HEADER SIGNALING PROTEIN/PROTEIN BINDING 17-JAN-11 2L8J TITLE GABARAPL-1 NBR1-LIR COMPLEX STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EARLY ESTROGEN-REGULATED PROTEIN, GABA(A) RECEPTOR- COMPND 5 ASSOCIATED PROTEIN-LIKE 1, GLANDULAR EPITHELIAL CELL PROTEIN 1, GEC- COMPND 6 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NBR1-LIR PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 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: GABARAPL1, GEC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: NEBT7; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX4T1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: NEBT7; SOURCE 17 EXPRESSION_SYSTEM_VECTOR: PET60M_UB KEYWDS SELECTIVE AUTOPHAGY, LC3 PROTEINS, SIGNALING PROTEIN, SIGNALING KEYWDS 2 PROTEIN-PROTEIN BINDING COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR V.V.ROGOV,A.ROZENKNOP,N.Y.ROGOVA,F.LOEHR,P.GUENTERT,I.DIKIC,V.DOETSCH REVDAT 3 14-JUN-23 2L8J 1 REMARK SEQADV REVDAT 2 06-JUL-11 2L8J 1 JRNL REVDAT 1 11-MAY-11 2L8J 0 JRNL AUTH A.ROZENKNOP,V.V.ROGOV,N.Y.ROGOVA,F.LOHR,P.GUNTERT,I.DIKIC, JRNL AUTH 2 V.DOTSCH JRNL TITL CHARACTERIZATION OF THE INTERACTION OF GABARAPL-1 WITH THE JRNL TITL 2 LIR MOTIF OF NBR1. JRNL REF J.MOL.BIOL. V. 410 477 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21620860 JRNL DOI 10.1016/J.JMB.2011.05.003 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, CYANA, OPAL REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA), LUGINBUHL, GUNTERT, BILLETER AND REMARK 3 WUTHRICH (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L8J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000102090. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-98% 15N] GABARAPL-1, REMARK 210 0.9 MM NBR1-LIR, 50 MM SODIUM REMARK 210 PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 4.6 MM SODIUM AZIDE, 1 REMARK 210 MM PROTEASE INHIBITOR COCKTAIL, REMARK 210 0.3 MM DSS, 95% H2O/5% D2O; 0.6 REMARK 210 MM [U-98% 13C; U-98% 15N] REMARK 210 GABARAPL-1, 0.9 MM NBR1-LIR, 50 REMARK 210 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 4.6 MM SODIUM REMARK 210 AZIDE, 1 MM PROTEASE INHIBITOR REMARK 210 COCKTAIL, 0.3 MM DSS, 95% H2O/5% REMARK 210 D2O; 0.9 MM GABARAPL-1, 0.6 MM REMARK 210 [U-98% 15N] NBR1-LIR, 50 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 4.6 MM SODIUM AZIDE, 1 REMARK 210 MM PROTEASE INHIBITOR COCKTAIL, REMARK 210 0.3 MM DSS, 95% H2O/5% D2O; 0.9 REMARK 210 MM GABARAPL-1, 0.6 MM [U-98% 13C; REMARK 210 U-98% 15N] NBR1-LIR, 50 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 4.6 MM SODIUM AZIDE, 1 REMARK 210 MM PROTEASE INHIBITOR COCKTAIL, REMARK 210 0.3 MM DSS, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HNCA; 3D HNCACB; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 