PDB Short entry for 2KQ0 HEADER LIGASE 23-OCT-09 2KQ0 TITLE HUMAN NEDD4 3RD WW DOMAIN COMPLEX WITH EBOLA ZAIRE VIRUS MATRIX TITLE 2 PROTEIN VP40 DERIVED PEPTIDE ILPTAPPEYMEA COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE NEDD4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 3RD WW DOMAIN, UNP RESIDUES 834-878; COMPND 5 SYNONYM: NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN- COMPND 6 REGULATED PROTEIN 4, NEDD-4, CELL PROLIFERATION-INDUCING GENE 53 COMPND 7 PROTEIN; COMPND 8 EC: 6.3.2.-; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 12-MER FROM MATRIX PROTEIN VP40; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: UNP RESIDUES 5-16; COMPND 14 SYNONYM: MEMBRANE-ASSOCIATED PROTEIN VP40; COMPND 15 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: NEDD4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PETM11; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HUMAN T-CELL LYMPHOTROPHIC VIRUS TYPE 1 ISOLATE SOURCE 14 MEL 15; SOURCE 15 ORGANISM_COMMON: HTLV-1; SOURCE 16 ORGANISM_TAXID: 402046; SOURCE 17 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS WW DOMAIN, COMPLEX, VIRUS L DOMAIN, NEDD4, EBOLA, HOST-VIRUS KEYWDS 2 INTERACTION, LIGASE, PHOSPHOPROTEIN, UBL CONJUGATION PATHWAY, CELL KEYWDS 3 MEMBRANE, RIBONUCLEOPROTEIN, RNA REPLICATION, RNA-BINDING, VIRAL KEYWDS 4 MATRIX PROTEIN, VIRION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.IGLESIAS-BEXIGA,M.MACIAS,R.BONET,F.J.BLANCO,E.S.COBOS,I.LUQUE REVDAT 2 26-FEB-20 2KQ0 1 REMARK SEQADV REVDAT 1 03-NOV-10 2KQ0 0 JRNL AUTH M.IGLESIAS-BEXIGA JRNL TITL HUMAN NEDD4 3RD WW DOMAIN COMPLEX WITH EBOLA ZAIRE VIRUS JRNL TITL 2 MATRIX PROTEIN VP40 DERIVED PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XEASY, CNSSOLVE REMARK 3 AUTHORS : BARTELS ET AL. (XEASY), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNSSOLVE) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KQ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000101429. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 7.00 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM [U-100% 15N] PROTEIN; 10MM REMARK 210 PEPTIDE; 20MM SODIUM PHOSPHATE; REMARK 210 0.02 V/V % SODIUM AZIDE; 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY, CNSSOLVE, TOPSPIN REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 120 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 764 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3556 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.3 KCAL/MOL 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 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 GLY A 1 REMARK 465 ALA A 2 REMARK 465 MET A 3 REMARK 465 GLY A 4 REMARK 465 PRO A 5 REMARK 465 SER A 6 REMARK 465 GLU A 7 REMARK 465 ILE A 8 REMARK 465 GLU A 9 REMARK 465 GLN A 10 REMARK 465 GLY A 11 REMARK 465 PRO A 47 REMARK 465 ALA A 48 REMARK 465 HIS A 49 REMARK 465 ILE B 109 REMARK 465 LEU B 110 REMARK 465 PRO B 