PDB Short entry for 2K3W HEADER PROTEIN TRANSPORT 19-MAY-08 2K3W TITLE NMR STRUCTURE OF VPS4A-MIT-CHMP6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATING PROTEIN 4A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MIT DOMAIN; COMPND 5 SYNONYM: PROTEIN SKD2, HVPS4, VPS4-1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CHARGED MULTIVESICULAR BODY PROTEIN 6; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 166-181; COMPND 11 SYNONYM: CHROMATIN-MODIFYING PROTEIN 6, VACUOLAR PROTEIN SORTING- COMPND 12 ASSOCIATED PROTEIN 20, HVPS20; COMPND 13 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: VPS4A, VPS4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET16; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: CHMP6, VPS20; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PET16 KEYWDS ESRCT-III, CHMP6, MIT, ATP-BINDING, MEMBRANE, NUCLEOTIDE-BINDING, KEYWDS 2 PROTEIN TRANSPORT, TRANSPORT, COILED COIL, ENDOSOME, LIPOPROTEIN, KEYWDS 3 MYRISTATE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.KIEFFER,J.J.SKALICKY,E.MORITA,I.DE DOMINI,D.M.WARD,J.KAPLAN, AUTHOR 2 W.I.SUNDQUIST REVDAT 3 16-MAR-22 2K3W 1 REMARK REVDAT 2 24-FEB-09 2K3W 1 VERSN REVDAT 1 28-OCT-08 2K3W 0 JRNL AUTH C.KIEFFER,J.J.SKALICKY,E.MORITA,I.DE DOMENICO,D.M.WARD, JRNL AUTH 2 J.KAPLAN,W.I.SUNDQUIST JRNL TITL TWO DISTINCT MODES OF ESCRT-III RECOGNITION ARE REQUIRED FOR JRNL TITL 2 VPS4 FUNCTIONS IN LYSOSOMAL PROTEIN TARGETING AND HIV-1 JRNL TITL 3 BUDDING JRNL REF DEV.CELL V. 15 62 2008 JRNL REFN ISSN 1534-5807 JRNL PMID 18606141 JRNL DOI 10.1016/J.DEVCEL.2008.05.014 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.19, X-PLOR NIH 2.19 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 2K3W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000100643. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.8 REMARK 210 IONIC STRENGTH : 75 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.4 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN, 1.8 MM PEPTIDE, 25 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 1 MM EDTA, 10 % D2O, REMARK 210 90% H2O/10% D2O; 1.22 MM [U-99% REMARK 210 13C; U-99% 15N] PEPTIDE, 1.55 MM REMARK 210 PROTEIN, 25 MM SODIUM PHOSPHATE, REMARK 210 50 MM SODIUM CHLORIDE, 1 MM EDTA, REMARK 210 10 % D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCA; 3D HNCACB; 3D HBHA(CO)NH; REMARK 210 3D HN(CO)CA; 3D HCCH-COSY; 3D REMARK 210 H(CCO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 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: 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 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 MET A 1 REMARK 465 THR A 2 REMARK 465 SER A 76 REMARK 465 LYS A 77 REMARK 465 GLU A 78 REMARK 465 LYS A 79 REMARK 465 HIS A 80 REMARK 465 GLY A 81 