TROSY-H(CCCO)NH-TOCSY; (H)CC(CO) REMARK 210 NH-TOCSY; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 700 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, TALOS, CSI, REMARK 210 CYANA REMARK 210 METHOD USED : ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 5 ARG A 47 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 11 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 12 ARG A 14 NE - CZ - NH2 ANGL. DEV. = -3.1 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 LYS A 38 -11.50 66.45 REMARK 500 1 ARG A 47 -51.27 -127.19 REMARK 500 1 ASN A 81 70.59 30.76 REMARK 500 1 ASN A 82 9.61 56.21 REMARK 500 2 GLU A 0 151.80 65.75 REMARK 500 2 HIS A 69 94.04 49.85 REMARK 500 2 HIS A 99 125.80 -37.88 REMARK 500 2 SER A 113 99.36 -65.21 REMARK 500 2 SER B 728 -176.22 -61.37 REMARK 500 3 GLU A 0 77.70 48.43 REMARK 500 3 LYS A 2 -26.66 -155.36 REMARK 500 3 LYS A 38 15.93 58.53 REMARK 500 3 HIS A 69 28.17 43.10 REMARK 500 3 ASN A 81 58.89 37.18 REMARK 500 3 HIS A 99 95.95 -43.17 REMARK 500 3 GLU B 738 3.70 -69.95 REMARK 500 4 PRO A -1 33.48 -76.14 REMARK 500 4 PHE A 1 74.58 48.18 REMARK 500 4 TYR A 25 78.53 -118.66 REMARK 500 4 ASP A 45 2.58 -66.39 REMARK 500 4 HIS A 69 47.71 37.52 REMARK 500 4 ASN A 81 66.55 31.40 REMARK 500 5 GLU A 0 -90.35 62.10 REMARK 500 5 LYS A 2 177.41 72.24 REMARK 500 5 LYS A 38 15.62 56.83 REMARK 500 5 ASN A 81 59.67 36.58 REMARK 500 5 HIS A 99 104.84 -39.81 REMARK 500 5 TYR A 103 15.23 44.95 REMARK 500 6 LYS A 2 -177.81 70.89 REMARK 500 6 LYS A 38 -10.17 70.38 REMARK 500 6 HIS A 69 50.06 37.57 REMARK 500 6 ASN A 81 65.17 27.84 REMARK 500 6 HIS A 99 125.82 -39.27 REMARK 500 6 SER A 113 98.88 -66.71 REMARK 500 6 ALA B 723 -169.68 -78.93 REMARK 500 7 GLU A 0 -169.80 66.16 REMARK 500 7 PHE A 1 -69.01 72.12 REMARK 500 7 LYS A 2 -73.85 67.64 REMARK 500 7 LYS A 38 -16.52 94.44 REMARK 500 7 ASN A 81 18.87 51.38 REMARK 500 7 ASN A 82 20.00 87.47 REMARK 500 7 ALA A 89 -168.86 -72.70 REMARK 500 7 SER B 728 -169.06 -75.04 REMARK 500 8 LYS A 38 -2.69 63.32 REMARK 500 8 ASP A 45 -80.64 -65.55 REMARK 500 8 HIS A 69 69.00 33.69 REMARK 500 8 HIS A 99 101.47 -45.22 REMARK 500 8 PRO B 737 -179.26 -64.89 REMARK 500 9 ASP A 45 -87.97 -59.35 REMARK 500 9 HIS A 69 39.58 38.19 REMARK 500 REMARK 500 THIS ENTRY HAS 106 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 TYR A 95 0.07 SIDE CHAIN REMARK 500 1 TYR B 732 0.09 SIDE CHAIN REMARK 500 2 TYR A 109 0.07 SIDE CHAIN REMARK 500 4 TYR A 5 0.09 SIDE CHAIN REMARK 500 5 ARG A 14 0.09 SIDE CHAIN REMARK 500 5 TYR A 95 0.08 SIDE CHAIN REMARK 500 5 TYR A 109 0.10 SIDE CHAIN REMARK 500 5 TYR A 115 0.07 SIDE CHAIN REMARK 500 6 ARG A 14 0.08 SIDE CHAIN REMARK 500 6 TYR A 95 0.09 SIDE CHAIN REMARK 500 7 TYR A 13 0.07 SIDE CHAIN REMARK 500 7 