HEADER PROTEIN BINDING/PEPTIDE 14-DEC-15 2N9X TITLE LC3 FUNDC1 COMPLEX STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AUTOPHAGY-RELATED PROTEIN LC3 B, AUTOPHAGY-RELATED COMPND 5 UBIQUITIN-LIKE MODIFIER LC3 B, MAP1 LIGHT CHAIN 3-LIKE PROTEIN 2, COMPND 6 MAP1A/MAP1B LIGHT CHAIN 3 B, MAP1A/MAP1B LC3 B, MICROTUBULE- COMPND 7 ASSOCIATED PROTEIN 1 LIGHT CHAIN 3 BETA; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: FUN14 DOMAIN-CONTAINING PROTEIN 1; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 10-26; 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: MAP1LC3B, MAP1ALC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET30A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS PROTEIN/PEPTIDE, LC3 INTERACTING REGION (LIR), PROTEIN BINDING- KEYWDS 2 PEPTIDE COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.XIA,Y.KUANG REVDAT 3 01-MAY-24 2N9X 1 REMARK REVDAT 2 07-JUN-17 2N9X 1 JRNL REVDAT 1 14-DEC-16 2N9X 0 JRNL AUTH Y.KUANG,K.MA,C.ZHOU,P.DING,Y.ZHU,Q.CHEN,B.XIA JRNL TITL STRUCTURAL BASIS FOR THE PHOSPHORYLATION OF FUNDC1 LIR AS A JRNL TITL 2 MOLECULAR SWITCH OF MITOPHAGY. JRNL REF AUTOPHAGY V. 12 2363 2016 JRNL REFN ESSN 1554-8635 JRNL PMID 27653272 JRNL DOI 10.1080/15548627.2016.1238552 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, AMBER REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), CASE, REMARK 3 DARDEN, CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 ... AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N9X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000104606. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-13C; U-15N] ENTITY_1 REMARK 210 -1, 1.8 MM ENTITY_2-2, 100 MM REMARK 210 SODIUM CHLORIDE-3, 25 MM SODIUM REMARK 210 PHOSPHATE-4, 10 % [U-2H] D2O-5, REMARK 210 1 % DSS-6, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HNCO; 3D HBHA(CO)NH; REMARK 210 3D HCCH-COSY; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D 1H-13C NOESY AROMATIC; 2D 1H- REMARK 210 1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 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 37 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 TYR B 18 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 21 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 TYR B 18 CB - CG - CD2 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 TYR B 18 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 5 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 5 ARG A 24 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 10 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 6 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 TYR B 18 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 TYR B 18 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES REMARK 500 10 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 16 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 21 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 TYR B 18 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 11 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 16 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 11 TYR B 18 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 12 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 13 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 16 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 13 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 14 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 14 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 15 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 15 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 