PDB Short entry for 2KR0 HEADER PROTEIN BINDING 25-NOV-09 2KR0 TITLE SOLUTION STRUCTURE OF THE PROTEASOME UBIQUITIN RECEPTOR RPN13 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASOMAL UBIQUITIN RECEPTOR ADRM1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADHESION-REGULATING MOLECULE 1, ARM-1, 110 KDA CELL MEMBRANE COMPND 5 GLYCOPROTEIN, GP110, RPN13 HOMOLOG, PROTEASOME REGULATORY PARTICLE COMPND 6 NON-ATPASE 13, HRPN13; COMPND 7 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: ADRM1, GP110; 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, UBIQUITIN, 19S REGULATOR, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 31 AUTHOR X.CHEN,B.LEE,D.FINLEY,K.J.WALTERS REVDAT 3 29-NOV-17 2KR0 1 HELIX REVDAT 2 23-DEC-15 2KR0 1 TITLE VERSN REVDAT 1 26-MAY-10 2KR0 0 JRNL AUTH X.CHEN,B.H.LEE,D.FINLEY,K.J.WALTERS JRNL TITL STRUCTURE OF PROTEASOME UBIQUITIN RECEPTOR HRPN13 AND ITS JRNL TITL 2 ACTIVATION BY THE SCAFFOLDING PROTEIN HRPN2. JRNL REF MOL.CELL V. 38 404 2010 JRNL REFN ISSN 1097-2765 JRNL PMID 20471946 JRNL DOI 10.1016/J.MOLCEL.2010.04.019 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ, X-PLOR_NIH REMARK 3 AUTHORS : VARIAN (VNMRJ), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR_NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE OF TWO FUNCTIONAL DOMAIN REMARK 3 OF THE PROTEIN IS CALCULATED BASED ON THEIR NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, HYDROGEN BONDS AND DIHEDRAL ANGLE RESTRAINTS. THE REMARK 3 PARAMAGNETIC RELAXATION ENHANCEMENT FROM SPIN-LABELING REMARK 3 EXPERIMENTS AND INTER-DOMAIN NOE HELP DEFINE THE STRUCTURE OF REMARK 3 FULL PROTEIN. REMARK 4 REMARK 4 2KR0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000101465. 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 : 20 MM PHOSPHATE, 50 MM NACL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 0.1 MM [U-15N] PROTEIN, 0.1 MM REMARK 210 [U-15N; U-50% 2H] PROTEIN, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE 2.5, XEASY 6.4, REMARK 210 CARA 1.8.4, X-PLOR_NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 31 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: THE SPECTRA TOOK IN BRUKER ADVANCE 700 MHZ ARE A SET OF REMARK 210 SPIN-LABELING EXPERIMENTS TO ACHIEVE PRE DATA. 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 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 1-31 REMARK 465 RES C SSSEQI REMARK 465 GLY A -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 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 HZ1 LYS A 30 OD2 ASP A 41 1.51 REMARK 500 OE2 GLU A 119 HZ3 LYS A 123 1.53 REMARK 500 OE1 GLU A 81 HZ1 LYS A 99 1.53 REMARK 500 HE ARG A 122 OE2 GLU A 126 1.54 REMARK 500 HZ3 LYS A 371 OD2 ASP A 373 1.55 REMARK 500 HH12 ARG A 84 OE2 GLU A 118 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 4 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 6 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 7 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 11 ARG A 309 