ARG A 22 0.08 SIDE CHAIN REMARK 500 8 ARG A 14 0.09 SIDE CHAIN REMARK 500 8 ARG A 28 0.08 SIDE CHAIN REMARK 500 8 ARG A 47 0.12 SIDE CHAIN REMARK 500 8 ARG A 71 0.08 SIDE CHAIN REMARK 500 8 TYR A 95 0.07 SIDE CHAIN REMARK 500 9 ARG A 67 0.10 SIDE CHAIN REMARK 500 10 ARG A 14 0.10 SIDE CHAIN REMARK 500 10 TYR A 61 0.08 SIDE CHAIN REMARK 500 11 ARG A 67 0.09 SIDE CHAIN REMARK 500 12 ARG A 28 0.11 SIDE CHAIN REMARK 500 12 TYR A 95 0.07 SIDE CHAIN REMARK 500 13 TYR B 732 0.10 SIDE CHAIN REMARK 500 14 ARG A 22 0.09 SIDE CHAIN REMARK 500 14 TYR A 49 0.08 SIDE CHAIN REMARK 500 15 ARG A 14 0.11 SIDE CHAIN REMARK 500 15 ARG A 40 0.08 SIDE CHAIN REMARK 500 15 ARG A 71 0.10 SIDE CHAIN REMARK 500 18 TYR A 13 0.08 SIDE CHAIN REMARK 500 18 ARG A 40 0.15 SIDE CHAIN REMARK 500 18 ARG A 47 0.12 SIDE CHAIN REMARK 500 18 TYR B 732 0.07 SIDE CHAIN REMARK 500 19 ARG A 14 0.11 SIDE CHAIN REMARK 500 20 TYR A 13 0.09 SIDE CHAIN REMARK 500 20 TYR A 106 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17412 RELATED DB: BMRB DBREF 2L8J A 2 115 UNP Q9H0R8 GBRL1_HUMAN 2 115 DBREF 2L8J B 726 738 UNP Q14596 NBR1_HUMAN 726 738 SEQADV 2L8J GLY A -3 UNP Q9H0R8 EXPRESSION TAG SEQADV 2L8J SER A -2 UNP Q9H0R8 EXPRESSION TAG SEQADV 2L8J PRO A -1 UNP Q9H0R8 EXPRESSION TAG SEQADV 2L8J GLU A 0 UNP Q9H0R8 EXPRESSION TAG SEQADV 2L8J PHE A 1 UNP Q9H0R8 EXPRESSION TAG SEQADV 2L8J GLY B 722 UNP Q14596 EXPRESSION TAG SEQADV 2L8J ALA B 723 UNP Q14596 EXPRESSION TAG SEQADV 2L8J MET B 724 UNP Q14596 EXPRESSION TAG SEQADV 2L8J GLY B 725 UNP Q14596 EXPRESSION TAG SEQADV 2L8J SER B 739 UNP Q14596 EXPRESSION TAG SEQRES 1 A 119 GLY SER PRO GLU PHE LYS PHE GLN TYR LYS GLU ASP HIS SEQRES 2 A 119 PRO PHE GLU TYR ARG LYS LYS GLU GLY GLU LYS ILE ARG SEQRES 3 A 119 LYS LYS TYR PRO ASP ARG VAL PRO VAL ILE VAL GLU LYS SEQRES 4 A 119 ALA PRO LYS ALA ARG VAL PRO ASP LEU ASP LYS ARG LYS SEQRES 5 A 119 TYR LEU VAL PRO SER ASP LEU THR VAL GLY GLN PHE TYR SEQRES 6 A 119 PHE LEU ILE ARG LYS ARG ILE HIS LEU ARG PRO GLU ASP SEQRES 7 A 119 ALA LEU PHE PHE PHE VAL ASN ASN THR ILE PRO PRO THR SEQRES 8 A 119 SER ALA THR MET GLY GLN LEU TYR GLU ASP ASN HIS GLU SEQRES 9 A 119 GLU ASP TYR PHE LEU TYR VAL ALA TYR SER ASP GLU SER SEQRES 10 A 119 VAL TYR SEQRES 1 B 18 GLY ALA MET GLY SER ALA SER SER GLU ASP TYR ILE ILE SEQRES 2 B 18 ILE LEU PRO GLU SER HELIX 1 1 GLN A 4 HIS A 9 1 6 HELIX 2 2 PRO A 10 TYR A 25 1 16 HELIX 3 3 THR A 56 HIS A 69 1 14 HELIX 4 4 THR A 90 ASN A 98 1 9 SHEET 1 A 5 PHE A 77 VAL A 80 0 SHEET 2 A 5 LEU A 105 SER A 110 -1 O ALA A 108 N PHE A 79 SHEET 3 A 5 ARG A 28 LYS A 35 1 N ILE A 32 O LEU A 105 SHEET 4 A 5 LYS A 48 PRO A 52 -1 O VAL A 51 N VAL A 29 SHEET 5 A 5 ILE B 733 ILE B 734 1 O ILE B 733 N LEU A 50 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