HEADER PEPTIDE BINDING PROTEIN 12-NOV-19 6LAN TITLE STRUCTURE OF CCDC50 AND LC3B COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: COILED-COIL DOMAIN-CONTAINING PROTEIN 50,MICROTUBULE- COMPND 3 ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PROTEIN YMER,AUTOPHAGY-RELATED PROTEIN LC3 B,AUTOPHAGY- COMPND 6 RELATED UBIQUITIN-LIKE MODIFIER LC3 B,MAP1 LIGHT CHAIN 3-LIKE PROTEIN COMPND 7 2,MAP1A/MAP1B LIGHT CHAIN 3 B,MAP1A/MAP1B LC3 B,MICROTUBULE- COMPND 8 ASSOCIATED PROTEIN 1 LIGHT CHAIN 3 BETA; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: THE FUSION PROTEIN OF CCDC50 PEPTIDE (RESIDUES -7-1) COMPND 11 AND LC3B PROTEIN (RESIDUES 2-125). SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CCDC50, C3ORF6, MAP1LC3B, MAP1ALC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AUTOPHAGY, COMPLEX, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.LIU,J.LI,P.HOU REVDAT 3 22-NOV-23 6LAN 1 REMARK REVDAT 2 20-JAN-21 6LAN 1 JRNL REVDAT 1 30-SEP-20 6LAN 0 JRNL AUTH P.HOU,K.YANG,P.JIA,L.LIU,Y.LIN,Z.LI,J.LI,S.CHEN,S.GUO,J.PAN, JRNL AUTH 2 J.WU,H.PENG,W.ZENG,C.LI,Y.LIU,D.GUO JRNL TITL A NOVEL SELECTIVE AUTOPHAGY RECEPTOR, CCDC50, DELIVERS K63 JRNL TITL 2 POLYUBIQUITINATION-ACTIVATED RIG-I/MDA5 FOR DEGRADATION JRNL TITL 3 DURING VIRAL INFECTION. JRNL REF CELL RES. V. 31 62 2021 JRNL REFN ISSN 1001-0602 JRNL PMID 32612200 JRNL DOI 10.1038/S41422-020-0362-1 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 24952 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.4000 - 3.4000 1.00 1806 156 0.1562 0.1656 REMARK 3 2 3.3900 - 2.7000 0.99 1743 151 0.1571 0.1752 REMARK 3 3 2.7000 - 2.3600 0.99 1736 152 0.1732 0.2042 REMARK 3 4 2.3600 - 2.1400 0.99 1745 151 0.1754 0.2356 REMARK 3 5 2.1400 - 1.9900 0.99 1714 148 0.1951 0.2412 REMARK 3 6 1.9900 - 1.8700 0.98 1716 149 0.2238 0.2364 REMARK 3 7 1.8700 - 1.7800 0.98 1707 147 0.2325 0.2533 REMARK 3 8 1.7800 - 1.7000 0.97 1702 148 0.2421 0.2833 REMARK 3 9 1.7000 - 1.6300 0.97 1696 148 0.2396 0.2805 REMARK 3 10 1.6300 - 1.5800 0.97 1692 147 0.2449 0.2486 REMARK 3 11 1.5800 - 1.5300 0.97 1688 146 0.2540 0.3334 REMARK 3 12 1.5300 - 1.4800 0.94 1632 141 0.2777 0.3240 REMARK 3 13 1.4800 - 1.4500 0.77 1326 115 0.2726 0.2937 REMARK 3 14 1.4500 - 1.4100 0.60 1059 91 0.3319 0.3590 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.176 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.326 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 1189 REMARK 3 ANGLE : 0.801 1614 REMARK 3 CHIRALITY : 0.072 175 REMARK 3 PLANARITY : 0.004 214 REMARK 3 DIHEDRAL : 30.459 467 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6LAN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014318. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24956 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 49.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.65000 REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3WAO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% V/V 2-PROPANOL, 0.1 M SODIUM REMARK 280 CITRATE PH 5.6, 20% W/V PEG 2000 MME, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 32.88800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.40200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.88800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.40200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 357 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -9 REMARK 465 PRO A -8 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 332 O HOH A 380 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O GLN A -6 HZ3 LYS A 51 4456 1.57 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 72 63.23 65.26 REMARK 500 HIS A 86 0.51 -152.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 481 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A 482 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 483 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A 484 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A 485 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A 486 DISTANCE = 7.17 ANGSTROMS DBREF 6LAN A -7 1 UNP Q8IVM0 CCD50_HUMAN 170 178 DBREF 6LAN A 2 125 UNP Q9GZQ8 MLP3B_HUMAN 2 125 SEQADV 6LAN GLY A -9 UNP Q8IVM0 EXPRESSION TAG SEQADV 6LAN PRO A -8 UNP Q8IVM0 EXPRESSION TAG SEQRES 1 A 135 GLY PRO ASP GLN GLU TRP TYR ASP ALA GLU ILE PRO SER SEQRES 2 A 135 GLU LYS THR PHE LYS GLN ARG ARG THR PHE GLU GLN ARG SEQRES 3 A 135 VAL GLU ASP VAL ARG LEU ILE ARG GLU GLN HIS PRO THR SEQRES 4 A 135 LYS ILE PRO VAL ILE ILE GLU ARG TYR LYS GLY GLU LYS SEQRES 5 A 135 GLN LEU PRO VAL LEU ASP LYS THR LYS PHE LEU VAL PRO SEQRES 6 A 135 ASP HIS VAL ASN MET SER GLU LEU ILE LYS ILE ILE ARG SEQRES 7 A 135 ARG ARG LEU GLN LEU ASN ALA ASN GLN ALA PHE PHE LEU SEQRES 8 A 135 LEU VAL ASN GLY HIS SER MET VAL SER VAL SER THR PRO SEQRES 9 A 135 ILE SER GLU VAL TYR GLU SER GLU LYS ASP GLU ASP GLY SEQRES 10 A 135 PHE LEU TYR MET VAL TYR ALA SER GLN GLU THR PHE GLY SEQRES 11 A 135 MET LYS LEU SER VAL FORMUL 2 HOH *286(H2 O) HELIX 1 AA1 THR A 6 ARG A 11 1 6 HELIX 2 AA2 THR A 12 HIS A 27 1 16 HELIX 3 AA3 ASN A 59 GLN A 72 1 14 HELIX 4 AA4 PRO A 94 LYS A 103 1 10 HELIX 5 AA5 SER A 115 VAL A 125 1 11 SHEET 1 AA1 4 LYS A 51 PRO A 55 0 SHEET 2 AA1 4 LYS A 30 ARG A 37 -1 N ILE A 31 O VAL A 54 SHEET 3 AA1 4 LEU A 109 ALA A 114 1 O LEU A 109 N ILE A 34 SHEET 4 AA1 4 PHE A 80 VAL A 83 -1 N PHE A 80 O ALA A 114 CRYST1 65.776 46.804 46.154 90.00 101.27 90.00 C 1 2 1 4 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 0.015203 0.000000 0.003029 0.00000 SCALE2 0.000000 0.021366 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022093 0.00000