HEADER PROTEIN TRANSPORT 15-JUL-10 2L0T TITLE SOLUTION STRUCTURE OF THE COMPLEX OF UBIQUITIN AND THE VHS DOMAIN OF TITLE 2 STAM2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SIGNAL TRANSDUCING ADAPTER MOLECULE 2; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: VHS DOMAIN (UNP RESIDUES 1-150); COMPND 9 SYNONYM: STAM-2, HRS-BINDING PROTEIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET4A; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: STAM2, HBP; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PETM60 KEYWDS UBIQUITIN, VHS, STAM2, ENDOSOME, TRANSPORT, PROTEIN TRANSPORT EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.LANGE,D.HOELLER,H.WIENK,O.MARCILLAT,J.LANCELIN,O.WALKER REVDAT 2 14-MAR-12 2L0T 1 JRNL VERSN REVDAT 1 15-DEC-10 2L0T 0 JRNL AUTH A.LANGE,D.HOELLER,H.WIENK,O.MARCILLAT,J.M.LANCELIN,O.WALKER JRNL TITL NMR REVEALS A DIFFERENT MODE OF BINDING OF THE STAM2 VHS JRNL TITL 2 DOMAIN TO UBIQUITIN AND DIUBIQUITIN. JRNL REF BIOCHEMISTRY V. 50 48 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21121635 JRNL DOI 10.1021/BI101594A REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS-HADDOCK 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES, READ, REMARK 3 DOMINGUEZ, BOELENS, BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L0T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-10. REMARK 100 THE RCSB ID CODE IS RCSB101813. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 250 UM [U-99% 15N] UBIQUITIN REMARK 210 PROTEIN, 250 UM [U-99% 15N] VHS REMARK 210 DOMAIN OF STAM2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 15N R1 AND R2; REMARK 210 15N{1H} NOE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; DRX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS-HADDOCK 1.2, SPARKY, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING, DISTANCE REMARK 210 GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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 19 HZ3 LYS B 42 1.52 REMARK 500 OD1 ASP B 38 HZ1 LYS B 42 1.58 REMARK 500 HE2 HIS A 68 OE1 GLU B 31 1.58 REMARK 500 HZ1 LYS A 63 OE2 GLU A 64 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 ASP A 58 -35.71 -38.77 REMARK 500 1 THR B 24 52.52 -105.43 REMARK 500 1 THR B 29 -66.34 -105.53 REMARK 500 1 TRP B 33 49.11 -80.22 REMARK 500 1 SER B 34 -71.93 -55.92 REMARK 500 2 THR B 30 -81.98 -145.06 REMARK 500 2 PHE B 127 39.51 -92.12 REMARK 500 2 ALA B 153 32.31 -85.01 REMARK 500 3 ASP B 32 100.68 50.09 REMARK 500 3 ASN B 62 37.99 -90.69 REMARK 500 4 THR A 7 -146.61 -77.40 REMARK 500 4 LEU A 8 -63.67 -90.49 REMARK 500 4 THR A 22 133.74 -38.61 REMARK 500 4 ALA A 46 -4.18 66.94 REMARK 500 4 THR B 30 -65.85 -145.38 REMARK 500 4 GLU B 31 -51.79 -129.76 REMARK 500 4 ASP B 32 69.02 61.47 REMARK 500 4 ASN B 62 42.69 -84.02 REMARK 500 4 LYS B 107 61.78 60.88 REMARK 500 4 ALA B 153 36.81 -97.29 REMARK 500 5 THR A 7 -156.94 -80.54 REMARK 500 5 THR A 9 29.35 -140.64 REMARK 500 5 ILE A 13 -113.29 -111.64 REMARK 500 5 LEU A 56 -54.67 -12.24 REMARK 500 5 ASP A 58 -78.45 -55.43 REMARK 500 5 TYR A 59 -16.32 -49.19 REMARK 500 5 ASN A 60 