 BETA-SUBUNIT VARIANTS ASSOCIATED WITH ARRHYTHMIAS. JRNL REF BIOELECTRICITY V. 2 269 2020 JRNL REFN ESSN 2576-3113 JRNL PMID 34476357 JRNL DOI 10.1089/BIOE.2020.0030 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15397 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.390 REMARK 3 FREE R VALUE TEST SET COUNT : 676 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 2.7699 - 2.1986 1.00 2935 141 0.2043 0.2413 REMARK 3 2 2.1986 - 1.9207 1.00 2927 119 0.1931 0.2202 REMARK 3 3 1.9207 - 1.7451 1.00 2889 135 0.2074 0.2381 REMARK 3 4 1.7451 - 1.6200 1.00 2862 143 0.2291 0.2499 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 21.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.55 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 : 0.012 1021 REMARK 3 ANGLE : 1.229 1399 REMARK 3 CHIRALITY : 0.081 163 REMARK 3 PLANARITY : 0.008 180 REMARK 3 DIHEDRAL : 3.446 812 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -9.4792 18.9772 4.2786 REMARK 3 T TENSOR REMARK 3 T11: 0.1113 T22: 0.1145 REMARK 3 T33: 0.1395 T12: -0.0160 REMARK 3 T13: -0.0144 T23: 0.0140 REMARK 3 L TENSOR REMARK 3 L11: 3.0334 L22: 3.0769 REMARK 3 L33: 4.6711 L12: 0.1889 REMARK 3 L13: -1.7633 L23: 0.4874 REMARK 3 S TENSOR REMARK 3 S11: 0.0217 S12: -0.0437 S13: -0.0552 REMARK 3 S21: 0.0870 S22: -0.0115 S23: 0.0641 REMARK 3 S31: -0.0172 S32: -0.0771 S33: 0.0076 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 6VSV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000247027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15397 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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: 4MZ2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 (M) MES, PH 6.5, 15-17% PEG200 REMARK 280 -MME, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 71.66133 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 35.83067 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 35.83067 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 71.66133 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A 36 REMARK 465 THR A 107 REMARK 465 LYS A 108 REMARK 465 GLU A 109 REMARK 465 LEU A 155 REMARK 465 GLU A 156 REMARK 465 GLU A 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 LYS A 110 CG CD CE NZ REMARK 470 ASN A 112 O 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 222 O HOH A 262 2.11 REMARK 500 O HOH A 332 O HOH A 345 2.11 REMARK 500 NZ LYS A 85 O HOH A 201 2.16 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 ASN A 112 28.79 -145.52 REMARK 500 ASP A 153 -86.75 -88.20 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 A 345 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 346 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 347 DISTANCE = 6.65 ANGSTROMS DBREF 6VSV A 32 157 UNP Q8IWT1 SCN4B_HUMAN 32 157 SEQADV 6VSV SER A 29 UNP Q8IWT1 EXPRESSION TAG SEQADV 6VSV ASN A 30 UNP Q8IWT1 EXPRESSION TAG SEQADV 6VSV ALA A 31 UNP Q8IWT1 EXPRESSION TAG SEQADV 6VSV ALA A 58 UNP Q8IWT1 CYS 58 CONFLICT SEQADV 6VSV THR A 80 UNP Q8IWT1 ILE 80 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 ALA 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 THR 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 CYS 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 FORMUL 2 HOH *147(H2 O) HELIX 1 AA1 GLU A 122 THR A 126 5 5 HELIX 2 AA2 PRO A 136 ASN A 139 5 4 SHEET 1 AA1 6 THR A 39 VAL A 44 0 SHEET 2 AA1 6 ILE A 147 VAL A 152 1 O PHE A 148 N THR A 39 SHEET 3 AA1 6 GLY A 127 ASN A 135 -1 N TYR A 129 O ILE A 147 SHEET 4 AA1 6 GLU A 62 ASN A 71 -1 N HIS A 65 O LYS A 134 SHEET 5 AA1 6 PHE A 76 ASN A 86 -1 O THR A 80 N TRP A 68 SHEET 6 AA1 6 LYS A 92 LYS A 96 -1 O LYS A 92 N THR A 83 SHEET 1 AA2 4 THR A 39 VAL A 44 0 SHEET 2 AA2 4 ILE A 147 VAL A 152 1 O PHE A 148 N THR A 39 SHEET 3 AA2 4 GLY A 127 ASN A 135 -1 N TYR A 129 O ILE A 147 SHEET 4 AA2 4 ASN A 140 HIS A 143 -1 O ASN A 140 N ASN A 135 SHEET 1 AA3 3 ILE A 49 LEU A 51 0 SHEET 2 AA3 3 ILE A 116 LEU A 118 -1 O ILE A 116 N LEU A 51 SHEET 3 AA3 3 ILE A 101 LEU A 103 -1 N THR A 102 O VAL A 117 SSBOND 1 CYS A 53 CYS A 131 1555 1555 2.05 CRYST1 43.123 43.123 107.492 90.00 90.00 120.00 P 32 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 0.023189 0.013388 0.000000 0.00000 SCALE2 0.000000 0.026777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009303 0.00000