HEADER PROTEIN BINDING/PROTEIN BINDING 19-AUG-12 2LXC TITLE SOLUTION STRUCTURE OF THE COMPLEX BETWEEN THE SGT2 HOMODIMERIZATION TITLE 2 DOMAIN AND THE GET5 UBL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE PROTEIN MDY2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBIQUITIN-LIKE DOMAIN; COMPND 5 SYNONYM: GOLGI TO ER TRAFFIC PROTEIN 5, MATING-DEFICIENT PROTEIN 2, COMPND 6 TRANSLATION MACHINERY-ASSOCIATED PROTEIN 24; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING COMPND 10 PROTEIN 2; COMPND 11 CHAIN: B, C; COMPND 12 FRAGMENT: N-TERMINAL DOMAIN; COMPND 13 SYNONYM: SGT/UBP, VIRAL PROTEIN U-BINDING PROTEIN; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: GET5, MDY2, TMA24, YOL111C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: NICO21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET33B; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 14 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 15 ORGANISM_TAXID: 559292; SOURCE 16 STRAIN: ATCC 204508 / S288C; SOURCE 17 GENE: SGT2, UNF346, YOR007C; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: NICO21(DE3); SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PET33B KEYWDS UBIQUITIN-LIKE DOMAIN, PROTEIN-PROTEIN INTERACTION, FOUR-HELIX KEYWDS 2 BUNDLE, GET PATHWAY, PROTEIN BINDING-PROTEIN BINDING COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.W.CHARTRON,D.G.VANDERVELDE,W.M.CLEMONS JR. REVDAT 4 14-JUN-23 2LXC 1 REMARK SEQADV REVDAT 3 16-JAN-13 2LXC 1 JRNL REVDAT 2 28-NOV-12 2LXC 1 JRNL REVDAT 1 21-NOV-12 2LXC 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. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ, ARIA 2.3 REMARK 3 AUTHORS : VARIAN (VNMRJ), LINGE, O'DONOGHUE AND NILGES REMARK 3 (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES OF ASYMMETRICALLY LABELED REMARK 3 COMPLEX (SAMPLE_1 AND SAMPLE_3) WERE USED TO DETERMINE THE REMARK 3 SEPERATE STRUCTURES OF GET5 OR SGT2, IN THEIR COMPLEX STATES. REMARK 3 STRUCTURES ARE REFINED IN EXPLICIT WATER. AMBIGUOUS INTERACTION REMARK 3 RESTRAINTS, RESIDUAL DIPOLAR COUPLINGS AND INTERMOLECULAR NOES REMARK 3 WERE USED TO DOCK THE STRUCTURES OF GET5 AND SGT2, DETERMINED IN REMARK 3 THEIR COMPLEX STATES. STRUCTURES ARE SELECTED FROM THE BEST REMARK 3 SCORING CLUSTER BY HADDOCK SCORES AND REFINED IN WATER. REMARK 4 REMARK 4 2LXC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000102949. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.1 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM GET5, 2 MM [U-100% 13C; U REMARK 210 -100% 15N] SGT2, 10 MM BIS-TRIS, REMARK 210 50 MM L-ARGININE, 50 MM L- REMARK 210 GLUTAMIC ACID, 0.02 % SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 1 MM REMARK 210 GET5, 2 MM [U-100% 13C; U-100% REMARK 210 15N] SGT2, 10 MM BIS-TRIS, 50 MM REMARK 210 L-ARGININE, 50 MM L-GLUTAMIC REMARK 210 ACID, 0.02 % SODIUM AZIDE, 3.5 % REMARK 210 POLYACRYLAMIDE, 90% H2O/10% D2O; REMARK 210 1 MM [U-100% 13C; U-100% 15N] REMARK 210 GET5, 2 MM SGT2, 10 MM BIS-TRIS, REMARK 210 50 MM L-ARGININE, 50 MM L- REMARK 210 GLUTAMIC ACID, 0.02 % SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 