HEADER TRANSCRIPTION 04-MAR-19 6O5W TITLE CRYSTAL STRUCTURE OF MORC3 CW DOMAIN FUSED WITH VIRAL INFLUENZA A NS1 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NS1-LINKED PEPTIDE,MORC FAMILY CW-TYPE ZINC FINGER PROTEIN COMPND 3 3; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: NUCLEAR MATRIX PROTEIN 2,ZINC FINGER CW-TYPE COILED-COIL COMPND 6 DOMAIN PROTEIN 3; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: NS1-LINKED PEPTIDE (225-230) LINKER(403-406) MORC COMPND 9 FAMILY CW-TYPE ZINC FINGER 3(407-455) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MORC3, KIAA0136, NXP2, ZCWCC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MORC3, ATPASE, NS1, VIRUS, HISTONE, CW, CHROMATIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.AHN,Y.ZHANG,K.R.VANN,T.KUTATELEADZE REVDAT 3 11-OCT-23 6O5W 1 REMARK REVDAT 2 12-JUN-19 6O5W 1 JRNL REVDAT 1 08-MAY-19 6O5W 0 JRNL AUTH Y.ZHANG,J.AHN,K.J.GREEN,K.R.VANN,J.BLACK,C.B.BROOKE, JRNL AUTH 2 T.G.KUTATELADZE JRNL TITL MORC3 IS A TARGET OF THE INFLUENZA A VIRAL PROTEIN NS1. JRNL REF STRUCTURE V. 27 1029 2019 JRNL REFN ISSN 0969-2126 JRNL PMID 31006586 JRNL DOI 10.1016/J.STR.2019.03.015 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.480 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 21392 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2140 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 26.3428 - 3.4795 0.95 1221 142 0.1525 0.1389 REMARK 3 2 3.4795 - 2.7627 0.99 1301 142 0.1575 0.1880 REMARK 3 3 2.7627 - 2.4138 0.99 1278 145 0.1745 0.1741 REMARK 3 4 2.4138 - 2.1932 1.00 1278 136 0.1528 0.1919 REMARK 3 5 2.1932 - 2.0361 1.00 1314 144 0.1443 0.1825 REMARK 3 6 2.0361 - 1.9161 1.00 1302 145 0.1554 0.1593 REMARK 3 7 1.9161 - 1.8201 1.00 1299 145 0.1443 0.1595 REMARK 3 8 1.8201 - 1.7409 1.00 1277 139 0.1535 0.1710 REMARK 3 9 1.7409 - 1.6739 1.00 1300 148 0.1588 0.1893 REMARK 3 10 1.6739 - 1.6161 1.00 1290 143 0.1403 0.1570 REMARK 3 11 1.6161 - 1.5656 1.00 1302 142 0.1350 0.1696 REMARK 3 12 1.5656 - 1.5209 0.98 1281 146 0.1461 0.1530 REMARK 3 13 1.5209 - 1.4808 1.00 1289 143 0.1436 0.1626 REMARK 3 14 1.4808 - 1.4447 0.98 1276 144 0.1482 0.1769 REMARK 3 15 1.4447 - 1.4119 0.95 1244 136 0.1475 0.1516 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.040 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 : 0.005 494 REMARK 3 ANGLE : 0.948 673 REMARK 3 CHIRALITY : 0.093 64 REMARK 3 PLANARITY : 0.007 93 REMARK 3 DIHEDRAL : 14.695 194 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 6O5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1000239343. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71940 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 92.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: 5SVX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 7.5 AND 1.4M SODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 15.45600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.15700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.71200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.15700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.45600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.71200 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: MONOMERIC 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 ASP A 454 REMARK 465 GLU A 455 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 676 O HOH A 690 2.17 REMARK 500 O HOH A 614 O HOH A 705 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 413 SG REMARK 620 2 CYS A 416 SG 108.1 REMARK 620 3 CYS A 435 SG 105.0 108.8 REMARK 620 4 CYS A 446 SG 109.4 108.7 116.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501 DBREF 6O5W A 225 230 PDB 6O5W 6O5W 225 230 DBREF 6O5W A 407 455 UNP Q14149 MORC3_HUMAN 407 455 SEQADV 6O5W GLY A 403 PDB LINKER SEQADV 6O5W GLY A 404 PDB LINKER SEQADV 6O5W SER A 405 PDB LINKER SEQADV 6O5W GLY A 406 PDB LINKER SEQRES 1 A 59 THR ALA ARG SER LYS VAL GLY GLY SER GLY ASP GLN THR SEQRES 2 A 59 TRP VAL GLN CYS ASP ALA CYS LEU LYS TRP ARG LYS LEU SEQRES 3 A 59 PRO ASP GLY MET ASP GLN LEU PRO GLU LYS TRP TYR CYS SEQRES 4 A 59 SER ASN ASN PRO ASP PRO GLN PHE ARG ASN CYS GLU VAL SEQRES 5 A 59 PRO GLU GLU PRO GLU ASP GLU HET ZN A 501 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *135(H2 O) HELIX 1 AA1 TYR A 434 ASN A 438 5 5 HELIX 2 AA2 ASP A 440 ARG A 444 5 5 SHEET 1 AA1 3 SER A 228 VAL A 230 0 SHEET 2 AA1 3 THR A 409 GLN A 412 -1 O TRP A 410 N LYS A 229 SHEET 3 AA1 3 TRP A 419 LYS A 421 -1 O ARG A 420 N VAL A 411 LINK SG CYS A 413 ZN ZN A 501 1555 1555 2.35 LINK SG CYS A 416 ZN ZN A 501 1555 1555 2.30 LINK SG CYS A 435 ZN ZN A 501 1555 1555 2.34 LINK SG CYS A 446 ZN ZN A 501 1555 1555 2.31 SITE 1 AC1 4 CYS A 413 CYS A 416 CYS A 435 CYS A 446 CRYST1 30.912 37.424 50.314 90.00 90.00 90.00 P 21 21 21 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 0.032350 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019875 0.00000