PDB Short entry for 2NBV HEADER PROTEIN BINDING 12-MAR-16 2NBV TITLE SOLUTION STRUCTURE OF THE RPN13 PRU DOMAIN ENGAGING THE HPLIC2 UBL TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASOMAL UBIQUITIN RECEPTOR ADRM1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-150; COMPND 5 SYNONYM: 110 KDA CELL MEMBRANE GLYCOPROTEIN, GP110, ADHESION- COMPND 6 REGULATING MOLECULE 1, ARM-1, PROTEASOME REGULATORY PARTICLE NON- COMPND 7 ATPASE 13, HRPN13, RPN13 HOMOLOG; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UBIQUILIN-2; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: RESIDUES 26-103; COMPND 13 SYNONYM: CHAP1, DSK2 HOMOLOG, PROTEIN LINKING IAP WITH CYTOSKELETON COMPND 14 2, PLIC-2, HPLIC-2, UBIQUITIN-LIKE PRODUCT CHAP1/DSK2; 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: ADRM1, GP110; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PRSET; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: UBQLN2, N4BP4, PLIC2, HRIHFB2157; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PGEX4T1 KEYWDS PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.CHEN,K.J.WALTERS REVDAT 3 14-JUN-23 2NBV 1 REMARK REVDAT 2 17-AUG-16 2NBV 1 JRNL REVDAT 1 20-JUL-16 2NBV 0 JRNL AUTH X.CHEN,L.RANDLES,K.SHI,S.G.TARASOV,H.AIHARA,K.J.WALTERS JRNL TITL STRUCTURES OF RPN1 T1:RAD23 AND HRPN13:HPLIC2 REVEAL JRNL TITL 2 DISTINCT BINDING MECHANISMS BETWEEN SUBSTRATE RECEPTORS AND JRNL TITL 3 SHUTTLE FACTORS OF THE PROTEASOME. JRNL REF STRUCTURE V. 24 1257 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27396824 JRNL DOI 10.1016/J.STR.2016.05.018 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, HADDOCK 2.2, CNS REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), ALEXANDRE BONVIN REMARK 3 (HADDOCK), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STARTING STRUCTURES ARE PDB ENRIES REMARK 3 1J8C AND 5IRS. REMARK 4 REMARK 4 2NBV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000104672. 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 : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-100% 15N] PROTEIN_1, REMARK 210 0.04-0.6 MM PROTEIN_2, 20 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 2 MM DTT, 0.1 % SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O; 0.04-0.6 REMARK 210 MM PROTEIN_1, 0.3 MM [U-100% 15N] REMARK 210 PROTEIN_2, 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 2 MM DTT, 0.1 % SODIUM AZIDE, REMARK 210 95% H2O/5% D2O; 0.5 MM PROTEIN_1, REMARK 210 0.5 MM [U-100% 15N, 100% REMARK 210 DEUTERIUM] PROTEIN_2, 20 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 2 MM DTT, 0.1 % SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 0.5 MM REMARK 210 [U-100% 15N, 100% DEUTERIUM] REMARK 210 PROTEIN_2, 