HEADER VIRAL PROTEIN 11-SEP-18 6HLN TITLE CRYSTAL STRUCTURE OF HUMAN ACBD3 GOLD DOMAIN IN COMPLEX WITH 3A TITLE 2 PROTEIN OF ENTEROVIRUS-D68 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GOLGI RESIDENT PROTEIN GCP60; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 3,GOLGI COMPLEX- COMPND 5 ASSOCIATED PROTEIN 1,GOCAP1,GOLGI PHOSPHOPROTEIN 1,GOLPH1,PBR- AND COMPND 6 PKA-ASSOCIATED PROTEIN 7,PERIPHERAL BENZODIAZEPINE RECEPTOR- COMPND 7 ASSOCIATED PROTEIN PAP7; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: GENOME POLYPROTEIN; COMPND 11 CHAIN: B; COMPND 12 EC: 3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48; COMPND 13 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: ACBD3, GCP60, GOCAP1, GOLPH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ENTEROVIRUS D68; SOURCE 10 ORGANISM_TAXID: 42789; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, GOLGI, ENTEROVIRUS, PICORNAVIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KLIMA,E.BOURA REVDAT 3 24-JAN-24 6HLN 1 SOURCE REVDAT 2 14-AUG-19 6HLN 1 JRNL REVDAT 1 24-JUL-19 6HLN 0 JRNL AUTH V.HOROVA,H.LYOO,B.ROZYCKI,D.CHALUPSKA,M.SMOLA, JRNL AUTH 2 J.HUMPOLICKOVA,J.R.P.M.STRATING,F.J.M.VAN KUPPEVELD,E.BOURA, JRNL AUTH 3 M.KLIMA JRNL TITL CONVERGENT EVOLUTION IN THE MECHANISMS OF ACBD3 RECRUITMENT JRNL TITL 2 TO PICORNAVIRUS REPLICATION SITES. JRNL REF PLOS PATHOG. V. 15 07962 2019 JRNL REFN ESSN 1553-7374 JRNL PMID 31381608 JRNL DOI 10.1371/JOURNAL.PPAT.1007962 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 18496 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 926 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 47.4607 - 4.0165 0.98 2556 135 0.1688 0.1964 REMARK 3 2 4.0165 - 3.1882 0.98 2519 133 0.2034 0.2397 REMARK 3 3 3.1882 - 2.7852 0.99 2515 132 0.2584 0.2834 REMARK 3 4 2.7852 - 2.5306 0.98 2497 132 0.2718 0.3329 REMARK 3 5 2.5306 - 2.3492 0.98 2478 130 0.2967 0.3183 REMARK 3 6 2.3492 - 2.2107 0.98 2487 132 0.3207 0.3251 REMARK 3 7 2.2107 - 2.1000 0.99 2518 132 0.3533 0.3682 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.70 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 1466 REMARK 3 ANGLE : 1.065 1996 REMARK 3 CHIRALITY : 0.047 211 REMARK 3 PLANARITY : 0.005 255 REMARK 3 DIHEDRAL : 14.159 530 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 6HLN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1200011879. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-18 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 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 : XDS 11-SEP-2018 REMARK 200 DATA SCALING SOFTWARE : XDS 11-SEP-2018 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18521 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 47.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.210 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 5LZ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 8000, 6% V/V 1,5 REMARK 280 -PENTANEDIOL, 14% V/V PEG 200, 10 MM SPERMINE, 10 MM SPERMIDINE, REMARK 280 10 MM DL-ORNITHINE, 10 MM 1,4-DIAMINOBUTANE, 300 MM NACL, 100 MM REMARK 280 GLYGLY/AMPD PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 48.43950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.94450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.43950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.94450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 ASP A 437 REMARK 465 SER A 438 REMARK 465 PRO A 439 REMARK 465 ASN A 440 REMARK 465 THR A 441 REMARK 465 ALA A 442 REMARK 465 VAL A 443 REMARK 465 SER A 444 REMARK 465 VAL A 445 REMARK 465 HIS A 446 REMARK 465 VAL A 447 REMARK 465 SER A 448 REMARK 465 GLU A 449 REMARK 465 SER A 450 REMARK 465 SER A 451 REMARK 