PDB Short entry for 2MJ5 HEADER PROTEIN BINDING 25-DEC-13 2MJ5 TITLE STRUCTURE OF THE UBA DOMAIN OF HUMAN NBR1 IN COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUSES 1-76; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NEXT TO BRCA1 GENE 1 PROTEIN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 916-959; COMPND 10 SYNONYM: CELL MIGRATION-INDUCING GENE 19 PROTEIN, MEMBRANE COMPONENT COMPND 11 CHROMOSOME 17 SURFACE MARKER 2, NEIGHBOR OF BRCA1 GENE 1 PROTEIN, COMPND 12 PROTEIN 1A1-3B; 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: UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-6P1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: NBR1, 1A13B, KIAA0049, M17S2, MIG19; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PGEX-6P1 KEYWDS AUTOPHAGY, PROTEIN DEGRADATION, UBIQUITIN BINDING, PROTEIN BINDING EXPDTA SOLUTION NMR AUTHOR E.WALINDA,D.MORIMOTO,K.SUGASE,M.KOMATSU,H.TOCHIO,M.SHIRAKAWA REVDAT 4 14-JUN-23 2MJ5 1 REMARK REVDAT 3 24-AUG-22 2MJ5 1 JRNL REMARK SEQADV REVDAT 2 25-JUN-14 2MJ5 1 JRNL REVDAT 1 09-APR-14 2MJ5 0 JRNL AUTH E.WALINDA,D.MORIMOTO,K.SUGASE,T.KONUMA,H.TOCHIO,M.SHIRAKAWA JRNL TITL SOLUTION STRUCTURE OF THE UBIQUITIN-ASSOCIATED (UBA) DOMAIN JRNL TITL 2 OF HUMAN AUTOPHAGY RECEPTOR NBR1 AND ITS INTERACTION WITH JRNL TITL 3 UBIQUITIN AND POLYUBIQUITIN. JRNL REF J.BIOL.CHEM. V. 289 13890 2014 JRNL REFN ESSN 1083-351X JRNL PMID 24692539 JRNL DOI 10.1074/JBC.M114.555441 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.0, HADDOCK REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MJ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000103675. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 20 MM POTASSIUM PHOSPHATE-1, 5 REMARK 210 MM POTASSIUM CHLORIDE-2, 1 MM REMARK 210 EDTA-3, 1 MM BENZAMIDINE-4, 1 MM REMARK 210 DTT-5, 0.02 % SODIUM AZIDE-6, REMARK 210 1.2 MM [U-100% 13C; U-100% 15N] REMARK 210 NBR1 RESIDUES 913-959-7, 95 % REMARK 210 H2O-8, 5 % D2O-9, 95% H2O/5% D2O; REMARK 210 20 MM POTASSIUM PHOSPHATE-10, 5 REMARK 210 MM POTASSIUM CHLORIDE-11, 1 MM REMARK 210 EDTA-12, 1 MM BENZAMIDINE-13, 1 REMARK 210 MM DTT-14, 0.02 % SODIUM AZIDE- REMARK 210 15, 0.5 MM [U-100% 13C; U-100% REMARK 210 15N] NBR1 RESIDUES 913-959-16, REMARK 210 12.5 MG/ML PF1 PHAGE-17, 150 MM REMARK 210 SODIUM CHLORIDE-18, 95 % H2O-19, REMARK 210 5 % D2O-20, 0.5 MM [U-100% 13C; REMARK 210 U-100% 15N] NBR1_UBA-21, 2 MM REMARK 210 UBIQUITIN-22, 12.5 MG/ML PF1 REMARK 210 PHAGE-23, 95% H2O/5% D2O; 20 MM REMARK 210 POTASSIUM PHOSPHATE-24, 5 MM REMARK 210 POTASSIUM CHLORIDE-25, 1 MM EDTA- REMARK 210 26, 1 MM BENZAMIDINE-27, 1 MM REMARK 210 DTT-28, 0.02 % SODIUM AZIDE-29, REMARK 210 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 NBR1 RESIDUES 913-959-30, 12.5 REMARK 210 MG/ML PF1 PHAGE-31, 150 MM REMARK 210 SODIUM CHLORIDE-32, 95 % H2O-33, REMARK 210 5 % D2O-34, 0.5 MM [U-100% 13C; REMARK 210 U-100% 15N] NBR1_UBA-35, 2 MM REMARK 210 UBIQUITIN-36, 12.5 MG/ML PF1 REMARK 210 PHAGE-37, 95% H2O/5% D2O; 2 MM REMARK 210 NBR1_UBA-38, 0.5 MM [U-100% 13C; REMARK 210 U-100% 15N] UBIQUITIN-39, 12.5 REMARK 210 MG/ML PF1 PHAGE-40, 95% H2O/5% REMARK 210 D2O; 1 MM [U-100% 15N] NBR1_UBA- REMARK 210 41, 4.5 MM UBIQUITIN-42, 95% H2O/ REMARK 210 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D H(CCO) REMARK 210 NH; 3D C(CO)NH; 3D HCCH-TOCSY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-15N REMARK 210 NOESY; 2D 1H-15N HSQC IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TALOS, CYANA, NMRPIPE, MAGRO REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 199 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 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 H3 MET A 1 OE2 GLU A 16 1.58 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 GLN A 62 -162.48 -107.77 REMARK 500 MET B 927 -80.77 -79.42 REMARK 500 PHE B 929 -58.96 -133.61 REMARK 500 TYR B 944 78.32 61.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2MGW RELATED DB: PDB REMARK 900 STARTING STRUCTURE FOR HADDOCK REMARK 900 RELATED ID: 19606 RELATED DB: BMRB REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 STARTING STRUCTURE FOR HADDOCK DBREF 2MJ5 A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 2MJ5 B 913 959 UNP Q14596 NBR1_HUMAN 913 959 SEQADV 2MJ5 GLY B 1 UNP Q14596 EXPRESSION TAG SEQADV 2MJ5 PRO B 2 UNP Q14596 EXPRESSION TAG SEQADV 2MJ5 LEU B 3 UNP Q14596 EXPRESSION TAG SEQADV 2MJ5 GLY B 4 UNP Q14596 EXPRESSION TAG SEQADV 2MJ5 SER B 5 UNP Q14596 EXPRESSION TAG SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 52 GLY PRO LEU GLY SER SER GLU ASP GLN THR ALA ALA LEU SEQRES 2 B 52 MET ALA HIS LEU PHE GLU MET GLY PHE CYS ASP ARG GLN SEQRES 3 B 52 LEU ASN LEU ARG LEU LEU LYS LYS HIS ASN TYR ASN ILE SEQRES 4 B 52 LEU GLN VAL VAL THR GLU LEU LEU GLN LEU ASN ASN ASN HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 THR A 55 ASN A 60 5 6 HELIX 3 3 ASP B 915 GLU B 926 1 12 HELIX 4 4 ASP B 931 LYS B 940 1 10 HELIX 5 5 ASN B 945 GLN B 955 1 11 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 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