HEADER LIGASE/SIGNALING PROTEIN 22-APR-05 1ZGU
TITLE SOLUTION STRUCTURE OF THE HUMAN MMS2-UBIQUITIN COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: MMS2, ENTEROCYTE DIFFERENTIATION ASSOCIATED FACTOR EDAF-1,
COMPND 5 ENTEROCYTE DIFFERENTIATION PROMOTING FACTOR, EDPF-1, VITAMIN D3
COMPND 6 INDUCIBLE PROTEIN, DDVIT 1;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: UBIQUITIN;
COMPND 10 CHAIN: B;
COMPND 11 ENGINEERED: YES;
COMPND 12 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: UBE2V2, MMS2;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P;
SOURCE 11 MOL_ID: 2;
SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 13 ORGANISM_COMMON: HUMAN;
SOURCE 14 ORGANISM_TAXID: 9606;
SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL;
SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET3A
KEYWDS UEV DOMAIN, UBIQUITIN BINDING MOTIF, LIGASE-SIGNALING PROTEIN COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR M.J.LEWIS,L.F.SALTIBUS,D.D.HAU,W.XIAO,L.SPYRACOPOULOS
REVDAT 3 20-OCT-21 1ZGU 1 REMARK SEQADV
REVDAT 2 24-FEB-09 1ZGU 1 VERSN
REVDAT 1 04-APR-06 1ZGU 0
JRNL AUTH M.J.LEWIS,L.F.SALTIBUS,D.D.HAU,W.XIAO,L.SPYRACOPOULOS
JRNL TITL STRUCTURAL BASIS FOR NON-COVALENT INTERACTION BETWEEN
JRNL TITL 2 UBIQUITIN AND THE UBIQUITIN CONJUGATING ENZYME VARIANT HUMAN
JRNL TITL 3 MMS2.
JRNL REF J.BIOMOL.NMR V. 34 89 2006
JRNL REFN ISSN 0925-2738
JRNL PMID 16518696
JRNL DOI 10.1007/S10858-005-5583-6
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 6.1C, HADDOCK 1.3
REMARK 3 AUTHORS : VARIAN, INC. (VNMR), DOMINGUEZ, C., BOELENS, R.,
REMARK 3 BONVIN, A.M.J.J. (HADDOCK)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HADDOCK ALGORITHM
REMARK 4
REMARK 4 1ZGU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-05.
REMARK 100 THE DEPOSITION ID IS D_1000032705.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293; 303
REMARK 210 PH : 7.5; 7.5
REMARK 210 IONIC STRENGTH : 150 MM NACL; 150 MM NACL
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : [U-15N; U-10% 13C]-HMMS2 +
REMARK 210 UBIQUITIN (1:4 RATIO) 90% H20 :
REMARK 210 10% D20; [U-13C; U-15N]-
REMARK 210 UBIQUITIN + HMMS2 (4:1 RATIO) 90%
REMARK 210 H20 : 10% D20; [U-13C; U-15N]-
REMARK 210 HMMS2 + UBIQUITIN (1:4 RATIO) 90%
REMARK 210 H20 : 10% D20
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : F1-FILTERED, F3-EDITED NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 2.3, SPARKY 3.110,
REMARK 210 HADDOCK 1.3
REMARK 210 METHOD USED : PROTEIN-PROTEIN DOCKING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
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 : 10
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: DIMERIC
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 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 OD2 ASP B 21 HZ1 LYS B 29 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 THR A 35 31.14 -93.52
REMARK 500 1 ASP A 43 -48.61 74.94
REMARK 500 1 LYS A 113 58.26 -108.62
REMARK 500 1 GLN B 62 -165.58 -102.80
REMARK 500 2 GLU A 41 -78.49 -77.42
REMARK 500 2 ARG A 60 -35.79 73.88
REMARK 500 2 LYS A 113 57.43 -111.33
REMARK 500 2 ASN A 136 -45.79 -135.06
REMARK 500 2 ARG B 74 98.76 -164.20
REMARK 500 3 ASP A 43 10.39 53.50
REMARK 500 3 LYS A 113 44.95 -109.32
REMARK 500 3 GLN B 62 -166.75 -109.80
REMARK 500 3 GLU B 64 -2.30 69.24
REMARK 500 4 ASP A 43 -44.59 75.54
REMARK 500 4 GLU A 64 109.32 -50.60
REMARK 500 4 LYS A 113 57.05 -115.87
REMARK 500 4 ASN A 136 -37.34 -137.12
REMARK 500 5 ASP A 42 -51.02 -163.71
REMARK 500 5 ASP A 43 -46.80 76.98
REMARK 500 5 LYS A 113 50.05 -115.62
REMARK 500 5 ASN A 136 -41.60 -136.22
REMARK 500 5 GLN B 62 -166.46 -101.54
REMARK 500 5 GLU B 64 -8.65 70.93
REMARK 500 5 LEU B 73 108.35 -59.07
REMARK 500 6 ASP A 43 -49.82 73.10
REMARK 500 7 ASP A 43 -80.79 57.41
REMARK 500 7 ARG A 60 -4.73 73.28
REMARK 500 7 ASN A 65 -5.83 76.89
REMARK 500 7 SER A 99 -62.48 -98.24
REMARK 500 7 LYS A 113 40.90 -108.35
REMARK 500 7 ASN A 136 -42.70 -131.37
REMARK 500 8 ASP A 33 -72.23 -62.55
REMARK 500 8 ASP A 43 -72.49 67.29
REMARK 500 9 LYS A 13 97.89 -69.58
REMARK 500 9 GLU A 41 -66.31 -92.45
REMARK 500 9 ASP A 43 -51.95 74.57
REMARK 500 9 LYS A 113 62.52 -112.97
REMARK 500 9 ASN A 136 -42.48 -130.13
REMARK 500 10 ASP A 43 -50.18 73.77
REMARK 500 10 ASN A 65 -10.80 72.53
REMARK 500 10 SER A 99 -60.83 -101.43
REMARK 500 10 LYS A 113 59.97 -107.90
REMARK 500 10 ASN A 136 -35.11 -134.11
REMARK 500 10 GLN B 62 -169.60 -117.32
REMARK 500
REMARK 500 REMARK: NULL
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 YEAST UBIQUITIN WAS USED TO OBTAIN RESTRAINT INFORMATION,
REMARK 999 WHILE HUMAN UBIQUITIN WAS USED TO MODEL THE INTERACTION.
