HEADER LIGASE 30-AUG-12 2LXP TITLE NMR STRUCTURE OF TWO DOMAINS IN UBIQUITIN LIGASE GP78, RING AND G2BR, TITLE 2 BOUND TO ITS CONJUGATING ENZYME UBE2G COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 G2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-165; COMPND 5 SYNONYM: UBIQUITIN CARRIER PROTEIN G2, UBIQUITIN-PROTEIN LIGASE G2; COMPND 6 EC: 6.3.2.19; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE AMFR; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 574-600; COMPND 12 SYNONYM: AUTOCRINE MOTILITY FACTOR RECEPTOR, ISOFORM 2, AMF RECEPTOR, COMPND 13 ISOFORM 2, RING FINGER PROTEIN 45, GP78; COMPND 14 EC: 6.3.2.-; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE AMFR; COMPND 18 CHAIN: C; COMPND 19 FRAGMENT: UNP RESIDUES 327-384; COMPND 20 SYNONYM: AUTOCRINE MOTILITY FACTOR RECEPTOR, ISOFORM 2, AMF RECEPTOR, COMPND 21 ISOFORM 2, RING FINGER PROTEIN 45, GP78; COMPND 22 EC: 6.3.2.-; COMPND 23 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET3A; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: AMFR, RNF45; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PET3A; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 GENE: AMFR, RNF45; SOURCE 22 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 24 EXPRESSION_SYSTEM_VECTOR: PET3A KEYWDS RING DOMAIN, UBIQUITIN, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.DAS,Y.LINAG,J.MARIANO,J.LI,T.HUANG,A.KING,A.WEISSMAN,X.JI,R.BYRD REVDAT 4 15-MAY-24 2LXP 1 REMARK REVDAT 3 14-JUN-23 2LXP 1 REMARK LINK REVDAT 2 02-OCT-13 2LXP 1 JRNL REVDAT 1 28-AUG-13 2LXP 0 JRNL AUTH R.DAS,Y.H.LIANG,J.MARIANO,J.LI,T.HUANG,A.KING,S.G.TARASOV, JRNL AUTH 2 A.M.WEISSMAN,X.JI,R.A.BYRD JRNL TITL ALLOSTERIC REGULATION OF E2:E3 INTERACTIONS PROMOTE A JRNL TITL 2 PROCESSIVE UBIQUITINATION MACHINE. JRNL REF EMBO J. V. 32 2504 2013 JRNL REFN ISSN 0261-4189 JRNL PMID 23942235 JRNL DOI 10.1038/EMBOJ.2013.174 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LXP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000102962. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7-1 MM [U-100% 13C; U-100% REMARK 210 15N] GP78RING, 50 MM TRIS, 2 MM REMARK 210 TCEP, 0.2 MM SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 C(CO)NH; 3D H(CCO)NH; 3D 1H-15N REMARK 210 NOESY; 3D 1H-15N TOCSY; 3D HNCO; REMARK 210 3D 1H-13C NOESY; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, NMRDRAW, CNS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST HADDOCK SCORES 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI 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 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 OE1 GLU A 38 HZ3 LYS B 586 1.58 REMARK 500 HZ3 LYS A 7 OD2 ASP C 346 1.59 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 ASN A 33 87.51 -157.07 REMARK 500 1 ASP A 46 17.44 80.64 REMARK 500 1 PRO A 65 31.30 -95.99 REMARK 500 1 PHE A 78 52.68 -140.09 REMARK 500 1 PRO A 96 33.72 -85.38 REMARK 500 1 PRO A 130 88.50 -64.80 REMARK 500 1 ASP C 339 37.87 -78.81 REMARK 500 1 ILE C 343 -69.40 -99.94 REMARK 500 1 TRP C 345 -161.91 62.16 REMARK 500 1 ASP C 346 -168.01 60.57 REMARK 500 1 CYS C 378 -38.76 -135.51 REMARK 500 2 PRO A 65 36.91 -98.73 REMARK 500 2 THR A 74 49.85 -97.38 REMARK 500 2 CYS A 75 -165.29 -162.73 REMARK 500 2 ALA A 107 -65.09 -108.25 REMARK 500 2 ASP A 132 102.25 -57.12 REMARK 500 2 GLU A 133 -71.48 -114.83 REMARK 500 2 ASP A 146 -79.20 -100.18 REMARK 500 2 ALA C 342 35.68 -75.83 REMARK 500 2 ILE C 343 -62.70 -138.13 REMARK 500 2 TRP C 345 -159.58 60.65 REMARK 500 2 ASP C 346 -146.70 58.50 REMARK 500 2 PRO C 376 -70.67 -42.64 REMARK 500 2 THR C 377 40.33 -79.16 REMARK 500 2 CYS C 378 -39.04 -148.10 REMARK 500 3 ASP A 46 36.41 70.31 REMARK 500 3 PRO A 65 34.54 -96.76 REMARK 500 3 THR A 74 55.43 -110.97 REMARK 500 3 PHE A 78 56.85 -145.78 REMARK 500 3 PRO A 96 101.26 -57.97 REMARK 500 3 ASP A 146 -81.64 -112.22 REMARK 500 3 ALA C 342 38.09 -76.31 REMARK 500 3 ILE C 343 -54.18 -140.32 REMARK 500 3 TRP C 345 -147.03 61.04 REMARK 500 3 ASP C 346 -153.86 59.81 REMARK 500 3 PRO C 376 -75.74 -42.46 REMARK 500 4 ASN A 33 86.92 -150.57 REMARK 500 4 PRO A 65 33.09 -95.95 REMARK 500 4 PHE A 78 55.55 -111.11 REMARK 500 4 ARG A 109 -161.02 -111.19 REMARK 500 4 ASP A 132 83.45 -67.05 REMARK 500 4 ASP A 146 -76.27 -138.32 REMARK 500 4 ASN C 338 78.57 -109.95 REMARK 500 4 ASP C 339 42.71 -83.40 REMARK 500 4 ALA C 342 23.23 -76.01 REMARK 500 4 ILE C 343 -54.96 -133.40 REMARK 500 4 TRP C 345 -168.98 65.46 REMARK 500 4 ASP C 346 -147.61 57.64 REMARK 500 4 GLN C 349 32.56 -85.35 REMARK 500 4 PRO C 376 -70.37 -44.32 REMARK 500 REMARK 500 THIS ENTRY HAS 267 RAMACHANDRAN OUTLIERS. 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 C 900 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 341 SG REMARK 620 2 CYS C 344 SG 101.5 REMARK 620 3 HIS C 361 ND1 93.0 138.8 REMARK 620 4 CYS C 364 SG 104.0 90.6 123.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 356 SG REMARK 620 2 HIS C 358 ND1 121.6 REMARK 620 3 CYS C 375 SG 92.8 114.3 REMARK 620 4 CYS C 378 SG 107.9 114.9 101.7 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 C 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18688 RELATED DB: BMRB DBREF 2LXP A 2 165 UNP P60604 UB2G2_HUMAN 2 165 DBREF 2LXP B 574 600 UNP Q9UKV5 AMFR2_HUMAN 574 600 DBREF 2LXP C 327 384 UNP Q9UKV5 AMFR2_HUMAN 327 384 SEQRES 1 A 164 ALA GLY THR ALA LEU LYS ARG LEU MET ALA GLU TYR LYS SEQRES 2 A 164 GLN LEU THR LEU ASN PRO PRO GLU GLY ILE VAL ALA GLY SEQRES 3 A 164 PRO MET ASN GLU GLU ASN PHE PHE GLU TRP GLU ALA LEU SEQRES 4 A 164 ILE MET GLY PRO GLU ASP THR CYS PHE GLU PHE GLY VAL SEQRES 5 A 164 PHE PRO ALA ILE LEU SER PHE PRO LEU ASP TYR PRO LEU