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 15 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 19 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 21 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 24 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 26 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 27 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 30 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES 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 2 -37.15 -136.07 REMARK 500 1 PHE A 8 -46.54 -135.28 REMARK 500 1 SER A 15 -130.96 -145.59 REMARK 500 1 ARG A 16 19.64 85.75 REMARK 500 1 ALA A 18 10.93 86.27 REMARK 500 1 LYS A 42 45.53 -74.84 REMARK 500 1 SER A 55 19.82 87.84 REMARK 500 1 ASP A 78 -1.49 76.58 REMARK 500 1 SER A 102 8.46 83.22 REMARK 500 1 MET A 133 64.09 65.53 REMARK 500 1 SER A 142 20.24 -144.46 REMARK 500 1 SER A 148 -47.54 -154.71 REMARK 500 1 ALA A 149 36.84 73.11 REMARK 500 1 LEU A 150 -177.70 85.79 REMARK 500 1 GLU A 153 143.55 88.65 REMARK 500 1 ALA A 175 -64.52 -146.61 REMARK 500 1 ALA A 185 -173.18 72.42 REMARK 500 1 ALA A 192 25.27 -143.60 REMARK 500 1 SER A 197 22.61 80.77 REMARK 500 1 PRO A 201 152.73 -49.50 REMARK 500 1 SER A 206 42.64 -144.81 REMARK 500 1 SER A 211 39.98 -151.78 REMARK 500 1 SER A 213 1.30 -152.48 REMARK 500 1 VAL A 216 48.07 -87.46 REMARK 500 1 SER A 220 -73.27 78.60 REMARK 500 1 THR A 222 30.50 -150.02 REMARK 500 1 ALA A 227 53.85 -159.71 REMARK 500 1 ALA A 245 -41.71 -139.66 REMARK 500 1 PRO A 246 -2.15 -58.56 REMARK 500 1 SER A 247 110.40 -35.14 REMARK 500 1 ASN A 250 61.98 87.73 REMARK 500 1 SER A 253 -41.50 -154.00 REMARK 500 1 THR A 254 104.34 -57.54 REMARK 500 1 GLN A 263 -3.55 74.80 REMARK 500 1 ASN A 275 -28.76 -154.20 REMARK 500 1 SER A 316 137.05 90.08 REMARK 500 1 ASN A 329 -37.91 -131.05 REMARK 500 1 THR A 332 -91.57 -109.76 REMARK 500 1 SER A 333 -52.32 -163.54 REMARK 500 1 ASN A 384 46.39 -99.39 REMARK 500 1 PRO A 387 -160.01 -73.67 REMARK 500 1 GLU A 388 58.23 -67.15 REMARK 500 1 GLN A 389 144.70 78.79 REMARK 500 1 ASP A 396 52.62 -151.80 REMARK 500 1 GLU A 400 167.13 83.84 REMARK 500 1 ASP A 403 -54.81 78.77 REMARK 500 2 THR A 3 -5.01 -140.09 REMARK 500 2 ALA A 6 -7.31 81.76 REMARK 500 2 PHE A 8 60.33 65.09 REMARK 500 2 ARG A 16 -13.95 89.95 REMARK 500 REMARK 500 THIS ENTRY HAS 1425 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 392 ASP A 393 9 148.69 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 22 TYR A 94 0.09 SIDE CHAIN REMARK 500 31 TYR A 48 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2R2Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PROTEASOMAL RPN13 PRU-DOMAIN REMARK 900 RELATED ID: 2Z4D RELATED DB: PDB REMARK 900 NMR STRUCTURES OF YEAST PROTEASOME COMPONENT RPN13 REMARK 900 RELATED ID: 2Z59 RELATED DB: PDB REMARK 900 COMPLEX STRUCTURES OF MOUSE RPN13 (22-130AA) AND UBIQUITIN REMARK 900 RELATED ID: 3IHR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UCH37 REMARK 900 RELATED ID: 2KQZ RELATED DB: PDB DBREF 2KR0 A 1 407 UNP Q16186 