HEADER SIGNALING PROTEIN 02-AUG-18 6H8C TITLE STRUCTURE OF THE HUMAN GABARAPL2 PROTEIN IN COMPLEX WITH THE UBA5 LIR TITLE 2 MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GABA(A) RECEPTOR-ASSOCIATED PROTEIN-LIKE 2,GANGLIOSIDE COMPND 5 EXPRESSION FACTOR 2,GEF-2,GENERAL PROTEIN TRANSPORT FACTOR P16,GOLGI- COMPND 6 ASSOCIATED ATPASE ENHANCER OF 16 KDA,GATE-16,MAP1 LIGHT CHAIN 3- COMPND 7 RELATED PROTEIN; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN- COMPND 10 LIKE 2 (GABARAPL2) RESIDUES 3-116, RESIDUES 1-2 ARE EXPRESSING TAG; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 5; COMPND 13 CHAIN: B; COMPND 14 SYNONYM: UBIQUITIN-ACTIVATING ENZYME 5,THIFP1,UFM1-ACTIVATING ENZYME, COMPND 15 UBIQUITIN-ACTIVATING ENZYME E1 DOMAIN-CONTAINING PROTEIN 1; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: UFM1-ACTIVATING ENZYME 5 (UBA5) LIR/UFIM CONTAINING COMPND 18 PEPTIDE (RESIDES 333-348). FIRST 3 RESIDUES (GLY-ALA-MET) ARE COMPND 19 EXPRESSION TAG. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GABARAPL2, FLC3A, GEF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: NEB T7 EXPRESS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET39; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: UBA5, UBE1DC1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 18 EXPRESSION_SYSTEM_VARIANT: NEB T7 EXPRESS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET39 KEYWDS GABARAPL2, UBA5 LIR MOTIF, PROTEIN COMPLEX, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.HUBER,F.LOEHR,J.GRUBER,M.AKUTSU,P.GUENTERT,V.DOETSCH,V.V.ROGOV REVDAT 4 29-JAN-20 6H8C 1 JRNL REVDAT 3 17-JUL-19 6H8C 1 HELIX SHEET REVDAT 2 08-MAY-19 6H8C 1 JRNL REMARK REVDAT 1 01-MAY-19 6H8C 0 JRNL AUTH J.HUBER,M.OBATA,J.GRUBER,M.AKUTSU,F.LOHR,N.ROGOVA,P.GUNTERT, JRNL AUTH 2 I.DIKIC,V.KIRKIN,M.KOMATSU,V.DOTSCH,V.V.ROGOV JRNL TITL AN ATYPICAL LIR MOTIF WITHIN UBA5 (UBIQUITIN LIKE MODIFIER JRNL TITL 2 ACTIVATING ENZYME 5) INTERACTS WITH GABARAP PROTEINS AND JRNL TITL 3 MEDIATES MEMBRANE LOCALIZATION OF UBA5. JRNL REF AUTOPHAGY V. 16 256 2020 JRNL REFN ESSN 1554-8635 JRNL PMID 30990354 JRNL DOI 10.1080/15548627.2019.1606637 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPAL REMARK 3 AUTHORS : LUGINBUHL, GUNTERT, BILLETER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AMBER94 REMARK 4 REMARK 4 6H8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011250. 