HEADER LIGASE/TRANSFERASE 15-JAN-21 7LEW TITLE CRYSTAL STRUCTURE OF UBE2G2 IN COMPLEX WITH THE UBE2G2-BINDING REGION TITLE 2 OF AUP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 G2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: E2 UBIQUITIN-CONJUGATING ENZYME G2,UBIQUITIN CARRIER PROTEIN COMPND 5 G2,UBIQUITIN-PROTEIN LIGASE G2; COMPND 6 EC: 2.3.2.23; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: LIPID DROPLET-REGULATING VLDL ASSEMBLY FACTOR AUP1; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UBE2G2-BINDING REGION (G2BR) OF AUP1; COMPND 12 SYNONYM: ANCIENT UBIQUITOUS PROTEIN 1; 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: UBE2G2, UBC7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETDUET-GST; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: AUP1; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PETDUET-GST KEYWDS ALPHA BETA, LIGASE, LIGASE-TRANSFERASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.-H.LIANG,C.E.SMITH,Y.C.TSAI,A.M.WEISSMAN,X.JI REVDAT 3 18-OCT-23 7LEW 1 REMARK REVDAT 2 25-MAY-22 7LEW 1 JRNL REVDAT 1 10-NOV-21 7LEW 0 JRNL AUTH C.E.SMITH,Y.C.TSAI,Y.H.LIANG,D.KHAGO,J.MARIANO,J.LI, JRNL AUTH 2 S.G.TARASOV,E.GERGEL,B.TSAI,M.VILLANEUVA,M.E.CLAPP, JRNL AUTH 3 V.MAGIDSON,R.CHARI,R.A.BYRD,X.JI,A.M.WEISSMAN JRNL TITL A STRUCTURALLY CONSERVED SITE IN AUP1 BINDS THE E2 ENZYME JRNL TITL 2 UBE2G2 AND IS ESSENTIAL FOR ER-ASSOCIATED DEGRADATION. JRNL REF PLOS BIOL. V. 19 01474 2021 JRNL REFN ESSN 1545-7885 JRNL PMID 34879065 JRNL DOI 10.1371/JOURNAL.PBIO.3001474 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.DAS,J.MARIANO,Y.C.TSAI,R.C.KALATHUR,Z.KOSTOVA,J.LI, REMARK 1 AUTH 2 S.G.TARASOV,R.L.MCFEETERS,A.S.ALTIERI,X.JI,R.A.BYRD, REMARK 1 AUTH 3 A.M.WEISSMAN REMARK 1 TITL ALLOSTERIC ACTIVATION OF E2-RING FINGER-MEDIATED REMARK 1 TITL 2 UBIQUITYLATION BY A STRUCTURALLY DEFINED SPECIFIC E2-BINDING REMARK 1 TITL 3 REGION OF GP78. REMARK 1 REF MOL CELL V. 34 674 2009 REMARK 1 REFN ISSN 1097-4164 REMARK 1 PMID 19560420 REMARK 1 DOI 10.1016/J.MOLCEL.2009.05.010 REMARK 2 REMARK 2 RESOLUTION. 1.74 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19527 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1003 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 37.8190 - 3.3207 0.99 2758 155 0.1774 0.1950 REMARK 3 2 3.3207 - 2.6360 1.00 2689 140 0.1847 0.2295 REMARK 3 3 2.6360 - 2.3028 1.00 2658 141 0.1984 0.2422 REMARK 3 4 2.3028 - 2.0923 1.00 2631 150 0.1976 0.2564 REMARK 3 5 2.0923 - 1.9423 1.00 2617 136 0.2112 0.2552 REMARK 3 6 1.9423 - 1.8278 1.00 2578 146 0.2322 0.2921 REMARK 3 7 1.8278 - 1.7363 0.98 2593 135 0.2477 0.3052 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.27 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 : 0.011 1560 REMARK 3 ANGLE : 1.116 2122 REMARK 3 CHIRALITY : 0.062 220 REMARK 3 PLANARITY : 0.009 282 REMARK 3 DIHEDRAL : 12.827 973 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 7LEW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000254157. