HEADER NUCLEAR PROTEIN 15-JUN-07 2Z4D
TITLE NMR STRUCTURES OF YEAST PROTEASOME COMPONENT RPN13
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 26S PROTEASOME REGULATORY SUBUNIT RPN13;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 6-101;
COMPND 5 SYNONYM: PROTEASOME COMPONENT RPN13, PROTEASOME NON-ATPASE SUBUNIT
COMPND 6 13;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 3 ORGANISM_COMMON: YEAST;
SOURCE 4 ORGANISM_TAXID: 4932;
SOURCE 5 GENE: RPN13;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET
KEYWDS PROTEASOME, PH DOMAIN, NUCLEAR PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR N.ZHANG,K.J.WALTERS
REVDAT 4 16-MAR-22 2Z4D 1 REMARK
REVDAT 3 19-JAN-10 2Z4D 1 JRNL
REVDAT 2 24-FEB-09 2Z4D 1 VERSN
REVDAT 1 20-MAY-08 2Z4D 0
JRNL AUTH K.HUSNJAK,S.ELSASSER,N.ZHANG,X.CHEN,L.RANDLES,Y.SHI,
JRNL AUTH 2 K.HOFMANN,K.J.WALTERS,D.FINLEY,I.DIKIC
JRNL TITL PROTEASOME SUBUNIT RPN13 IS A NOVEL UBIQUITIN RECEPTOR.
JRNL REF NATURE V. 453 481 2008
JRNL REFN ISSN 0028-0836
JRNL PMID 18497817
JRNL DOI 10.1038/NATURE06926
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE 2006, X-PLOR 3.851
REMARK 3 AUTHORS : FRANK DELAGLIO, STEPHAN GRZESIEK, GUANG ZHU,
REMARK 3 GEERTEN W. VUISTER, JOHN PFEIFER AND AD BAX
REMARK 3 (NMRPIPE), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 1084 RESTRAINTS, 949 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 79
REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 56 DISTANCE RESTRAINTS FROM HYDROGEN
REMARK 3 BONDS.
REMARK 4
REMARK 4 2Z4D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUN-07.
REMARK 100 THE DEPOSITION ID IS D_1000027505.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : 20MM PHOSPHATE, 50MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.4MM RPN13 U-15N, 13C; U-70%
REMARK 210 2H; 20MM PHOSPHATE BUFFER; 50MM
REMARK 210 NACL; 4MM DTT; 90% H2O, 10% D2O;
REMARK 210 0.5MM RPN13 U-15N; U-50% 2H;
REMARK 210 20MM PHOSPHATE BUFFER; 50MM NACL;
REMARK 210 4MM DTT; 90% H2O, 10% D2O;
REMARK 210 0.5MM RPN13 U-13C; 20MM
REMARK 210 PHOSPHATE BUFFER; 50MM NACL; 4MM
REMARK 210 DTT; 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCACB, HNCA/HN(CO)CA,
REMARK 210 HNCO/HN(CA)CO; 3D_15N-SEPARATED_
REMARK 210 NOESY; 3D_13C-SEPARATED_NOESY;
REMARK 210 HCCH-TOCSY
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 : XEASY 1996, X-PLOR 3.851
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 35
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8
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: 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: 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 ALA A 12 -158.65 -150.15
REMARK 500 1 VAL A 14 -142.27 -103.88
REMARK 500 1 CYS A 15 108.30 -163.75
REMARK 500 1 ASN A 38 164.63 65.02