465 ASP A 452 REMARK 465 ASP A 453 REMARK 465 ASP A 454 REMARK 465 GLU A 455 REMARK 465 GLU A 456 REMARK 465 GLU A 457 REMARK 465 GLU A 458 REMARK 465 GLU A 459 REMARK 465 ASN A 460 REMARK 465 ILE A 461 REMARK 465 GLY A 462 REMARK 465 CYS A 463 REMARK 465 GLU A 464 REMARK 465 GLU A 465 REMARK 465 LYS A 466 REMARK 465 ALA A 467 REMARK 465 LYS A 468 REMARK 465 LYS A 469 REMARK 465 ASN A 470 REMARK 465 ALA A 471 REMARK 465 ASN A 472 REMARK 465 GLY B -2 REMARK 465 ALA B -1 REMARK 465 MET B 0 REMARK 465 GLY B 1 REMARK 465 PRO B 2 REMARK 465 PRO B 3 REMARK 465 GLN B 4 REMARK 465 PHE B 5 REMARK 465 LYS B 6 REMARK 465 GLU B 7 REMARK 465 ILE B 8 REMARK 465 LYS B 9 REMARK 465 ILE B 10 REMARK 465 SER B 11 REMARK 465 VAL B 12 REMARK 465 ALA B 13 REMARK 465 PRO B 14 REMARK 465 ASP B 15 REMARK 465 SER B 59 REMARK 465 ARG B 60 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 381 CG CD CE NZ REMARK 470 LYS A 473 CG CD CE NZ DBREF 6HLN A 364 528 UNP Q9H3P7 GCP60_HUMAN 364 528 DBREF 6HLN B 1 60 UNP Q68T42 Q68T42_9ENTO 1438 1497 SEQADV 6HLN MET A 363 UNP Q9H3P7 INITIATING METHIONINE SEQADV 6HLN GLY B -2 UNP Q68T42 EXPRESSION TAG SEQADV 6HLN ALA B -1 UNP Q68T42 EXPRESSION TAG SEQADV 6HLN MET B 0 UNP Q68T42 EXPRESSION TAG SEQRES 1 A 166 MET GLU SER LEU PRO VAL ILE ALA ALA PRO SER MET TRP SEQRES 2 A 166 THR ARG PRO GLN ILE LYS ASP PHE LYS GLU LYS ILE GLN SEQRES 3 A 166 GLN ASP ALA ASP SER VAL ILE THR VAL GLY ARG GLY GLU SEQRES 4 A 166 VAL VAL THR VAL ARG VAL PRO THR HIS GLU GLU GLY SER SEQRES 5 A 166 TYR LEU PHE TRP GLU PHE ALA THR ASP ASN TYR ASP ILE SEQRES 6 A 166 GLY PHE GLY VAL TYR PHE GLU TRP THR ASP SER PRO ASN SEQRES 7 A 166 THR ALA VAL SER VAL HIS VAL SER GLU SER SER ASP ASP SEQRES 8 A 166 ASP GLU GLU GLU GLU GLU ASN ILE GLY CYS GLU GLU LYS SEQRES 9 A 166 ALA LYS LYS ASN ALA ASN LYS PRO LEU LEU ASP GLU ILE SEQRES 10 A 166 VAL PRO VAL TYR ARG ARG ASP CYS HIS GLU GLU VAL TYR SEQRES 11 A 166 ALA GLY SER HIS GLN TYR PRO GLY ARG GLY VAL TYR LEU SEQRES 12 A 166 LEU LYS PHE ASP ASN SER TYR SER LEU TRP ARG SER LYS SEQRES 13 A 166 SER VAL TYR TYR ARG VAL TYR TYR THR ARG SEQRES 1 B 63 GLY ALA MET GLY PRO PRO GLN PHE LYS GLU ILE LYS ILE SEQRES 2 B 63 SER VAL ALA PRO ASP THR PRO ALA PRO ASP ALA ILE ASN SEQRES 3 B 63 ASP LEU LEU ARG SER VAL ASP SER GLN GLU VAL ARG ASP SEQRES 4 B 63 TYR CYS GLN LYS LYS GLY TRP ILE VAL ILE HIS PRO SER SEQRES 5 B 63 ASN GLU LEU VAL VAL GLU LYS HIS ILE SER ARG FORMUL 3 HOH *33(H2 O) HELIX 1 AA1 GLN A 379 GLN A 389 1 11 HELIX 2 AA2 ASP A 390 ASP A 392 5 3 HELIX 3 AA3 ALA B 18 ASP B 30 1 13 HELIX 4 AA4 SER B 31 LYS B 41 1 11 HELIX 5 AA5 PRO B 48 LEU B 52 5 5 SHEET 1 AA1 5 SER A 373 ARG A 377 0 SHEET 2 AA1 5 VAL A 491 GLN A 497 -1 O ALA A 493 N TRP A 375 SHEET 3 AA1 5 TYR A 415 THR A 422 -1 N PHE A 420 O TYR A 492 SHEET 4 AA1 5 LYS A 518 TYR A 526 -1 O TYR A 521 N ALA A 421 SHEET 5 AA1 5 VAL A 394 VAL A 397 -1 N ILE A 395 O VAL A 520 SHEET 1 AA2 5 SER A 373 ARG A 377 0 SHEET 2 AA2 5 VAL A 491 GLN A 497 -1 O ALA A 493 N TRP A 375 SHEET 3 AA2 5 TYR A 415 THR A 422 -1 N PHE A 420 O TYR A 492 SHEET 4 AA2 5 LYS A 518 TYR A 526 -1 O TYR A 521 N ALA A 421 SHEET 5 AA2 5 VAL B 45 ILE B 46 -1 O VAL B 45 N TYR A 526 SHEET 1 AA3 5 LEU A 476 ARG A 485 0 SHEET 2 AA3 5 ILE A 427 TRP A 435 -1 N VAL A 431 O VAL A 480 SHEET 3 AA3 5 GLY A 502 ASP A 509 -1 O VAL A 503 N GLU A 434 SHEET 4 AA3 5 VAL A 402 PRO A 408 -1 N VAL A 403 O PHE A 508 SHEET 5 AA3 5 VAL B 53 HIS B 57 -1 O GLU B 55 N THR A 404 CRYST1 96.879 55.889 64.493 90.00 112.05 90.00 C 1 2 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 0.010322 0.000000 0.004181 0.00000 SCALE2 0.000000 0.017893 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016729 0.00000