REMARK 465 LYS A 82 REMARK 465 LYS A 83 REMARK 465 PRO A 84 REMARK 465 GLU B 166 REMARK 465 GLN B 167 REMARK 465 GLU B 180 REMARK 465 LYS B 181 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 ASN A 24 69.38 -102.14 REMARK 500 1 PRO B 177 49.28 -92.19 REMARK 500 2 ASN A 24 68.40 -100.18 REMARK 500 3 PRO B 177 47.65 -68.64 REMARK 500 4 ASN A 24 68.29 -107.99 REMARK 500 4 ALA A 47 -98.40 -82.92 REMARK 500 4 HIS A 48 178.82 85.97 REMARK 500 4 PRO B 177 57.09 -67.99 REMARK 500 5 ALA A 47 84.23 -17.50 REMARK 500 5 HIS A 48 -143.25 -79.38 REMARK 500 5 PRO B 177 46.55 -70.74 REMARK 500 6 ALA A 47 100.01 -7.89 REMARK 500 6 PRO B 177 20.43 -66.84 REMARK 500 7 ASN A 24 67.03 -100.77 REMARK 500 8 ASN A 24 71.20 -103.18 REMARK 500 8 PRO B 177 70.13 -68.12 REMARK 500 9 ASN A 24 69.49 -102.28 REMARK 500 9 PRO B 177 31.06 -65.41 REMARK 500 9 LEU B 178 151.94 -43.50 REMARK 500 10 GLU A 46 -123.30 -85.99 REMARK 500 10 ALA A 47 15.89 174.49 REMARK 500 10 HIS A 48 151.66 -47.73 REMARK 500 10 PRO B 177 46.64 -72.93 REMARK 500 11 ASN A 24 69.98 -104.09 REMARK 500 11 PRO B 177 49.32 -89.02 REMARK 500 12 GLU A 46 -118.85 -85.87 REMARK 500 12 ALA A 47 33.20 164.75 REMARK 500 12 HIS A 48 -161.90 -54.30 REMARK 500 12 PRO B 177 39.72 -93.98 REMARK 500 13 GLU A 46 -112.79 -84.07 REMARK 500 13 ALA A 47 63.66 159.13 REMARK 500 14 GLU A 46 -118.52 -92.52 REMARK 500 14 ALA A 47 -89.92 -165.03 REMARK 500 14 HIS A 48 -179.25 63.79 REMARK 500 14 PRO B 177 29.23 -63.78 REMARK 500 15 GLU A 46 -110.25 -88.06 REMARK 500 15 ALA A 47 72.41 156.47 REMARK 500 15 PRO B 177 55.91 -93.23 REMARK 500 16 GLU A 46 -120.17 -87.19 REMARK 500 16 ALA A 47 32.75 164.33 REMARK 500 16 HIS A 48 -162.62 -54.78 REMARK 500 16 PRO B 177 47.43 -87.27 REMARK 500 16 LEU B 178 155.57 -44.02 REMARK 500 17 PRO B 177 37.88 -65.30 REMARK 500 18 ASN A 24 69.11 -104.05 REMARK 500 18 PRO B 177 43.58 -70.62 REMARK 500 19 ALA A 47 129.63 -20.47 REMARK 500 19 HIS A 48 -143.71 -122.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 2K3W A 1 84 UNP Q9UN37 VPS4A_HUMAN 1 84 DBREF 2K3W B 166 181 UNP Q96FZ7 CHMP6_HUMAN 166 181 SEQRES 1 A 84 MET THR THR SER THR LEU GLN LYS ALA ILE ASP LEU VAL SEQRES 2 A 84 THR LYS ALA THR GLU GLU ASP LYS ALA LYS ASN TYR GLU SEQRES 3 A 84 GLU ALA LEU ARG LEU TYR GLN HIS ALA VAL GLU TYR PHE SEQRES 4 A 84 LEU HIS ALA ILE LYS TYR GLU ALA HIS SER ASP LYS ALA SEQRES 5 A 84 LYS GLU SER ILE ARG ALA LYS CYS VAL GLN TYR LEU ASP SEQRES 6 A 84 ARG ALA GLU LYS LEU LYS ASP TYR LEU ARG SER LYS GLU SEQRES 7 A 84 LYS HIS GLY LYS LYS PRO SEQRES 1 B 16 GLU GLN ILE GLU LEU PRO GLU VAL PRO SER GLU PRO LEU SEQRES 2 B 16 PRO GLU LYS HELIX 1 1 SER A 4 ALA A 22 1 19 HELIX 2 2 ASN A 24 GLU A 46 1 23 HELIX 3 3 SER A 49 ARG A 75 1 27 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