REMARK 999 THE SEQUENCE DIFFERENCES BETWEEN YEAST AND HUMAN
REMARK 999 UBIQUITIN ARE ABSENT FROM THE PROTEIN-PROTEIN BINDING
REMARK 999 INTERFACE.
DBREF 1ZGU A 12 150 UNP Q15819 U2V2_HUMAN 7 145
DBREF 1ZGU B 1 76 UNP P61864 UBIQ_YEAST 1 76
SEQADV 1ZGU PRO B 19 UNP P61864 SER 19 SEE REMARK 999
SEQADV 1ZGU GLU B 24 UNP P61864 ASP 24 SEE REMARK 999
SEQADV 1ZGU ALA B 28 UNP P61864 SER 28 SEE REMARK 999
SEQADV 1ZGU ARG B 48 UNP P61864 LYS 48 ENGINEERED MUTATION
SEQRES 1 A 139 VAL LYS VAL PRO ARG ASN PHE ARG LEU LEU GLU GLU LEU
SEQRES 2 A 139 GLU GLU GLY GLN LYS GLY VAL GLY ASP GLY THR VAL SER
SEQRES 3 A 139 TRP GLY LEU GLU ASP ASP GLU ASP MET THR LEU THR ARG
SEQRES 4 A 139 TRP THR GLY MET ILE ILE GLY PRO PRO ARG THR ASN TYR
SEQRES 5 A 139 GLU ASN ARG ILE TYR SER LEU LYS VAL GLU CYS GLY PRO
SEQRES 6 A 139 LYS TYR PRO GLU ALA PRO PRO SER VAL ARG PHE VAL THR
SEQRES 7 A 139 LYS ILE ASN MET ASN GLY ILE ASN ASN SER SER GLY MET
SEQRES 8 A 139 VAL ASP ALA ARG SER ILE PRO VAL LEU ALA LYS TRP GLN
SEQRES 9 A 139 ASN SER TYR SER ILE LYS VAL VAL LEU GLN GLU LEU ARG
SEQRES 10 A 139 ARG LEU MET MET SER LYS GLU ASN MET LYS LEU PRO GLN
SEQRES 11 A 139 PRO PRO GLU GLY GLN THR TYR ASN ASN
SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE
SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL
SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP
SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY ARG GLN LEU GLU ASP
SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER
SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY
HELIX 1 1 LYS A 13 GLY A 30 1 18
HELIX 2 2 ILE A 108 LYS A 113 1 6
HELIX 3 3 SER A 119 MET A 132 1 14
HELIX 4 4 SER A 133 LYS A 138 1 6
HELIX 5 5 THR B 22 GLU B 34 1 13
HELIX 6 6 PRO B 37 ASP B 39 5 3
HELIX 7 7 THR B 55 ASN B 60 5 6
SHEET 1 A 4 VAL A 36 LEU A 40 0
SHEET 2 A 4 TRP A 51 ILE A 56 -1 O THR A 52 N GLY A 39
SHEET 3 A 4 ILE A 67 GLU A 73 -1 O LEU A 70 N GLY A 53
SHEET 4 A 4 SER A 84 PHE A 87 -1 O ARG A 86 N LYS A 71
SHEET 1 B 5 THR B 12 GLU B 16 0
SHEET 2 B 5 GLN B 2 THR B 7 -1 N VAL B 5 O ILE B 13
SHEET 3 B 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6
SHEET 4 B 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70
SHEET 5 B 5 ARG B 48 GLN B 49 -1 O ARG B 48 N PHE B 45
CISPEP 1 TYR A 78 PRO A 79 1 0.20
CISPEP 2 TYR A 78 PRO A 79 2 0.04
CISPEP 3 TYR A 78 PRO A 79 3 -0.19
CISPEP 4 TYR A 78 PRO A 79 4 0.73
CISPEP 5 TYR A 78 PRO A 79 5 0.50
CISPEP 6 TYR A 78 PRO A 79 6 0.29
CISPEP 7 TYR A 78 PRO A 79 7 0.28
CISPEP 8 TYR A 78 PRO A 79 8 -0.24
CISPEP 9 TYR A 78 PRO A 79 9 0.44
CISPEP 10 TYR A 78 PRO A 79 10 -0.08
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