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.9794 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19573 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.736 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 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) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.50200 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: PHENIX REMARK 200 STARTING MODEL: 3H8K REMARK 200 REMARK 200 REMARK: ROD-SHAPED CRYSTALS OF DIMENSIONS 0.08 MM X 0.08 MM X 0.3 REMARK 200 MM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, AMMONIUM ACETATE ETC., PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 24.86950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.69600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.11300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.69600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.86950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.11300 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: 1770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 MET A 1 REMARK 465 GLY A 97 REMARK 465 ASP A 98 REMARK 465 ASP A 99 REMARK 465 PRO A 100 REMARK 465 MET A 101 REMARK 465 GLY A 102 REMARK 465 TYR A 103 REMARK 465 GLU A 104 REMARK 465 SER A 105 REMARK 465 SER A 106 REMARK 465 ARG B 405 REMARK 465 ALA B 406 REMARK 465 GLN B 407 REMARK 465 GLU B 408 REMARK 465 ALA B 409 REMARK 465 ASP B 410 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 OD2 ASP A 85 NH2 ARG A 87 2.04 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 NE2 GLN A 157 OH TYR B 396 4445 2.08 REMARK 500 REMARK 500 REMARK: NULL DBREF 7LEW A 1 165 UNP P60604 UB2G2_HUMAN 1 165 DBREF 7LEW B 379 410 UNP Q9Y679 AUP1_HUMAN 379 410 SEQADV 7LEW GLY B 377 UNP Q9Y679 EXPRESSION TAG SEQADV 7LEW PRO B 378 UNP Q9Y679 EXPRESSION TAG SEQRES 1 A 165 MET ALA GLY THR ALA LEU LYS ARG LEU MET ALA GLU TYR SEQRES 2 A 165 LYS GLN LEU THR LEU ASN PRO PRO GLU GLY ILE VAL ALA SEQRES 3 A 165 GLY PRO MET ASN GLU GLU ASN PHE PHE GLU TRP GLU ALA SEQRES 4 A 165 LEU ILE MET GLY PRO GLU ASP THR CYS PHE GLU PHE GLY SEQRES 5 A 165 VAL PHE PRO ALA ILE LEU SER PHE PRO LEU ASP TYR PRO SEQRES 6 A 165 LEU SER PRO PRO LYS MET ARG PHE THR CYS GLU MET PHE SEQRES 7 A 165 HIS PRO ASN ILE TYR PRO ASP GLY ARG VAL CYS ILE SER SEQRES 8 A 165 ILE LEU HIS ALA PRO GLY ASP ASP PRO MET GLY TYR GLU SEQRES 9 A 165 SER SER ALA GLU ARG TRP SER PRO VAL GLN SER VAL GLU SEQRES 10 A 165 LYS ILE LEU LEU SER VAL VAL SER MET LEU ALA GLU PRO SEQRES 11 A 165 ASN ASP GLU SER GLY ALA ASN VAL ASP ALA SER LYS MET SEQRES 12 A 165 TRP ARG ASP ASP ARG GLU GLN PHE TYR LYS ILE ALA LYS SEQRES 13 A 165 GLN ILE VAL GLN LYS SER LEU GLY LEU SEQRES 1 B 34 GLY PRO SER TRP ALA ARG GLN GLU SER LEU GLN GLU ARG SEQRES 2 B 34 LYS GLN ALA LEU TYR GLU TYR ALA ARG ARG ARG PHE THR SEQRES 3 B 34 GLU ARG ARG ALA GLN GLU ALA ASP FORMUL 3 HOH *158(H2 O) HELIX 1 AA1 GLY A 3 ASN A 19 1 17 HELIX 2 AA2 ILE A 90 HIS A 94 5 5 HELIX 3 AA3 SER A 115 GLU A 129 1 15 HELIX 4 AA4 ASN A 137 ASP A 147 1 11 HELIX 5 AA5 ASP A 147 GLY A 164 1 18 HELIX 6 AA6 PRO B 378 GLU B 403 1 26 SHEET 1 AA1 4 ILE A 24 PRO A 28 0 SHEET 2 AA1 4 GLU A 36 MET A 42 -1 O LEU A 40 N VAL A 25 SHEET 3 AA1 4 VAL A 53 SER A 59 -1 O PHE A 54 N ILE A 41 SHEET 4 AA1 4 LYS A 70 PHE A 73 -1 O ARG A 72 N ILE A 57 CISPEP 1 TYR A 64 PRO A 65 0 7.80 CRYST1 49.739 58.226 63.392 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 0.020105 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017174 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015775 0.00000