HEADER PROTEIN BINDING 16-DEC-09 2KRE
TITLE SOLUTION STRUCTURE OF E4B/UFD2A U-BOX DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UBIQUITIN CONJUGATION FACTOR E4 B;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 1208-1302;
COMPND 5 SYNONYM: UBIQUITIN FUSION DEGRADATION PROTEIN 2, HOMOZYGOUSLY DELETED
COMPND 6 IN NEUROBLASTOMA 1;
COMPND 7 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: HDNB1, KIAA0684, UBE4B, UFD2;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET15B
KEYWDS U-BOX DOMAIN, E3 UBIQUITIN LIGASE, E4 POLYUBIQUITIN CHAIN ELONGATION
KEYWDS 2 FACTOR, PHOSPHOPROTEIN, UBL CONJUGATION PATHWAY, PROTEIN BINDING
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR Y.NOMINE,E.WASIELEWSKI,M.BOTUYAN,G.MER
REVDAT 2 25-AUG-10 2KRE 1 JRNL
REVDAT 1 29-DEC-09 2KRE 0
JRNL AUTH R.C.BENIRSCHKE,J.R.THOMPSON,Y.NOMINE,E.WASIELEWSKI,
JRNL AUTH 2 N.JURANIC,S.MACURA,S.HATAKEYAMA,K.I.NAKAYAMA,M.V.BOTUYAN,
JRNL AUTH 3 G.MER
JRNL TITL MOLECULAR BASIS FOR THE ASSOCIATION OF HUMAN E4B U BOX
JRNL TITL 2 UBIQUITIN LIGASE WITH E2-CONJUGATING ENZYMES UBCH5C AND
JRNL TITL 3 UBC4.
JRNL REF STRUCTURE V. 18 955 2010
JRNL REFN ISSN 0969-2126
JRNL PMID 20696396
JRNL DOI 10.1016/J.STR.2010.04.017
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XPLOR-NIH 2.11.1
REMARK 3 AUTHORS : SCHWIETERS & CLORE
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2KRE COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-DEC-09.
REMARK 100 THE RCSB ID CODE IS RCSB101479.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 50 MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1-2 MM [U-100% 13C; U-100% 15N]
REMARK 210 E4B U-BOX DOMAIN-1, 20 MM SODIUM
REMARK 210 PHOSPHATE-2, 50 MM SODIUM
REMARK 210 CHLORIDE-3, 2 MM DTT-4, 93% H2O/
REMARK 210 7% D2O; 1-2 MM [U-100% 15N] E4B U
REMARK 210 -BOX DOMAIN-5, 20 MM SODIUM
REMARK 210 PHOSPHATE-6, 50 MM SODIUM
REMARK 210 CHLORIDE-7, 2 MM DTT-8, 93% H2O/
REMARK 210 7% D2O; 1-2 MM [U-100% 13C; U-
REMARK 210 100% 15N] E4B U-BOX DOMAIN-9, 20
REMARK 210 MM SODIUM PHOSPHATE-10, 50 MM
REMARK 210 SODIUM CHLORIDE-11, 100% D2O; 2
REMARK 210 MM E4B U-BOX DOMAIN-12, 20 MM
REMARK 210 SODIUM PHOSPHATE-13, 50 MM SODIUM
REMARK 210 CHLORIDE-14, 2 MM DTT-15, 93%
REMARK 210 H2O/7% D2O; 1-2 MM E4B U-BOX
REMARK 210 DOMAIN-16, 20 MM SODIUM PHOSPHATE
REMARK 210 -17, 50 MM SODIUM CHLORIDE-18, 2
REMARK 210 MM DTT-19, 100% D2O; 1-2 MM [U-
REMARK 210 100% 13C; U-100% 15N; U-80% 2H]
REMARK 210 E4B U-BOX DOMAIN-20, 20 MM SODIUM
REMARK 210 PHOSPHATE-21, 50 MM SODIUM
REMARK 210 CHLORIDE-22, 2 MM DTT-23, 93%
REMARK 210 H2O/7% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_ 15N-
REMARK 210 SEPARATED_NOESY; 2D 1H-1H NOESY;
REMARK 210 HBOND-J; 3J(NC(GAMMA)); 2D 1H-15N
REMARK 210 HSQC; 2D 1H-13C HSQC; 3D HNCO; 3D
REMARK 210 HN(CA)CO; 3D HNCA; 3D HN(CO)CA;
REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D
REMARK 210 HBHA(CO)NH; 3D H(CCO)NH; 3D
REMARK 210 CCONH; 3D HCCH-TOCSY; 2D 1H-1H
REMARK 210 TOCSY; 3D 1H-15N TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : CYANA 2.1
REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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: A
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 H THR A 1242 OD2 ASP A 1254 1.31
REMARK 500 O PHE A 1270 H ARG A 1272 1.45