ADRM1_HUMAN 1 407 SEQADV 2KR0 GLY A -3 UNP Q16186 EXPRESSION TAG SEQADV 2KR0 PRO A -2 UNP Q16186 EXPRESSION TAG SEQADV 2KR0 GLY A -1 UNP Q16186 EXPRESSION TAG SEQADV 2KR0 SER A 0 UNP Q16186 EXPRESSION TAG SEQRES 1 A 411 GLY PRO GLY SER MET THR THR SER GLY ALA LEU PHE PRO SEQRES 2 A 411 SER LEU VAL PRO GLY SER ARG GLY ALA SER ASN LYS TYR SEQRES 3 A 411 LEU VAL GLU PHE ARG ALA GLY LYS MET SER LEU LYS GLY SEQRES 4 A 411 THR THR VAL THR PRO ASP LYS ARG LYS GLY LEU VAL TYR SEQRES 5 A 411 ILE GLN GLN THR ASP ASP SER LEU ILE HIS PHE CYS TRP SEQRES 6 A 411 LYS ASP ARG THR SER GLY ASN VAL GLU ASP ASP LEU ILE SEQRES 7 A 411 ILE PHE PRO ASP ASP CYS GLU PHE LYS ARG VAL PRO GLN SEQRES 8 A 411 CYS PRO SER GLY ARG VAL TYR VAL LEU LYS PHE LYS ALA SEQRES 9 A 411 GLY SER LYS ARG LEU PHE PHE TRP MET GLN GLU PRO LYS SEQRES 10 A 411 THR ASP GLN ASP GLU GLU HIS CYS ARG LYS VAL ASN GLU SEQRES 11 A 411 TYR LEU ASN ASN PRO PRO MET PRO GLY ALA LEU GLY ALA SEQRES 12 A 411 SER GLY SER SER GLY HIS GLU LEU SER ALA LEU GLY GLY SEQRES 13 A 411 GLU GLY GLY LEU GLN SER LEU LEU GLY ASN MET SER HIS SEQRES 14 A 411 SER GLN LEU MET GLN LEU ILE GLY PRO ALA GLY LEU GLY SEQRES 15 A 411 GLY LEU GLY GLY LEU GLY ALA LEU THR GLY PRO GLY LEU SEQRES 16 A 411 ALA SER LEU LEU GLY SER SER GLY PRO PRO GLY SER SER SEQRES 17 A 411 SER SER SER SER SER ARG SER GLN SER ALA ALA VAL THR SEQRES 18 A 411 PRO SER SER THR THR SER SER THR ARG ALA THR PRO ALA SEQRES 19 A 411 PRO SER ALA PRO ALA ALA ALA SER ALA THR SER PRO SER SEQRES 20 A 411 PRO ALA PRO SER SER GLY ASN GLY ALA SER THR ALA ALA SEQRES 21 A 411 SER PRO THR GLN PRO ILE GLN LEU SER ASP LEU GLN SER SEQRES 22 A 411 ILE LEU ALA THR MET ASN VAL PRO ALA GLY PRO ALA GLY SEQRES 23 A 411 GLY GLN GLN VAL ASP LEU ALA SER VAL LEU THR PRO GLU SEQRES 24 A 411 ILE MET ALA PRO ILE LEU ALA ASN ALA ASP VAL GLN GLU SEQRES 25 A 411 ARG LEU LEU PRO TYR LEU PRO SER GLY GLU SER LEU PRO SEQRES 26 A 411 GLN THR ALA ASP GLU ILE GLN ASN THR LEU THR SER PRO SEQRES 27 A 411 GLN PHE GLN GLN ALA LEU GLY MET PHE SER ALA ALA LEU SEQRES 28 A 411 ALA SER GLY GLN LEU GLY PRO LEU MET CYS GLN PHE GLY SEQRES 29 A 411 LEU PRO ALA GLU ALA VAL GLU ALA ALA ASN LYS GLY ASP SEQRES 30 A 411 VAL GLU ALA PHE ALA LYS ALA MET GLN ASN ASN ALA LYS SEQRES 31 A 411 PRO GLU GLN LYS GLU GLY ASP THR LYS ASP LYS LYS ASP SEQRES 32 A 411 GLU GLU GLU ASP MET SER LEU ASP HELIX 1 1 ASP A 117 ASN A 129 1 13 HELIX 2 2 LEU A 264 MET A 274 1 11 HELIX 3 3 GLN A 285 LEU A 288 1 4 HELIX 4 4 ALA A 298 LEU A 301 1 4 HELIX 5 5 ALA A 304 LEU A 310 1 7 HELIX 6 6 ALA A 324 ASN A 329 1 6 HELIX 7 7 PHE A 336 SER A 349 1 14 HELIX 8 8 GLY A 353 MET A 356 1 4 HELIX 9 9 GLU A 364 LYS A 371 1 8 HELIX 10 10 VAL A 374 ASN A 384 1 11 SHEET 1 1 1 TYR A 22 LYS A 34 0 SHEET 1 2 1 THR A 37 THR A 39 0 SHEET 1 3 1 GLY A 45 GLN A 51 0 SHEET 1 4 1 ILE A 57 ASP A 63 0 SHEET 1 5 1 VAL A 69 ILE A 75 0 SHEET 1 6 1 CYS A 80 ARG A 84 0 SHEET 1 7 1 VAL A 93 PHE A 98 0 SHEET 1 8 1 ARG A 104 MET A 109 0 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