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 : 100 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-99% 13C; U-99% 15N] REMARK 210 GABARAPL2, 1.0 MM NO UBIQUITIN- REMARK 210 LIKE MODIFIER-ACTIVATING ENZYME REMARK 210 5 (UBA5) LIR MOTIF, 50 MM NO REMARK 210 SODIUM PHOSPHATE, 100 MM NO REMARK 210 SODIUM CHLORIDE, 4.6 MM NO REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O; REMARK 210 1.0 MM NO GABARAPL2, 0.6 MM [U- REMARK 210 99% 13C; U-99% 15N] UBIQUITIN- REMARK 210 LIKE MODIFIER-ACTIVATING ENZYME REMARK 210 5 (UBA5) LIR MOTIF, 50 MM NO REMARK 210 SODIUM PHOSPHATE, 100 MM NO REMARK 210 SODIUM CHLORIDE, 4.6 MM NO REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D (HCA)CO(CA)NH; 3D REMARK 210 H(CC)(CO)NH-TOCSY; 3D (H)CC(CO) REMARK 210 NH-TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; 3D NOESY-[13C,1H]- REMARK 210 HSQC 13C/15N FILTERED IN F1 REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 900 MHZ; 800 MHZ; 700 REMARK 210 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : BRUKER AVANCE 950 MHZ; BRUKER REMARK 210 AVANCE 900 MHZ; BRUKER AVANCE REMARK 210 800 MHZ; BRUKER AVANCE 700 MHZ; REMARK 210 BRUKER AVANCE 600 MHZ; BRUKER REMARK 210 AVANCE 500 MHZ REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.1, SPARKY 1.114, CYANA REMARK 210 3.97 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 1 ARG A 65 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 6 ARG A 28 CD - NE - CZ ANGL. DEV. = 10.9 DEGREES REMARK 500 6 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.3 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 ASP A 8 -74.95 -72.96 REMARK 500 1 SER A 10 -65.14 -130.73 REMARK 500 1 TYR A 25 71.95 -119.94 REMARK 500 1 MET B 332 48.17 -82.73 REMARK 500 1 TRP B 341 65.00 67.43 REMARK 500 2 ASP A 8 -76.99 -71.10 REMARK 500 2 SER A 10 -65.60 -124.02 REMARK 500 2 ASP B 338 -73.29 -56.45 REMARK 500 3 ASP A 8 -75.48 -82.09 REMARK 500 3 SER A 10 -53.29 -130.65 REMARK 500 3 GLU B 333 50.37 -108.15 REMARK 500 4 ASP A 8 -75.45 -82.64 REMARK 500 4 SER A 10 -65.48 -104.68 REMARK 500 4 ALA B 331 106.32 -165.19 REMARK 500 4 GLU B 333 51.46 -67.43 REMARK 500 4 GLU B 337 109.21 -55.33 REMARK 500 5 ASP A 8 -77.29 -74.73 REMARK 500 5 HIS A 9 117.85 -161.66 REMARK 500 5 LYS A 99 120.16 -33.38 REMARK 500 6 ASP A 8 -73.25 -75.96 REMARK 500 6 SER A 10 -64.97 -128.01 REMARK 500 6 LYS A 99 121.03 -33.23 REMARK 500 7 ASP A 8 -70.64 -85.18 REMARK 500 7 SER A 10 -66.15 -128.83 REMARK 500 7 ALA B 331 22.91 -147.74 REMARK 500 7 MET B 332 49.30 -83.03 REMARK 500 8 ASP A 8 -74.33 -69.57 REMARK 500 8 SER A 10 -66.39 -120.68 REMARK 500 8 HIS B 336 61.26 -112.30 REMARK 500 9 ASP A 8 -75.97 -76.83 REMARK 500 9 SER A 10 -67.25 -102.36 REMARK 500 9 LYS A 99 121.78 -36.26 REMARK 500 9 ALA B 331 96.25 68.00 REMARK 500 10 ASP A 8 -71.34 -68.70 REMARK 500 10 SER A 10 -66.15 -124.90 REMARK 500 11 ASP A 8 -75.87 -69.48 REMARK 500 11 SER A 10 -58.66 -130.20 REMARK 500 11 LYS A 99 121.72 -39.23 REMARK 500 12 ASP A 8 -75.12 -79.02 REMARK 500 12 MET B 332 70.49 -108.32 REMARK 500 12 HIS B 336 50.24 -113.10 