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 2 MM DTT, 0.1 % SODIUM AZIDE, REMARK 210 90% H2O/10% D2O; 0.5 MM [U-13C] REMARK 210 PROTEIN_1, 0.5 MM [U-100% 15N, REMARK 210 100% DEUTERIUM] PROTEIN_2,20 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 2 MM DTT, 0.1 % SODIUM REMARK 210 AZIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 2D 1H-13C HSQC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, XEASY, PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 THR A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 ALA A 6 REMARK 465 LEU A 7 REMARK 465 PHE A 8 REMARK 465 PRO A 9 REMARK 465 SER A 10 REMARK 465 LEU A 11 REMARK 465 VAL A 12 REMARK 465 PRO A 13 REMARK 465 GLY A 14 REMARK 465 SER A 15 REMARK 465 ARG A 16 REMARK 465 GLY A 17 REMARK 465 ALA A 18 REMARK 465 SER A 19 REMARK 465 ASN A 20 REMARK 465 PRO A 131 REMARK 465 PRO A 132 REMARK 465 MET A 133 REMARK 465 PRO A 134 REMARK 465 GLY A 135 REMARK 465 ALA A 136 REMARK 465 LEU A 137 REMARK 465 GLY A 138 REMARK 465 ALA A 139 REMARK 465 SER A 140 REMARK 465 GLY A 141 REMARK 465 SER A 142 REMARK 465 SER A 143 REMARK 465 GLY A 144 REMARK 465 HIS A 145 REMARK 465 GLU A 146 REMARK 465 LEU A 147 REMARK 465 SER A 148 REMARK 465 ALA A 149 REMARK 465 LEU A 150 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 36 15.60 -152.68 REMARK 500 1 THR A 65 -63.37 -96.74 REMARK 500 1 GLU A 70 -74.75 -81.55 REMARK 500 1 ASP A 79 6.69 -155.61 REMARK 500 1 GLU B 29 96.06 65.64 REMARK 500 1 LYS B 41 -48.44 -170.41 REMARK 500 1 GLU B 50 31.64 -81.33 REMARK 500 1 ASN B 51 45.16 -159.25 REMARK 500 1 LYS B 66 74.17 59.95 REMARK 500 1 SER B 67 -87.47 -134.31 REMARK 500 1 THR B 69 -52.03 -127.51 REMARK 500 1 ALA B 77 87.55 57.02 REMARK 500 1 ASP B 85 -152.94 -107.08 REMARK 500 1 HIS B 90 -42.56 -141.68 REMARK 500 1 ASP B 94 88.87 -170.01 REMARK 500 2 THR A 36 13.82 -155.28 REMARK 500 2 ASP A 79 -58.24 -148.82 REMARK 500 2 GLU B 29 89.46 58.65 REMARK 500 2 PRO B 30 32.37 -76.75 REMARK 500 2 LYS B 41 -76.43 -163.30 REMARK 500 2 GLU B 50 25.77 -72.36 REMARK 500 2 ASN B 51 13.34 -140.86 REMARK 500 2 LYS B 66 89.12 60.26 REMARK 500 2 SER B 67 -79.24 -152.03 REMARK 500 2 THR B 69 -47.12 -134.87 REMARK 500 2 ALA B 77 87.30 53.32 REMARK 500 2 ASP B 83 24.68 -75.70 REMARK 500 2 ASP B 85 -143.88 -124.92 REMARK 500 2 GLN B 89 -63.79 -99.97 REMARK 500 2 ASP B 94 -3.58 -141.98 REMARK 500 3 ASP A 78 19.40 56.25 REMARK 500 3 GLU B 29 85.36 55.38 REMARK 500 3 PRO B 30 34.15 -75.88 REMARK 500 3 LYS B 41 -61.06 -171.34 REMARK 500 3 GLU B 50 46.03 -74.49 REMARK 500 3 ASN B 51 4.28 -150.92 REMARK 500 3 LYS B 66 78.71 61.51 REMARK 500 3 SER B 67 -57.17 -134.16 REMARK 500 3 THR B 69 -68.77 -126.30 REMARK 500 3 ALA B 77 81.93 56.74 REMARK 500 3 LYS B 82 -159.82 -143.24 