13C; U-100% 15N] GET5, 2 MM REMARK 210 SGT2, 10 MM BIS-TRIS, 50 MM L- REMARK 210 ARGININE, 50 MM L-GLUTAMIC ACID, REMARK 210 0.02 % SODIUM AZIDE, 3.5 % REMARK 210 POLYACRYLAMIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCACB; 3D HNCO; 3D REMARK 210 HCCH-TOCSY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANALYSIS, NMRPIPE, TALOS+, ARIA REMARK 210 2.3, HADDOCK 2.1, TOPSPIN, PALES REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 EXPERIMENTALLY DRIVEN DOCKING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 H2 SER B -1 OD1 ASP B 1 1.56 REMARK 500 HE2 HIS A 127 OD2 ASP B 28 1.58 REMARK 500 HZ3 LYS A 122 OD2 ASP C 38 1.58 REMARK 500 HZ1 LYS A 102 OD2 ASP A 128 1.59 REMARK 500 HZ1 LYS A 149 OD2 ASP B 38 1.60 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 1 SER A 112 -61.35 -94.46 REMARK 500 1 LYS A 122 59.39 36.43 REMARK 500 1 LYS A 136 99.38 67.94 REMARK 500 1 ASN A 141 -72.61 -132.83 REMARK 500 1 ASP B 1 106.78 -56.40 REMARK 500 1 GLU B 24 33.68 -90.60 REMARK 500 1 LYS B 57 23.63 -157.72 REMARK 500 1 SER B 58 35.53 -81.61 REMARK 500 1 GLU B 59 73.04 50.82 REMARK 500 1 PHE B 60 94.93 -67.23 REMARK 500 1 GLN B 63 90.56 -67.34 REMARK 500 1 ALA B 66 19.83 59.51 REMARK 500 1 ASN B 70 41.67 -100.74 REMARK 500 1 VAL C 0 50.37 -106.54 REMARK 500 1 ASP C 1 96.32 -68.96 REMARK 500 1 LYS C 57 28.75 -151.35 REMARK 500 1 SER C 58 30.82 -87.55 REMARK 500 1 GLU C 59 86.33 61.05 REMARK 500 1 ASN C 70 44.71 -92.16 REMARK 500 1 SER C 71 31.58 -94.21 REMARK 500 2 LYS A 136 99.18 63.07 REMARK 500 2 ASP B 1 -79.18 -171.11 REMARK 500 2 SER B 2 -31.72 -155.53 REMARK 500 2 LEU B 69 -67.80 70.66 REMARK 500 2 ASN B 70 -14.43 -148.88 REMARK 500 2 ASP C 1 -58.93 -135.39 REMARK 500 2 SER C 2 -21.53 -157.01 REMARK 500 2 HIS C 64 113.16 -161.67 REMARK 500 2 LEU C 69 -73.95 69.53 REMARK 500 3 LYS A 136 92.20 63.43 REMARK 500 3 ASN A 141 -75.02 -128.63 REMARK 500 3 SER A 142 13.27 57.66 REMARK 500 3 VAL B 0 -162.57 -118.31 REMARK 500 3 ASP B 1 -84.67 -156.96 REMARK 500 3 SER B 2 12.91 -162.94 REMARK 500 3 ILE B 68 97.26 -68.70 REMARK 500 3 LEU B 69 -96.37 63.80 REMARK 500 3 ASP C 1 -77.63 -150.09 REMARK 500 3 SER C 2 9.56 -170.35 REMARK 500 3 LEU C 69 -74.62 68.36 REMARK 500 3 ASN C 70 -26.48 -150.26 REMARK 500 4 LYS A 136 91.96 65.85 REMARK 500 4 ASN A 141 -63.88 -136.48 REMARK 500 4 ASP B 1 -86.92 -156.99 REMARK 500 4 PHE B 60 -41.09 -166.54 REMARK 500 4 ASP C 1 -90.29 -68.15 REMARK 500 4 PHE C 60 -62.63 -168.72 REMARK 500 4 ALA C 66 28.72 -152.40 REMARK 500 4 SER C 71 47.49 -108.87 REMARK 500 5 SER A 112 -61.36 -101.10 REMARK 500 REMARK 500 THIS ENTRY HAS 132 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GOC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GET5 UBIQUITIN LIKE DOMAIN REMARK 900 RELATED ID: 2LXA RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GET5 UBIQUITIN LIKE DOMAIN REMARK 900 RELATED ID: 2LXB RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF SGT2 HOMODIMERIZATION DOMAIN REMARK 900 RELATED ID: 4GOD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SGTA HOMODIMERIZATION DOMAIN, THE