REMARK 500 12 GLU B 340 -63.41 -92.45 REMARK 500 13 SER A 10 -65.72 -130.57 REMARK 500 13 LYS A 99 121.42 -37.92 REMARK 500 13 ALA B 331 85.20 -170.26 REMARK 500 13 GLU B 333 47.72 -67.98 REMARK 500 14 ASP A 8 -76.22 -75.02 REMARK 500 14 HIS A 9 119.68 -160.96 REMARK 500 14 SER A 10 -65.92 -106.89 REMARK 500 14 ALA B 331 -7.27 -153.40 REMARK 500 REMARK 500 THIS ENTRY HAS 79 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 HIS A 9 0.10 SIDE CHAIN REMARK 500 1 ARG A 22 0.08 SIDE CHAIN REMARK 500 5 ARG A 65 0.09 SIDE CHAIN REMARK 500 6 TYR A 106 0.09 SIDE CHAIN REMARK 500 7 ARG A 47 0.10 SIDE CHAIN REMARK 500 8 TYR A 25 0.08 SIDE CHAIN REMARK 500 10 TYR A 95 0.07 SIDE CHAIN REMARK 500 12 ARG A 28 0.12 SIDE CHAIN REMARK 500 12 ARG A 47 0.08 SIDE CHAIN REMARK 500 13 TYR A 95 0.08 SIDE CHAIN REMARK 500 15 ARG A 65 0.07 SIDE CHAIN REMARK 500 15 TYR A 95 0.10 SIDE CHAIN REMARK 500 15 TYR A 109 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34307 RELATED DB: BMRB REMARK 900 STRUCTURE OF THE HUMAN GABARAPL2 PROTEIN IN COMPLEX WITH THE UBA5 REMARK 900 LIR MOTIF REMARK 900 RELATED ID: 6HB9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN GABARAP PROTEIN IN COMPLEX WITH THE REMARK 900 UBA5 LIR MOTIF DBREF 6H8C A 3 116 UNP P60520 GBRL2_HUMAN 3 116 DBREF 6H8C B 333 348 UNP Q9GZZ9 UBA5_HUMAN 333 348 SEQADV 6H8C MET A 1 UNP P60520 INITIATING METHIONINE SEQADV 6H8C GLY A 2 UNP P60520 EXPRESSION TAG SEQADV 6H8C GLY B 330 UNP Q9GZZ9 EXPRESSION TAG SEQADV 6H8C ALA B 331 UNP Q9GZZ9 EXPRESSION TAG SEQADV 6H8C MET B 332 UNP Q9GZZ9 EXPRESSION TAG SEQRES 1 A 116 MET GLY TRP MET PHE LYS GLU ASP HIS SER LEU GLU HIS SEQRES 2 A 116 ARG CYS VAL GLU SER ALA LYS ILE ARG ALA LYS TYR PRO SEQRES 3 A 116 ASP ARG VAL PRO VAL ILE VAL GLU LYS VAL SER GLY SER SEQRES 4 A 116 GLN ILE VAL ASP ILE ASP LYS ARG LYS TYR LEU VAL PRO SEQRES 5 A 116 SER ASP ILE THR VAL ALA GLN PHE MET TRP ILE ILE ARG SEQRES 6 A 116 LYS ARG ILE GLN LEU PRO SER GLU LYS ALA ILE PHE LEU SEQRES 7 A 116 PHE VAL ASP LYS THR VAL PRO GLN SER SER LEU THR MET SEQRES 8 A 116 GLY GLN LEU TYR GLU LYS GLU LYS ASP GLU ASP GLY PHE SEQRES 9 A 116 LEU TYR VAL ALA TYR SER GLY GLU ASN THR PHE GLY SEQRES 1 B 19 GLY ALA MET GLU ILE ILE HIS GLU ASP ASN GLU TRP GLY SEQRES 2 B 19 ILE GLU LEU VAL SER GLU HELIX 1 AA1 TRP A 3 HIS A 9 1 7 HELIX 2 AA2 SER A 10 TYR A 25 1 16 HELIX 3 AA3 THR A 56 GLN A 69 1 14 HELIX 4 AA4 THR A 90 LYS A 99 1 10 SHEET 1 AA1 5 PHE A 77 VAL A 80 0 SHEET 2 AA1 5 LEU A 105 SER A 110 -1 O SER A 110 N PHE A 77 SHEET 3 AA1 5 ARG A 28 LYS A 35 1 N ILE A 32 O VAL A 107 SHEET 4 AA1 5 ARG A 47 PRO A 52 -1 O VAL A 51 N VAL A 29 SHEET 5 AA1 5 GLY B 342 LEU B 345 1 O GLU B 344 N LYS A 48 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