SEQRES 6 A 164 SER PRO PRO LYS MET ARG PHE THR CYS GLU MET PHE HIS SEQRES 7 A 164 PRO ASN ILE TYR PRO ASP GLY ARG VAL CYS ILE SER ILE SEQRES 8 A 164 LEU HIS ALA PRO GLY ASP ASP PRO MET GLY TYR GLU SER SEQRES 9 A 164 SER ALA GLU ARG TRP SER PRO VAL GLN SER VAL GLU LYS SEQRES 10 A 164 ILE LEU LEU SER VAL VAL SER MET LEU ALA GLU PRO ASN SEQRES 11 A 164 ASP GLU SER GLY ALA ASN VAL ASP ALA SER LYS MET TRP SEQRES 12 A 164 ARG ASP ASP ARG GLU GLN PHE TYR LYS ILE ALA LYS GLN SEQRES 13 A 164 ILE VAL GLN LYS SER LEU GLY LEU SEQRES 1 B 27 SER ALA ASP GLU ARG GLN ARG MET LEU VAL GLN ARG LYS SEQRES 2 B 27 ASP GLU LEU LEU GLN GLN ALA ARG LYS ARG PHE LEU ASN SEQRES 3 B 27 LYS SEQRES 1 C 58 ALA VAL ALA THR PRO GLU GLU LEU ALA VAL ASN ASN ASP SEQRES 2 C 58 ASP CYS ALA ILE CYS TRP ASP SER MET GLN ALA ALA ARG SEQRES 3 C 58 LYS LEU PRO CYS GLY HIS LEU PHE HIS ASN SER CYS LEU SEQRES 4 C 58 ARG SER TRP LEU GLU GLN ASP THR SER CYS PRO THR CYS SEQRES 5 C 58 ARG MET SER LEU ASN ILE HET ZN C 900 1 HET ZN C 901 1 HETNAM ZN ZINC ION FORMUL 4 ZN 2(ZN 2+) HELIX 1 1 GLY A 3 THR A 17 1 15 HELIX 2 2 ILE A 90 HIS A 94 5 5 HELIX 3 3 SER A 115 GLU A 129 1 15 HELIX 4 4 ASN A 137 ASP A 147 1 11 HELIX 5 5 ASP A 147 GLY A 164 1 18 HELIX 6 6 ASP B 576 LYS B 600 1 25 HELIX 7 7 PRO C 331 ASN C 338 1 8 HELIX 8 8 ASN C 362 ASP C 372 1 11 SHEET 1 A 4 ILE A 24 ASN A 30 0 SHEET 2 A 4 ASN A 33 MET A 42 -1 O GLU A 38 N GLY A 27 SHEET 3 A 4 VAL A 53 SER A 59 -1 O ALA A 56 N ALA A 39 SHEET 4 A 4 LYS A 70 PHE A 73 -1 O ARG A 72 N ILE A 57 SHEET 1 B 2 ALA C 351 LEU C 354 0 SHEET 2 B 2 HIS C 358 HIS C 361 -1 O HIS C 358 N LEU C 354 LINK SG CYS C 341 ZN ZN C 900 1555 1555 2.48 LINK SG CYS C 344 ZN ZN C 900 1555 1555 2.15 LINK SG CYS C 356 ZN ZN C 901 1555 1555 2.26 LINK ND1 HIS C 358 ZN ZN C 901 1555 1555 1.80 LINK ND1 HIS C 361 ZN ZN C 900 1555 1555 1.84 LINK SG CYS C 364 ZN ZN C 900 1555 1555 2.24 LINK SG CYS C 375 ZN ZN C 901 1555 1555 2.23 LINK SG CYS C 378 ZN ZN C 901 1555 1555 2.14 CISPEP 1 TYR A 64 PRO A 65 1 0.82 CISPEP 2 TYR A 64 PRO A 65 2 0.55 CISPEP 3 TYR A 64 PRO A 65 3 0.56 CISPEP 4 TYR A 64 PRO A 65 4 0.40 CISPEP 5 TYR A 64 PRO A 65 5 0.94 CISPEP 6 TYR A 64 PRO A 65 6 0.42 CISPEP 7 TYR A 64 PRO A 65 7 0.22 CISPEP 8 TYR A 64 PRO A 65 8 0.42 CISPEP 9 TYR A 64 PRO A 65 9 0.06 CISPEP 10 TYR A 64 PRO A 65 10 0.08 CISPEP 11 TYR A 64 PRO A 65 11 0.57 CISPEP 12 TYR A 64 PRO A 65 12 0.57 CISPEP 13 TYR A 64 PRO A 65 13 -0.30 CISPEP 14 TYR A 64 PRO A 65 14 0.75 CISPEP 15 TYR A 64 PRO A 65 15 0.71 CISPEP 16 TYR A 64 PRO A 65 16 0.93 CISPEP 17 TYR A 64 PRO A 65 17 0.36 CISPEP 18 TYR A 64 PRO A 65 18 0.04 CISPEP 19 TYR A 64 PRO A 65 19 0.27 CISPEP 20 TYR A 64 PRO A 65 20 0.80 SITE 1 AC1 4 CYS C 341 CYS C 344 HIS C 361 CYS C 364 SITE 1 AC2 4 CYS C 356 HIS C 358 CYS C 375 CYS C 378 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