HUMAN HOMOLOG REMARK 900 RELATED ID: 4GOE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SGTA HOMODIMERIZATION DOMAIN, THE HUMAN HOMOLOG REMARK 900 RELATED ID: 4GOF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SGTA HOMODIMERIZATION DOMAIN, THE HUMAN HOMOLOG REMARK 900 RELATED ID: 18671 RELATED DB: BMRB DBREF 2LXC A 74 151 UNP Q12285 MDY2_YEAST 74 151 DBREF 2LXC B 2 72 UNP Q12118 SGT2_YEAST 2 72 DBREF 2LXC C 2 72 UNP Q12118 SGT2_YEAST 2 72 SEQADV 2LXC MET A 73 UNP Q12285 INITIATING METHIONINE SEQADV 2LXC LEU A 152 UNP Q12285 EXPRESSION TAG SEQADV 2LXC GLU A 153 UNP Q12285 EXPRESSION TAG SEQADV 2LXC SER B -1 UNP Q12118 EXPRESSION TAG SEQADV 2LXC VAL B 0 UNP Q12118 EXPRESSION TAG SEQADV 2LXC ASP B 1 UNP Q12118 EXPRESSION TAG SEQADV 2LXC SER C -1 UNP Q12118 EXPRESSION TAG SEQADV 2LXC VAL C 0 UNP Q12118 EXPRESSION TAG SEQADV 2LXC ASP C 1 UNP Q12118 EXPRESSION TAG SEQRES 1 A 81 MET VAL HIS LEU THR LEU LYS LYS ILE GLN ALA PRO LYS SEQRES 2 A 81 PHE SER ILE GLU HIS ASP PHE SER PRO SER ASP THR ILE SEQRES 3 A 81 LEU GLN ILE LYS GLN HIS LEU ILE SER GLU GLU LYS ALA SEQRES 4 A 81 SER HIS ILE SER GLU ILE LYS LEU LEU LEU LYS GLY LYS SEQRES 5 A 81 VAL LEU HIS ASP ASN LEU PHE LEU SER ASP LEU LYS VAL SEQRES 6 A 81 THR PRO ALA ASN SER THR ILE THR VAL MET ILE LYS PRO SEQRES 7 A 81 ASN LEU GLU SEQRES 1 B 74 SER VAL ASP SER ALA SER LYS GLU GLU ILE ALA ALA LEU SEQRES 2 B 74 ILE VAL ASN TYR PHE SER SER ILE VAL GLU LYS LYS GLU SEQRES 3 B 74 ILE SER GLU ASP GLY ALA ASP SER LEU ASN VAL ALA MET SEQRES 4 B 74 ASP CYS ILE SER GLU ALA PHE GLY PHE GLU ARG GLU ALA SEQRES 5 B 74 VAL SER GLY ILE LEU GLY LYS SER GLU PHE LYS GLY GLN SEQRES 6 B 74 HIS LEU ALA ASP ILE LEU ASN SER ALA SEQRES 1 C 74 SER VAL ASP SER ALA SER LYS GLU GLU ILE ALA ALA LEU SEQRES 2 C 74 ILE VAL ASN TYR PHE SER SER ILE VAL GLU LYS LYS GLU SEQRES 3 C 74 ILE SER GLU ASP GLY ALA ASP SER LEU ASN VAL ALA MET SEQRES 4 C 74 ASP CYS ILE SER GLU ALA PHE GLY PHE GLU ARG GLU ALA SEQRES 5 C 74 VAL SER GLY ILE LEU GLY LYS SER GLU PHE LYS GLY GLN SEQRES 6 C 74 HIS LEU ALA ASP ILE LEU ASN SER ALA HELIX 1 1 THR A 97 GLU A 108 1 12 HELIX 2 2 HIS A 113 SER A 115 5 3 HELIX 3 3 PHE A 131 LYS A 136 1 6 HELIX 4 4 SER B 4 LYS B 22 1 19 HELIX 5 5 SER B 26 PHE B 44 1 19 HELIX 6 6 GLU B 47 GLU B 49 5 3 HELIX 7 7 ALA B 50 LEU B 55 1 6 HELIX 8 8 SER C 4 LYS C 22 1 19 HELIX 9 9 SER C 26 GLY C 45 1 20 HELIX 10 10 GLU C 47 GLU C 49 5 3 HELIX 11 11 ALA C 50 LEU C 55 1 6 SHEET 1 A 5 PHE A 86 PHE A 92 0 SHEET 2 A 5 VAL A 74 LYS A 80 -1 N VAL A 74 O PHE A 92 SHEET 3 A 5 THR A 143 ILE A 148 1 O ILE A 144 N LYS A 79 SHEET 4 A 5 ILE A 117 LEU A 121 -1 N LEU A 120 O THR A 145 SHEET 5 A 5 LYS A 124 VAL A 125 -1 O LYS A 124 N LEU A 121 CISPEP 1 ALA A 83 PRO A 84 1 -1.35 CISPEP 2 ALA A 83 PRO A 84 2 -1.31 CISPEP 3 ALA A 83 PRO A 84 3 -1.11 CISPEP 4 ALA A 83 PRO A 84 4 -1.64 CISPEP 5 ALA A 83 PRO A 84 5 -1.25 CISPEP 6 ALA A 83 PRO A 84 6 -1.66 CISPEP 7 ALA A 83 PRO A 84 7 -1.77 CISPEP 8 ALA A 83 PRO A 84 8 -1.40 CISPEP 9 ALA A 83 PRO A 84 9 -1.47 CISPEP 10 ALA A 83 PRO A 84 10 -0.74 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1