REMARK 500 O PRO A 1266 H LEU A 1275 1.53
REMARK 500 O PRO A 1229 H GLU A 1231 1.55
REMARK 500 O ARG A 1260 H LEU A 1263 1.58
REMARK 500 OD1 ASP A 1234 H LEU A 1236 1.58
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 A1204 108.11 -165.71
REMARK 500 1 HIS A1205 -93.89 -46.38
REMARK 500 1 PHE A1207 -85.08 -96.77
REMARK 500 1 GLU A1209 -19.31 -38.12
REMARK 500 1 LYS A1210 93.35 -56.80
REMARK 500 1 GLU A1212 -135.27 -159.46
REMARK 500 1 ILE A1214 78.82 -67.58
REMARK 500 1 VAL A1215 -91.32 -124.03
REMARK 500 1 ALA A1216 84.39 -34.58
REMARK 500 1 ASN A1218 -6.14 -160.96
REMARK 500 1 ALA A1219 63.19 -160.40
REMARK 500 1 ARG A1220 -134.35 30.44
REMARK 500 1 ASP A1224 -75.77 -25.15
REMARK 500 1 TYR A1225 72.93 -59.18
REMARK 500 1 ASP A1227 -55.94 -134.18
REMARK 500 1 ALA A1228 156.87 77.98
REMARK 500 1 PRO A1229 174.36 -46.90
REMARK 500 1 ASP A1230 48.02 -68.55
REMARK 500 1 GLU A1231 -80.04 -135.32
REMARK 500 1 PHE A1232 -2.09 -56.84
REMARK 500 1 ASP A1238 7.62 50.15
REMARK 500 1 ASP A1243 86.72 -170.68
REMARK 500 1 ARG A1255 -17.13 -39.07
REMARK 500 1 SER A1265 95.41 153.16
REMARK 500 1 ASP A1268 142.88 -22.43
REMARK 500 1 PHE A1270 -105.87 -102.41
REMARK 500 1 ASN A1271 35.48 -62.06
REMARK 500 1 ARG A1272 63.26 24.72
REMARK 500 1 THR A1274 120.54 -39.86
REMARK 500 1 GLU A1277 170.26 -59.37
REMARK 500 1 SER A1278 -28.03 69.84
REMARK 500 1 GLU A1285 -8.18 -57.44
REMARK 500 1 ALA A1292 -80.67 -70.94
REMARK 500 1 GLU A1296 -2.57 -52.90
REMARK 500 1 ASN A1299 44.82 35.24
REMARK 500 1 SER A1300 83.92 -163.41
REMARK 500 2 SER A1204 -96.81 -35.47
REMARK 500 2 LYS A1206 -177.47 49.60
REMARK 500 2 GLU A1209 -138.04 -115.10
REMARK 500 2 GLU A1213 -152.84 -148.68
REMARK 500 2 VAL A1215 -77.69 75.63
REMARK 500 2 ALA A1216 134.09 60.82
REMARK 500 2 LYS A1217 -85.88 -41.73
REMARK 500 2 ASN A1218 134.14 -34.45
REMARK 500 2 ARG A1220 -63.61 -141.17
REMARK 500 2 GLU A1222 -169.70 -103.97
REMARK 500 2 ASP A1224 -64.50 63.64
REMARK 500 2 SER A1226 -39.84 -22.90
REMARK 500 2 ALA A1228 -179.99 -57.81
REMARK 500 2 ASP A1234 117.84 -35.96
REMARK 500
REMARK 500 THIS ENTRY HAS 725 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 2KRE A 1208 1302 UNP O95155 UBE4B_HUMAN 1208 1302
SEQADV 2KRE GLY A 1203 UNP O95155 EXPRESSION TAG
SEQADV 2KRE SER A 1204 UNP O95155 EXPRESSION TAG
SEQADV 2KRE HIS A 1205 UNP O95155 EXPRESSION TAG
SEQADV 2KRE LYS A 1206 UNP O95155 EXPRESSION TAG
SEQADV 2KRE PHE A 1207 UNP O95155 EXPRESSION TAG
SEQRES 1 A 100 GLY SER HIS LYS PHE ALA GLU LYS VAL GLU GLU ILE VAL
SEQRES 2 A 100 ALA LYS ASN ALA ARG ALA GLU ILE ASP TYR SER ASP ALA
SEQRES 3 A 100 PRO ASP GLU PHE ARG ASP PRO LEU MET ASP THR LEU MET
SEQRES 4 A 100 THR ASP PRO VAL ARG LEU PRO SER GLY THR ILE MET ASP
SEQRES 5 A 100 ARG SER ILE ILE LEU ARG HIS LEU LEU ASN SER PRO THR
SEQRES 6 A 100 ASP PRO PHE ASN ARG GLN THR LEU THR GLU SER MET LEU
SEQRES 7 A 100 GLU PRO VAL PRO GLU LEU LYS GLU GLN ILE GLN ALA TRP
SEQRES 8 A 100 MET ARG GLU LYS GLN ASN SER ASP HIS
HELIX 1 1 ARG A 1255 LEU A 1262 1 8
HELIX 2 2 VAL A 1283 GLU A 1296 1 14
SHEET 1 A 3 THR A1251 ASP A1254 0
SHEET 2 A 3 PRO A1244 LEU A1247 -1 N VAL A1245 O MET A1253
SHEET 3 A 3 GLU A1281 PRO A1282 -1 O GLU A1281 N ARG A1246
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
(ATOM LINES ARE NOT SHOWN.)
END
