HEADER PROTEIN BINDING 19-AUG-12 4GOD TITLE CRYSTAL STRUCTURE OF THE SGTA HOMODIMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING COMPND 3 PROTEIN ALPHA; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: ALPHA-SGT, VPU-BINDING PROTEIN, UBP; 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 GENE: SGT, SGT1, SGTA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: NICO(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET33B KEYWDS FOUR-HELIX BUNDLE, PROTEIN-PROTEIN INTERACTION, UBL4A UBIQUITIN-LIKE KEYWDS 2 DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.W.CHARTRON,D.G.VANDERVELDE,W.M.CLEMONS JR. REVDAT 4 28-FEB-24 4GOD 1 REMARK SEQADV REVDAT 3 16-JAN-13 4GOD 1 JRNL REVDAT 2 02-JAN-13 4GOD 1 JRNL REVDAT 1 21-NOV-12 4GOD 0 JRNL AUTH J.W.CHARTRON,D.G.VANDERVELDE,W.M.CLEMONS JRNL TITL STRUCTURES OF THE SGT2/SGTA DIMERIZATION DOMAIN WITH THE JRNL TITL 2 GET5/UBL4A UBL DOMAIN REVEAL AN INTERACTION THAT FORMS A JRNL TITL 3 CONSERVED DYNAMIC INTERFACE. JRNL REF CELL REP V. 2 1620 2012 JRNL REFN ESSN 2211-1247 JRNL PMID 23142665 JRNL DOI 10.1016/J.CELREP.2012.10.010 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.780 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 17666 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.250 REMARK 3 FREE R VALUE TEST SET COUNT : 1281 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 28.2273 - 2.9112 0.97 1939 142 0.1904 0.2119 REMARK 3 2 2.9112 - 2.3111 0.95 1792 143 0.1856 0.1779 REMARK 3 3 2.3111 - 2.0190 0.99 1845 147 0.1769 0.1885 REMARK 3 4 2.0190 - 1.8345 0.98 1790 156 0.1903 0.1996 REMARK 3 5 1.8345 - 1.7030 0.98 1814 131 0.2116 0.2311 REMARK 3 6 1.7030 - 1.6026 0.99 1825 132 0.2086 0.2232 REMARK 3 7 1.6026 - 1.5223 0.99 1815 140 0.2279 0.2664 REMARK 3 8 1.5223 - 1.4561 0.99 1812 130 0.2374 0.2570 REMARK 3 9 1.4561 - 1.4000 0.99 1753 160 0.2711 0.2598 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.050 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 : 0.006 749 REMARK 3 ANGLE : 1.015 1009 REMARK 3 CHIRALITY : 0.058 118 REMARK 3 PLANARITY : 0.003 127 REMARK 3 DIHEDRAL : 20.062 273 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 4GOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074436. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17693 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 28.222 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% 2-METHYL-2,4-PENTANEDIOL, 0.2 M REMARK 280 AMMONIUM ACETATE, 0.1 M TRIS, PH 8.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.52250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.47400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.52250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.47400 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: 2160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 SER A 50 REMARK 465 ASP A 51 REMARK 465 LEU A 52 REMARK 465 ALA A 53 REMARK 465 LEU A 54 REMARK 465 ASP B 49 REMARK 465 SER B 50 REMARK 465 ASP B 51 REMARK 465 LEU B 52 REMARK 465 ALA B 53 REMARK 465 LEU B 54 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 OE1 GLN B 18 O HOH B 138 1.82 REMARK 500 O HOH A 240 O HOH A 248 1.94 REMARK 500 O HOH A 249 O HOH A 253 1.96 REMARK 500 O HOH A 251 O HOH A 269 2.02 REMARK 500 O HOH A 243 O HOH A 258 2.02 REMARK 500 O HOH A 255 O HOH A 261 2.13 REMARK 500 O HOH A 240 O HOH A 251 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 265 O HOH A 265 2566 2.17 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 MPD A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GOC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GET5 UBL, THE YEAST HOMOLOG OF THE SGTA REMARK 900 BINDING PARTNER, UBL4A REMARK 900 RELATED ID: 4GOE RELATED DB: PDB REMARK 900 RELATED ID: 4GOF RELATED DB: PDB DBREF 4GOD A 4 54 UNP O43765 SGTA_HUMAN 4 54 DBREF 4GOD B 4 54 UNP O43765 SGTA_HUMAN 4 54 SEQADV 4GOD MET A 3 UNP O43765 EXPRESSION TAG SEQADV 4GOD MET B 3 UNP O43765 EXPRESSION TAG SEQRES 1 A 52 MET LYS LYS ARG LEU ALA TYR ALA ILE ILE GLN PHE LEU SEQRES 2 A 52 HIS ASP GLN LEU ARG HIS GLY GLY LEU SER SER ASP ALA SEQRES 3 A 52 GLN GLU SER LEU GLU VAL ALA ILE GLN CYS LEU GLU THR SEQRES 4 A 52 ALA PHE GLY VAL THR VAL GLU ASP SER ASP LEU ALA LEU SEQRES 1 B 52 MET LYS LYS ARG LEU ALA TYR ALA ILE ILE GLN PHE LEU SEQRES 2 B 52 HIS ASP GLN LEU ARG HIS GLY GLY LEU SER SER ASP ALA SEQRES 3 B 52 GLN GLU SER LEU GLU VAL ALA ILE GLN CYS LEU GLU THR SEQRES 4 B 52 ALA PHE GLY VAL THR VAL GLU ASP SER ASP LEU ALA LEU HET MPD A 101 8 HET MPD A 102 8 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 MPD 2(C6 H14 O2) FORMUL 5 HOH *110(H2 O) HELIX 1 1 LYS A 4 GLY A 22 1 19 HELIX 2 2 SER A 25 GLY A 44 1 20 HELIX 3 3 LYS B 4 GLY B 22 1 19 HELIX 4 4 SER B 25 GLY B 44 1 20 SITE 1 AC1 4 ALA A 10 PHE A 14 HOH A 262 GLN B 37 SITE 1 AC2 1 GLN B 37 CRYST1 23.603 57.045 64.948 90.00 90.00 90.00 P 2 21 21 8 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 0.042367 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017530 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015397 0.00000