111 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 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 PRO A 14 139.95 -35.93 REMARK 500 1 LYS A 35 73.57 58.32 REMARK 500 1 ALA B 113 97.77 72.45 REMARK 500 1 MET B 118 91.53 -163.35 REMARK 500 2 PRO A 23 3.65 -64.36 REMARK 500 2 LYS A 35 97.19 -57.68 REMARK 500 2 PRO A 42 -9.44 -58.23 REMARK 500 2 MET B 118 105.75 -160.03 REMARK 500 2 GLU B 119 123.52 -173.49 REMARK 500 3 PRO A 23 5.85 -67.67 REMARK 500 3 LYS A 35 81.12 57.71 REMARK 500 3 MET B 118 103.65 -162.46 REMARK 500 4 PRO A 23 10.64 -67.33 REMARK 500 4 LYS A 35 78.13 56.02 REMARK 500 4 MET B 118 48.87 -152.38 REMARK 500 5 PRO A 14 150.30 -41.19 REMARK 500 5 PRO A 23 6.15 -66.22 REMARK 500 5 LYS A 35 73.48 59.54 REMARK 500 5 MET B 118 88.38 -155.19 REMARK 500 6 LYS A 35 89.82 55.21 REMARK 500 6 MET B 118 95.45 -162.23 REMARK 500 6 GLU B 119 -87.37 -105.91 REMARK 500 7 PRO A 14 131.57 -33.15 REMARK 500 7 PRO A 23 14.10 -68.58 REMARK 500 7 LYS A 35 72.58 54.13 REMARK 500 7 GLU A 40 -93.94 -78.34 REMARK 500 7 ASP A 41 122.82 -177.02 REMARK 500 7 PRO A 42 -9.47 -56.56 REMARK 500 7 MET B 118 95.45 -170.05 REMARK 500 8 PRO A 23 2.77 -62.20 REMARK 500 8 LYS A 35 76.42 60.49 REMARK 500 8 MET B 118 80.53 -161.45 REMARK 500 9 PRO A 23 6.86 -66.99 REMARK 500 9 LYS A 35 98.98 -34.91 REMARK 500 10 PRO A 14 -131.35 -43.75 REMARK 500 10 LYS A 35 70.75 49.93 REMARK 500 10 PRO A 42 -9.85 -57.47 REMARK 500 10 LYS A 45 112.26 -173.94 REMARK 500 10 MET B 118 99.64 -170.99 REMARK 500 11 PRO A 23 12.53 -67.48 REMARK 500 11 LYS A 35 83.50 53.69 REMARK 500 11 ASP A 41 105.20 66.20 REMARK 500 11 MET B 118 99.71 -164.20 REMARK 500 12 LYS A 35 83.14 58.60 REMARK 500 12 MET B 118 105.96 -179.52 REMARK 500 13 PRO A 23 12.00 -67.72 REMARK 500 13 MET B 118 105.07 -168.42 REMARK 500 14 LYS A 15 -90.79 38.79 REMARK 500 14 PRO A 23 6.27 -65.23 REMARK 500 14 LYS A 35 88.59 54.53 REMARK 500 REMARK 500 THIS ENTRY HAS 80 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16575 RELATED DB: BMRB REMARK 900 RELATED ID: 2KPZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ANOTHER PEPTIDE DBREF 2KQ0 A 5 49 UNP P46934 NEDD4_HUMAN 834 878 DBREF 2KQ0 B 109 120 UNP Q05128 VP40_EBOZM 5 16 SEQADV 2KQ0 GLY A 1 UNP P46934 EXPRESSION TAG SEQADV 2KQ0 ALA A 2 UNP P46934 EXPRESSION TAG SEQADV 2KQ0 MET A 3 UNP P46934 EXPRESSION TAG SEQADV 2KQ0 GLY A 4 UNP P46934 EXPRESSION TAG SEQRES 1 A 49 GLY ALA MET GLY PRO SER GLU ILE GLU GLN GLY PHE LEU SEQRES 2 A 49 PRO LYS GLY TRP GLU VAL ARG HIS ALA PRO ASN GLY ARG SEQRES 3 A 49 PRO PHE PHE ILE ASP HIS ASN THR LYS THR THR THR TRP SEQRES 4 A 49 GLU ASP PRO ARG LEU LYS ILE PRO ALA HIS SEQRES 1 B 12 ILE LEU PRO THR ALA PRO PRO GLU TYR MET GLU ALA HELIX 1 1 PHE A 12 LYS A 45 0 34 SHEET 1 A 3 TRP A 17 ALA A 22 0 SHEET 2 A 3 ARG A 26 ASP A 31 -1 O ARG A 26 N ALA A 22 SHEET 3 A 3 THR A 36 THR A 38 -1 O THR A 38 N PHE A 29 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