REMARK 500 1 GLU A 40 38.33 -147.82
REMARK 500 1 ARG A 51 146.32 -177.50
REMARK 500 1 GLU A 54 -169.09 -116.20
REMARK 500 1 PRO A 56 -167.34 -78.29
REMARK 500 1 VAL A 57 49.88 -148.59
REMARK 500 1 LEU A 61 -162.15 -116.53
REMARK 500 1 GLU A 72 -68.29 -133.10
REMARK 500 1 LYS A 79 49.33 -104.67
REMARK 500 1 SER A 80 -173.61 53.27
REMARK 500 1 SER A 81 -168.08 52.43
REMARK 500 1 ARG A 85 94.06 -162.45
REMARK 500 1 PHE A 91 -79.65 -92.03
REMARK 500 1 SER A 92 -39.59 -172.82
REMARK 500 1 SER A 93 -81.58 -83.64
REMARK 500 1 ASN A 94 15.76 -150.82
REMARK 500 1 GLU A 95 49.53 -90.51
REMARK 500 2 ALA A 12 -155.04 -170.72
REMARK 500 2 VAL A 14 -141.51 -89.55
REMARK 500 2 CYS A 15 110.13 -162.99
REMARK 500 2 ASN A 38 150.16 62.45
REMARK 500 2 GLU A 40 -154.38 -133.74
REMARK 500 2 ARG A 51 146.20 -175.44
REMARK 500 2 GLU A 72 -76.87 -60.47
REMARK 500 2 THR A 73 -153.06 -71.71
REMARK 500 2 LYS A 79 50.38 -94.80
REMARK 500 2 ARG A 85 134.81 62.49
REMARK 500 2 PHE A 91 -61.62 -100.99
REMARK 500 2 SER A 92 -50.92 -142.53
REMARK 500 2 SER A 93 -29.23 -178.85
REMARK 500 3 VAL A 7 59.53 -111.20
REMARK 500 3 ALA A 12 -160.68 -161.81
REMARK 500 3 VAL A 14 -138.87 -95.53
REMARK 500 3 PRO A 37 55.41 -93.14
REMARK 500 3 ASN A 38 175.16 60.29
REMARK 500 3 TRP A 46 81.87 -66.78
REMARK 500 3 ARG A 51 146.89 179.55
REMARK 500 3 GLU A 54 -169.59 -100.62
REMARK 500 3 VAL A 57 30.69 -148.41
REMARK 500 3 LEU A 61 -163.46 -103.73
REMARK 500 3 GLU A 72 -80.55 -61.86
REMARK 500 3 SER A 81 -156.08 49.39
REMARK 500 3 LYS A 82 49.80 -98.99
REMARK 500 3 SER A 83 -76.26 -117.82
REMARK 500 3 ARG A 85 86.77 50.64
REMARK 500 3 PHE A 91 -70.85 -117.32
REMARK 500 3 SER A 92 -68.04 -133.94
REMARK 500
REMARK 500 THIS ENTRY HAS 128 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 ARG A 11 0.29 SIDE CHAIN
REMARK 500 1 ARG A 22 0.32 SIDE CHAIN
REMARK 500 1 ARG A 51 0.23 SIDE CHAIN
REMARK 500 1 ARG A 59 0.23 SIDE CHAIN
REMARK 500 1 ARG A 85 0.27 SIDE CHAIN
REMARK 500 1 ARG A 96 0.28 SIDE CHAIN
REMARK 500 2 ARG A 11 0.32 SIDE CHAIN
REMARK 500 2 ARG A 22 0.31 SIDE CHAIN
REMARK 500 2 ARG A 51 0.25 SIDE CHAIN
REMARK 500 2 ARG A 59 0.32 SIDE CHAIN
REMARK 500 2 ARG A 85 0.25 SIDE CHAIN
REMARK 500 2 ARG A 96 0.32 SIDE CHAIN
REMARK 500 3 ARG A 11 0.22 SIDE CHAIN
REMARK 500 3 ARG A 22 0.31 SIDE CHAIN
REMARK 500 3 ARG A 51 0.24 SIDE CHAIN
REMARK 500 3 ARG A 59 0.31 SIDE CHAIN
REMARK 500 3 ARG A 85 0.26 SIDE CHAIN
REMARK 500 3 ARG A 96 0.27 SIDE CHAIN
REMARK 500 4 ARG A 11 0.30 SIDE CHAIN
REMARK 500 4 ARG A 22 0.26 SIDE CHAIN
REMARK 500 4 ARG A 51 0.32 SIDE CHAIN
REMARK 500 4 ARG A 59 0.25 SIDE CHAIN
REMARK 500 4 ARG A 85 0.26 SIDE CHAIN
REMARK 500 4 ARG A 96 0.16 SIDE CHAIN
REMARK 500 5 ARG A 11 0.21 SIDE CHAIN
REMARK 500 5 ARG A 22 0.25 SIDE CHAIN
REMARK 500 5 ARG A 51 0.31 SIDE CHAIN