REMARK 500 3 ASP B 94 -57.17 -154.96 REMARK 500 4 THR A 36 12.45 -152.30 REMARK 500 4 THR A 52 -166.08 -102.75 REMARK 500 4 ASP A 79 -11.37 -143.06 REMARK 500 4 ASN A 129 -42.81 -139.62 REMARK 500 4 GLU B 29 100.40 66.54 REMARK 500 4 PRO B 30 41.12 -78.59 REMARK 500 4 LYS B 41 -77.90 -162.04 REMARK 500 4 LYS B 66 81.17 64.63 REMARK 500 REMARK 500 THIS ENTRY HAS 267 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25995 RELATED DB: BMRB REMARK 900 RELATED ID: 2NBU RELATED DB: PDB REMARK 900 RELATED ID: 2NBW RELATED DB: PDB DBREF 2NBV A 1 150 UNP Q16186 ADRM1_HUMAN 1 150 DBREF 2NBV B 26 103 UNP Q9UHD9 UBQL2_HUMAN 26 103 SEQRES 1 A 150 MET THR THR SER GLY ALA LEU PHE PRO SER LEU VAL PRO SEQRES 2 A 150 GLY SER ARG GLY ALA SER ASN LYS TYR LEU VAL GLU PHE SEQRES 3 A 150 ARG ALA GLY LYS MET SER LEU LYS GLY THR THR VAL THR SEQRES 4 A 150 PRO ASP LYS ARG LYS GLY LEU VAL TYR ILE GLN GLN THR SEQRES 5 A 150 ASP ASP SER LEU ILE HIS PHE CYS TRP LYS ASP ARG THR SEQRES 6 A 150 SER GLY ASN VAL GLU ASP ASP LEU ILE ILE PHE PRO ASP SEQRES 7 A 150 ASP CYS GLU PHE LYS ARG VAL PRO GLN CYS PRO SER GLY SEQRES 8 A 150 ARG VAL TYR VAL LEU LYS PHE LYS ALA GLY SER LYS ARG SEQRES 9 A 150 LEU PHE PHE TRP MET GLN GLU PRO LYS THR ASP GLN ASP SEQRES 10 A 150 GLU GLU HIS CYS ARG LYS VAL ASN GLU TYR LEU ASN ASN SEQRES 11 A 150 PRO PRO MET PRO GLY ALA LEU GLY ALA SER GLY SER SER SEQRES 12 A 150 GLY HIS GLU LEU SER ALA LEU SEQRES 1 B 78 ALA PRO ALA GLU PRO LYS ILE ILE LYS VAL THR VAL LYS SEQRES 2 B 78 THR PRO LYS GLU LYS GLU GLU PHE ALA VAL PRO GLU ASN SEQRES 3 B 78 SER SER VAL GLN GLN PHE LYS GLU ALA ILE SER LYS ARG SEQRES 4 B 78 PHE LYS SER GLN THR ASP GLN LEU VAL LEU ILE PHE ALA SEQRES 5 B 78 GLY LYS ILE LEU LYS ASP GLN ASP THR LEU ILE GLN HIS SEQRES 6 B 78 GLY ILE HIS ASP GLY LEU THR VAL HIS LEU VAL ILE LYS HELIX 1 1 LYS A 113 ASP A 115 5 3 HELIX 2 2 GLN A 116 ASN A 130 1 15 HELIX 3 3 SER B 53 PHE B 65 1 13 SHEET 1 A 5 THR A 37 PRO A 40 0 SHEET 2 A 5 VAL A 24 LYS A 34 -1 N SER A 32 O THR A 39 SHEET 3 A 5 GLY A 45 GLN A 51 -1 O VAL A 47 N PHE A 26 SHEET 4 A 5 ILE A 57 ASP A 63 -1 O HIS A 58 N GLN A 50 SHEET 5 A 5 VAL A 69 ILE A 75 -1 O LEU A 73 N PHE A 59 SHEET 1 B 5 THR A 37 PRO A 40 0 SHEET 2 B 5 VAL A 24 LYS A 34 -1 N SER A 32 O THR A 39 SHEET 3 B 5 ARG A 104 MET A 109 -1 O TRP A 108 N GLY A 29 SHEET 4 B 5 VAL A 93 PHE A 98 -1 N LEU A 96 O LEU A 105 SHEET 5 B 5 CYS A 80 ARG A 84 -1 N LYS A 83 O VAL A 95 SHEET 1 C 5 LYS B 43 PRO B 49 0 SHEET 2 C 5 ILE B 32 LYS B 38 -1 N VAL B 35 O PHE B 46 SHEET 3 C 5 LEU B 96 VAL B 101 1 O VAL B 98 N THR B 36 SHEET 4 C 5 VAL B 73 ILE B 75 -1 N VAL B 73 O VAL B 101 SHEET 5 C 5 ILE B 80 LEU B 81 -1 O LEU B 81 N LEU B 74 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