45.89 74.67 REMARK 500 5 THR B 29 -59.76 -123.40 REMARK 500 5 PHE B 127 37.90 -99.90 REMARK 500 6 THR A 7 -118.05 -76.84 REMARK 500 6 LEU A 8 -58.44 -122.19 REMARK 500 6 THR A 9 -80.05 -66.53 REMARK 500 6 GLN A 62 -168.54 -102.20 REMARK 500 6 THR B 24 63.04 -119.27 REMARK 500 6 THR B 29 -86.11 -89.11 REMARK 500 6 GLU B 31 -61.03 -160.44 REMARK 500 6 ASP B 32 67.68 63.05 REMARK 500 6 ASN B 62 42.32 -94.46 REMARK 500 7 ARG A 74 95.53 -171.99 REMARK 500 7 SER B 6 -169.11 -112.05 REMARK 500 7 THR B 29 -78.53 -105.16 REMARK 500 7 ASP B 32 65.48 31.48 REMARK 500 7 SER B 34 -72.18 -90.89 REMARK 500 8 GLU A 64 -8.07 74.92 REMARK 500 8 ASP B 32 72.50 48.30 REMARK 500 8 TRP B 33 49.94 -76.61 REMARK 500 8 SER B 34 -75.80 -90.79 REMARK 500 8 ASN B 62 37.00 -85.39 REMARK 500 8 HIS B 109 117.65 -173.59 REMARK 500 9 THR A 7 -162.30 -79.03 REMARK 500 REMARK 500 THIS ENTRY HAS 68 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF UBIQUITIN REMARK 900 RELATED ID: 1X5B RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE VHS DOMAIN OF STAM1 DBREF 2L0T A 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 2L0T B 8 157 UNP O75886 STAM2_HUMAN 1 150 SEQADV 2L0T GLY B 1 UNP O75886 EXPRESSION TAG SEQADV 2L0T SER B 2 UNP O75886 EXPRESSION TAG SEQADV 2L0T SER B 3 UNP O75886 EXPRESSION TAG SEQADV 2L0T GLY B 4 UNP O75886 EXPRESSION TAG SEQADV 2L0T SER B 5 UNP O75886 EXPRESSION TAG SEQADV 2L0T SER B 6 UNP O75886 EXPRESSION TAG SEQADV 2L0T GLY B 7 UNP O75886 EXPRESSION TAG SEQADV 2L0T SER B 158 UNP O75886 EXPRESSION TAG SEQADV 2L0T GLY B 159 UNP O75886 EXPRESSION TAG SEQADV 2L0T PRO B 160 UNP O75886 EXPRESSION TAG SEQADV 2L0T SER B 161 UNP O75886 EXPRESSION TAG SEQADV 2L0T SER B 162 UNP O75886 EXPRESSION TAG SEQADV 2L0T GLY B 163 UNP O75886 EXPRESSION TAG SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 163 GLY SER SER GLY SER SER GLY MET PRO LEU PHE THR ALA SEQRES 2 B 163 ASN PRO PHE GLU GLN ASP VAL GLU LYS ALA THR ASN GLU SEQRES 3 B 163 TYR ASN THR THR GLU ASP TRP SER LEU ILE MET ASP ILE SEQRES 4 B 163 CYS ASP LYS VAL GLY SER THR PRO ASN GLY ALA LYS ASP SEQRES 5 B 163 CYS LEU LYS ALA ILE MET LYS ARG VAL ASN HIS LYS VAL SEQRES 6 B 163 PRO HIS VAL ALA LEU GLN ALA LEU THR LEU LEU GLY ALA SEQRES 7 B 163 CYS VAL ALA ASN CYS GLY LYS ILE PHE HIS LEU GLU VAL SEQRES 8 B 163 CYS SER ARG ASP PHE ALA THR GLU VAL ARG ALA VAL ILE SEQRES 9 B 163 LYS ASN LYS ALA HIS PRO LYS VAL CYS GLU LYS LEU LYS SEQRES 10 B 163 SER LEU MET VAL GLU TRP SER GLU GLU PHE GLN LYS ASP SEQRES 11 B 163 PRO GLN PHE SER LEU ILE SER ALA THR ILE LYS SER MET SEQRES 12 B 163 LYS GLU GLU GLY ILE THR PHE PRO PRO ALA GLY SER GLN SEQRES 13 B 163 THR SER GLY PRO SER SER GLY HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 ASN B 14 THR B 24 1 11 HELIX 3 3 TRP B 33 THR B 46 1 14 HELIX 4 4 ASN B 48 ASN B 62 1 15 HELIX 5 5 VAL B 65 CYS B 83 1 19 HELIX 6 6 GLY B 84 CYS B 92 1 9 HELIX 7 7 SER B 93 LYS B 107 1 15 HELIX 8 8 HIS B 109 PHE B 127 1 19 HELIX 9 9 PHE B 133 GLU B 145 1 13 SHEET 1 A 5 LYS A 11 GLU A 16 0 SHEET 2 A 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 156 0 0 9 5 0 0 6 0 0 0 19 END