REMARK 500 5 ARG A 59 0.32 SIDE CHAIN
REMARK 500 5 ARG A 85 0.32 SIDE CHAIN
REMARK 500 5 ARG A 96 0.23 SIDE CHAIN
REMARK 500 6 ARG A 11 0.25 SIDE CHAIN
REMARK 500 6 ARG A 22 0.28 SIDE CHAIN
REMARK 500 6 ARG A 51 0.31 SIDE CHAIN
REMARK 500 6 ARG A 59 0.32 SIDE CHAIN
REMARK 500 6 ARG A 85 0.23 SIDE CHAIN
REMARK 500 6 ARG A 96 0.22 SIDE CHAIN
REMARK 500 7 ARG A 11 0.30 SIDE CHAIN
REMARK 500 7 ARG A 22 0.27 SIDE CHAIN
REMARK 500 7 ARG A 51 0.23 SIDE CHAIN
REMARK 500 7 ARG A 59 0.32 SIDE CHAIN
REMARK 500 7 ARG A 85 0.25 SIDE CHAIN
REMARK 500 7 ARG A 96 0.27 SIDE CHAIN
REMARK 500 8 ARG A 11 0.28 SIDE CHAIN
REMARK 500 8 ARG A 22 0.29 SIDE CHAIN
REMARK 500 8 ARG A 51 0.28 SIDE CHAIN
REMARK 500 8 ARG A 59 0.25 SIDE CHAIN
REMARK 500 8 ARG A 85 0.25 SIDE CHAIN
REMARK 500 8 ARG A 96 0.24 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1UBQ RELATED DB: PDB
REMARK 900 STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION
REMARK 900 RELATED ID: 2COC RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE C-TERMINAL PH DOMAIN OF FYVE, RHOGEF AND
REMARK 900 PH DOMAIN CONTAINING PROTEIN 3 (FGD3) FROM HUMAN
REMARK 900 RELATED ID: 2DHK RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE PH DOMAIN OF TBC1 DOMAIN FAMILY MEMBER 2
REMARK 900 PROTEIN FROM HUMAN
REMARK 900 RELATED ID: 2HTH RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS FOR UBIQUITIN RECOGNITION BY THE HUMAN EAP45/ESCRT-
REMARK 900 II GLUE DOMAIN
REMARK 900 RELATED ID: 1FHO RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE PH DOMAIN FROM THE C. ELEGANS MUSCLE
REMARK 900 PROTEIN UNC-89
REMARK 900 RELATED ID: 2D9V RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE PH DOMAIN OF PLECKSTRIN HOMOLOGY DOMAIN-
REMARK 900 CONTAINING PROTEIN FAMILY B MEMBER 1 FROM MOUSE
DBREF 2Z4D A 6 101 UNP O13563 RPN13_YEAST 6 101
SEQRES 1 A 96 THR VAL ILE LYS PHE ARG ALA GLY VAL CYS GLU TYR ASN
SEQRES 2 A 96 GLU ASP SER ARG LEU CYS THR PRO ILE PRO VAL GLN GLY
SEQRES 3 A 96 GLU ILE GLU ILE LYS PRO ASN GLU GLU GLU GLU LEU GLY
SEQRES 4 A 96 PHE TRP ASP PHE GLU TRP ARG PRO THR GLU LYS PRO VAL
SEQRES 5 A 96 GLY ARG GLU LEU ASP PRO ILE SER LEU ILE LEU ILE PRO
SEQRES 6 A 96 GLY GLU THR MET TRP VAL PRO ILE LYS SER SER LYS SER
SEQRES 7 A 96 GLY ARG ILE PHE ALA LEU VAL PHE SER SER ASN GLU ARG
SEQRES 8 A 96 TYR PHE PHE TRP LEU
SHEET 1 A 4 ILE A 8 PHE A 10 0
SHEET 2 A 4 ILE A 33 PRO A 37 -1 O ILE A 33 N PHE A 10
SHEET 3 A 4 TRP A 46 TRP A 50 -1 O GLU A 49 N GLU A 34
SHEET 4 A 4 ILE A 64 LEU A 66 -1 O LEU A 66 N PHE A 48
SHEET 1 B 2 CYS A 15 ASN A 18 0
SHEET 2 B 2 LEU A 23 PRO A 26 -1 O LEU A 23 N ASN A 18
SHEET 1 C 3 MET A 74 VAL A 76 0
SHEET 2 C 3 ILE A 86 VAL A 90 -1 O VAL A 90 N MET A 74
SHEET 3 C 3 TYR A 97 TRP A 100 -1 O TYR A 97 N LEU A 89
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