TYR B 18 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 17 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 21 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 20 ARG A 11 NE - CZ - NH2 ANGL. DEV. = 3.8 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 6 135.10 -39.92 REMARK 500 1 PHE A 7 -39.32 -37.50 REMARK 500 1 LYS A 42 45.51 -78.45 REMARK 500 1 VAL A 46 33.33 -75.16 REMARK 500 1 ASP A 48 88.35 -61.30 REMARK 500 1 THR A 50 -45.94 61.58 REMARK 500 1 PHE A 119 -37.64 -147.18 REMARK 500 1 TYR B 11 -54.37 -154.81 REMARK 500 1 GLU B 12 -141.87 53.61 REMARK 500 1 ASP B 14 -85.69 -160.44 REMARK 500 1 ASP B 16 -94.08 49.44 REMARK 500 2 GLU A 4 -16.57 59.64 REMARK 500 2 ARG A 10 -51.39 -136.78 REMARK 500 2 GLU A 41 77.99 -151.34 REMARK 500 2 LYS A 42 38.28 -74.57 REMARK 500 2 LEU A 47 -110.99 49.45 REMARK 500 2 THR A 50 -33.78 -139.56 REMARK 500 2 SER B 13 10.87 52.33 REMARK 500 2 ASP B 14 -116.85 -86.58 REMARK 500 2 ASP B 16 -98.41 53.49 REMARK 500 2 VAL B 20 164.05 68.75 REMARK 500 3 GLU A 4 -31.11 62.70 REMARK 500 3 LYS A 42 41.81 -77.62 REMARK 500 3 LYS A 49 -10.84 60.05 REMARK 500 3 THR A 50 -19.88 59.10 REMARK 500 3 ASN A 74 152.67 -49.39 REMARK 500 3 PHE A 108 -107.82 60.29 REMARK 500 3 GLU B 12 -115.76 42.16 REMARK 500 3 ASP B 16 106.87 60.80 REMARK 500 3 SER B 17 77.91 55.35 REMARK 500 4 LYS A 5 157.66 67.30 REMARK 500 4 VAL A 46 39.28 -81.65 REMARK 500 4 ASP A 48 -23.03 61.62 REMARK 500 4 GLN A 72 40.11 -75.90 REMARK 500 4 PHE A 108 -81.55 -78.35 REMARK 500 4 TYR B 11 -72.31 61.70 REMARK 500 4 GLU B 12 -147.30 41.51 REMARK 500 4 ASP B 14 -113.04 -89.49 REMARK 500 4 ASP B 16 -92.74 58.72 REMARK 500 4 VAL B 20 -41.94 63.89 REMARK 500 5 LYS A 5 152.42 65.43 REMARK 500 5 GLU A 41 59.86 -148.84 REMARK 500 5 LYS A 42 32.82 -71.39 REMARK 500 5 THR A 50 -46.97 -159.21 REMARK 500 5 GLN A 72 37.92 -76.23 REMARK 500 5 PHE A 108 144.15 66.33 REMARK 500 5 SER B 13 -31.22 -165.08 REMARK 500 5 ASP B 14 -102.03 -64.18 REMARK 500 5 ASP B 16 -92.82 55.58 REMARK 500 5 VAL B 20 -48.74 64.10 REMARK 500 REMARK 500 THIS ENTRY HAS 200 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 3 ARG A 68 0.09 SIDE CHAIN REMARK 500 5 TYR B 18 0.10 SIDE CHAIN REMARK 500 11 ARG A 24 0.07 SIDE CHAIN REMARK 500 14 TYR B 18 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25919 RELATED DB: BMRB DBREF 2N9X A 1 120 UNP Q9GZQ8 MLP3B_HUMAN 1 120 DBREF 2N9X B 10 26 UNP Q8IVP5 FUND1_HUMAN 10 26 SEQRES 1 A 120 MET PRO SER GLU LYS THR PHE LYS GLN ARG ARG THR PHE SEQRES 2 A 120 GLU GLN ARG VAL GLU ASP VAL ARG LEU ILE ARG GLU GLN SEQRES 3 A 120 HIS PRO THR LYS ILE PRO VAL ILE ILE GLU ARG TYR LYS SEQRES 4 A 120 GLY GLU LYS GLN LEU PRO VAL LEU ASP LYS THR LYS PHE SEQRES 5 A 120 LEU VAL PRO ASP HIS VAL ASN MET SER GLU LEU ILE LYS SEQRES 6 A 120 ILE ILE ARG ARG ARG LEU GLN LEU ASN ALA ASN GLN ALA SEQRES 7 A 120 PHE PHE LEU LEU VAL ASN GLY HIS SER MET VAL SER VAL SEQRES 8 A 120 SER THR PRO ILE SER GLU VAL TYR GLU SER GLU LYS ASP SEQRES 9 A 120 GLU ASP GLY PHE LEU TYR MET VAL TYR ALA SER GLN GLU SEQRES 10 A 120 THR PHE GLY SEQRES 1 B 17 ASP TYR GLU SER ASP ASP ASP SER TYR GLU VAL LEU ASP SEQRES 2 B 17 LEU THR GLU TYR HELIX 1 1 THR A 6 ARG A 10 5 5 HELIX 2 2 THR A 12 HIS A 27 1 16 HELIX 3 3 ASN A 59 LEU A 71 1 13 HELIX 4 4 PRO A 94 LYS A 103 1 10 SHEET 1 A 5 LYS A 51 PRO A 55 0 SHEET 2 A 5 LYS A 30 ARG A 37 -1 N ILE A 31 O VAL A 54 SHEET 3 A 5 LEU A 109 ALA A 114 1 O LEU A 109 N ILE A 34 SHEET 4 A 5 PHE A 80 VAL A 83 -1 N LEU A 82 O VAL A 112 SHEET 5 A 5 HIS A 86 SER A 87 -1 O HIS A 86 N VAL A 83 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