HEADER LIGASE 27-AUG-12 2LXH TITLE NMR STRUCTURE OF THE RING DOMAIN IN UBIQUITIN LIGASE GP78 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE AMFR; COMPND 3 CHAIN: C; COMPND 4 FRAGMENT: RING-TYPE ZINC FINGER RESIDUES 313-393; COMPND 5 SYNONYM: AUTOCRINE MOTILITY FACTOR RECEPTOR, ISOFORM 2, AMF RECEPTOR, COMPND 6 ISOFORM 2, RING FINGER PROTEIN 45, GP78; COMPND 7 EC: 6.3.2.-; COMPND 8 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: AMFR, RNF45; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 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 3 14-JUN-23 2LXH 1 REMARK LINK REVDAT 2 02-OCT-13 2LXH 1 JRNL REVDAT 1 28-AUG-13 2LXH 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 2LXH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000102954. 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 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 LYS C 313 REMARK 465 ASN C 314 REMARK 465 TYR C 315 REMARK 465 LEU C 316 REMARK 465 ARG C 317 REMARK 465 VAL C 318 REMARK 465 VAL C 319 REMARK 465 GLY C 320 REMARK 465 ASN C 321 REMARK 465 MET C 322 REMARK 465 GLU C 323 REMARK 465 ALA C 324 REMARK 465 ARG C 325 REMARK 465 PHE C 326 REMARK 465 ALA C 385 REMARK 465 ASP C 386 REMARK 465 ASN C 387 REMARK 465 ASN C 388 REMARK 465 ARG C 389 REMARK 465 VAL C 390 REMARK 465 ARG C 391 REMARK 465 GLU C 392 REMARK 465 GLU C 393 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 H ARG C 352 O PHE C 360 1.50 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 ASP C 340 126.69 179.68 REMARK 500 1 ILE C 343 -69.72 -93.02 REMARK 500 1 TRP C 345 -178.77 58.82 REMARK 500 1 ASP C 346 -159.24 64.28 REMARK 500 1 MET C 348 -112.05 -143.91 REMARK 500 1 GLN C 349 -64.51 -139.17 REMARK 500 1 THR C 373 55.02 -97.81 REMARK 500 1 THR C 377 -62.05 -104.95 REMARK 500 1 ARG C 379 19.57 59.21 REMARK 500 2 ASP C 340 129.79 -171.86 REMARK 500 2 ILE C 343 -67.03 -91.79 REMARK 500 2 TRP C 345 21.34 41.52 REMARK 500 2 ASP C 346 -169.94 -102.24 REMARK 500 2 THR C 377 -62.52 -107.09 REMARK 500 2 ARG C 379 -0.34 65.00 REMARK 500 3 ASN C 338 62.74 -111.37 REMARK 500 3 ILE C 343 -66.54 -91.83 REMARK 500 3 TRP C 345 24.01 41.24 REMARK 500 3 ASP C 346 -161.50 -106.02 REMARK 500 3 ASP C 372 -112.82 -116.51 REMARK 500 3 THR C 373 -11.43 161.66 REMARK 500 3 THR C 377 -80.78 -88.38 REMARK 500 4 ASN C 338 62.31 -119.05 REMARK 500 4 ASP C 340 131.10 -170.54 REMARK 500 4 ILE C 343 -75.44 -92.31 REMARK 500 4 TRP C 345 36.98 73.41 REMARK 500 4 ASP C 346 -163.26 -124.85 REMARK 500 4 THR C 377 -60.06 -104.56 REMARK 500 5 ASN C 338 57.94 -149.86 REMARK 500 5 ASP C 339 49.53 -73.94 REMARK 500 5 ASP C 340 127.19 -176.47 REMARK 500 5 TRP C 345 22.53 40.65 REMARK 500 5 ASP C 346 -156.49 -98.51 REMARK 500 5 MET C 348 -127.25 -173.02 REMARK 500 5 GLN C 349 -65.01 -136.37 REMARK 500 5 ALA C 350 136.42 -35.87 REMARK 500 5 THR C 377 -67.22 -109.25 REMARK 500 5 ARG C 379 16.10 58.98 REMARK 500 5 ASN C 383 96.52 53.13 REMARK 500 6 ASN C 338 58.98 -111.86 REMARK 500 6 ASP C 340 139.47 -171.19 REMARK 500 6 ILE C 343 -75.01 -92.85 REMARK 500 6 TRP C 345 63.73 63.34 REMARK 500 6 ASP C 346 -152.10 -155.92 REMARK 500 6 MET C 348 -133.68 -170.85 REMARK 500 6 ASP C 372 -127.52 -104.45 REMARK 500 6 THR C 373 -7.11 159.74 REMARK 500 6 THR C 377 -66.69 -103.87 REMARK 500 6 LEU C 382 -167.43 -63.15 REMARK 500 7 ASN C 338 58.51 -147.24 REMARK 500 REMARK 500 THIS ENTRY HAS 148 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 93.9 REMARK 620 3 HIS C 361 ND1 115.0 134.3 REMARK 620 4 CYS C 364 SG 111.7 81.3 115.6 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 78.9 REMARK 620 3 CYS C 375 SG 103.6 140.0 REMARK 620 4 CYS C 378 SG 107.3 124.5 93.3 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: 18677 RELATED DB: BMRB DBREF 2LXH C 313 393 UNP Q9UKV5 AMFR2_HUMAN 313 393 SEQRES 1 C 81 LYS ASN TYR LEU ARG VAL VAL GLY ASN MET GLU ALA ARG SEQRES 2 C 81 PHE ALA VAL ALA THR PRO GLU GLU LEU ALA VAL ASN ASN SEQRES 3 C 81 ASP ASP CYS ALA ILE CYS TRP ASP SER MET GLN ALA ALA SEQRES 4 C 81 ARG LYS LEU PRO CYS GLY HIS LEU PHE HIS ASN SER CYS SEQRES 5 C 81 LEU ARG SER TRP LEU GLU GLN ASP THR SER CYS PRO THR SEQRES 6 C 81 CYS ARG MET SER LEU ASN ILE ALA ASP ASN ASN ARG VAL SEQRES 7 C 81 ARG GLU GLU HET ZN C 900 1 HET ZN C 901 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 PRO C 331 ASN C 338 1 8 HELIX 2 2 HIS C 361 ASP C 372 1 12 SHEET 1 A 2 ARG C 352 LYS C 353 0 SHEET 2 A 2 LEU C 359 PHE C 360 -1 O PHE C 360 N ARG C 352 LINK SG CYS C 341 ZN ZN C 900 1555 1555 2.21 LINK SG CYS C 344 ZN ZN C 900 1555 1555 2.37 LINK SG CYS C 356 ZN ZN C 901 1555 1555 2.24 LINK ND1 HIS C 358 ZN ZN C 901 1555 1555 2.09 LINK ND1 HIS C 361 ZN ZN C 900 1555 1555 2.08 LINK SG CYS C 364 ZN ZN C 900 1555 1555 2.25 LINK SG CYS C 375 ZN ZN C 901 1555 1555 2.19 LINK SG CYS C 378 ZN ZN C 901 1555 1555 2.36 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