HEADER SIGNALING PROTEIN 01-NOV-17 5YPA TITLE P62/SQSTM1 ZZ DOMAIN WITH LYS-PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 78 KDA GLUCOSE-REGULATED PROTEIN,SEQUESTOSOME-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GRP-78,EBI3-ASSOCIATED PROTEIN OF 60 KDA,P60, COMPND 5 PHOSPHOTYROSINE-INDEPENDENT LIGAND FOR THE LCK SH2 DOMAIN OF 62 KDA, COMPND 6 UBIQUITIN-BINDING PROTEIN P62; COMPND 7 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: HSPA5, GRP78, SQSTM1, ORCA, OSIL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS COMPLEX, P62/SQSTM1, ZZ DOMAIN, AUTOPHAGY, N-END RULE, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.H.KWON,L.KIM,H.K.SONG REVDAT 3 27-MAR-24 5YPA 1 REMARK REVDAT 2 03-OCT-18 5YPA 1 TITLE REVDAT 1 29-AUG-18 5YPA 0 JRNL AUTH D.H.KWON,O.H.PARK,L.KIM,Y.O.JUNG,Y.PARK,H.JEONG,J.HYUN, JRNL AUTH 2 Y.K.KIM,H.K.SONG JRNL TITL INSIGHTS INTO DEGRADATION MECHANISM OF N-END RULE SUBSTRATES JRNL TITL 2 BY P62/SQSTM1 AUTOPHAGY ADAPTER. JRNL REF NAT COMMUN V. 9 3291 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30120248 JRNL DOI 10.1038/S41467-018-05825-X REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 2939 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 294 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 21.9941 - 3.1511 0.95 1426 158 0.2131 0.2498 REMARK 3 2 3.1511 - 2.5023 0.87 1219 136 0.2054 0.3031 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 778 REMARK 3 ANGLE : 0.982 1050 REMARK 3 CHIRALITY : 0.061 112 REMARK 3 PLANARITY : 0.006 140 REMARK 3 DIHEDRAL : 9.194 472 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 5YPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2939 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.502 REMARK 200 RESOLUTION RANGE LOW (A) : 21.993 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-2000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, CACL2, HEPES, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 14.54250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.60950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.91100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.60950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.54250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.91100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 PHE A 48 REMARK 465 GLY A 49 REMARK 465 HIS A 50 REMARK 465 LEU A 51 REMARK 465 SER A 52 REMARK 465 GLU A 53 REMARK 465 GLY A 54 REMARK 465 PHE A 55 REMARK 465 SER A 56 REMARK 465 PHE B 48 REMARK 465 GLY B 49 REMARK 465 HIS B 50 REMARK 465 LEU B 51 REMARK 465 SER B 52 REMARK 465 GLU B 53 REMARK 465 GLY B 54 REMARK 465 PHE B 55 REMARK 465 SER B 56 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 VAL A 20 -60.20 -109.87 REMARK 500 ASP B 23 62.39 39.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 4 SG REMARK 620 2 CYS A 7 SG 105.1 REMARK 620 3 CYS A 27 SG 106.5 126.8 REMARK 620 4 CYS A 30 SG 98.2 114.0 102.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 CYS A 21 SG 128.6 REMARK 620 3 HIS A 36 NE2 113.6 105.3 REMARK 620 4 HIS A 39 ND1 103.9 99.3 101.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 4 SG REMARK 620 2 CYS B 7 SG 108.3 REMARK 620 3 CYS B 27 SG 118.5 109.4 REMARK 620 4 CYS B 30 SG 100.4 107.9 111.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 18 SG REMARK 620 2 CYS B 21 SG 117.9 REMARK 620 3 HIS B 36 NE2 107.1 102.5 REMARK 620 4 HIS B 39 ND1 113.0 112.8 101.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 102 REMARK 999 REMARK 999 SEQUENCE REMARK 999 LYS (-3 POSITION) IS SYNTHETIC RESIDUE GENERATED BY SPECIAL ENZYME DBREF 5YPA A -2 1 UNP P11021 GRP78_HUMAN 19 22 DBREF 5YPA A 2 56 UNP Q13501 SQSTM_HUMAN 126 180 DBREF 5YPA B -2 1 UNP P11021 GRP78_HUMAN 19 22 DBREF 5YPA B 2 56 UNP Q13501 SQSTM_HUMAN 126 180 SEQADV 5YPA LYS A -3 UNP P11021 SEE SEQUENCE DETAILS SEQADV 5YPA LYS B -3 UNP P11021 SEE SEQUENCE DETAILS SEQRES 1 A 60 LYS GLU GLU GLU ASP VAL ILE CYS ASP GLY CYS ASN GLY SEQRES 2 A 60 PRO VAL VAL GLY THR ARG TYR LYS CYS SER VAL CYS PRO SEQRES 3 A 60 ASP TYR ASP LEU CYS SER VAL CYS GLU GLY LYS GLY LEU SEQRES 4 A 60 HIS ARG GLY HIS THR LYS LEU ALA PHE PRO SER PRO PHE SEQRES 5 A 60 GLY HIS LEU SER GLU GLY PHE SER SEQRES 1 B 60 LYS GLU GLU GLU ASP VAL ILE CYS ASP GLY CYS ASN GLY SEQRES 2 B 60 PRO VAL VAL GLY THR ARG TYR LYS CYS SER VAL CYS PRO SEQRES 3 B 60 ASP TYR ASP LEU CYS SER VAL CYS GLU GLY LYS GLY LEU SEQRES 4 B 60 HIS ARG GLY HIS THR LYS LEU ALA PHE PRO SER PRO PHE SEQRES 5 B 60 GLY HIS LEU SER GLU GLY PHE SER HET ZN A 101 1 HET ZN A 102 1 HET ZN B 101 1 HET ZN B 102 1 HETNAM ZN ZINC ION FORMUL 3 ZN 4(ZN 2+) FORMUL 7 HOH *23(H2 O) HELIX 1 AA1 CYS A 27 LYS A 33 1 7 HELIX 2 AA2 CYS B 27 LYS B 33 1 7 SHEET 1 AA1 6 ASP A 25 LEU A 26 0 SHEET 2 AA1 6 GLY A 13 CYS A 18 -1 N TYR A 16 O LEU A 26 SHEET 3 AA1 6 LYS A 41 SER A 46 -1 O LEU A 42 N LYS A 17 SHEET 4 AA1 6 LYS B 41 SER B 46 -1 O LYS B 41 N ALA A 43 SHEET 5 AA1 6 GLY B 13 CYS B 18 -1 N ARG B 15 O PHE B 44 SHEET 6 AA1 6 ASP B 25 LEU B 26 -1 O LEU B 26 N TYR B 16 LINK SG CYS A 4 ZN ZN A 101 1555 1555 2.38 LINK SG CYS A 7 ZN ZN A 101 1555 1555 2.36 LINK SG CYS A 18 ZN ZN A 102 1555 1555 2.27 LINK SG CYS A 21 ZN ZN A 102 1555 1555 2.11 LINK SG CYS A 27 ZN ZN A 101 1555 1555 2.22 LINK SG CYS A 30 ZN ZN A 101 1555 1555 2.31 LINK NE2 HIS A 36 ZN ZN A 102 1555 1555 2.01 LINK ND1 HIS A 39 ZN ZN A 102 1555 1555 2.20 LINK SG CYS B 4 ZN ZN B 101 1555 1555 2.26 LINK SG CYS B 7 ZN ZN B 101 1555 1555 2.27 LINK SG CYS B 18 ZN ZN B 102 1555 1555 2.24 LINK SG CYS B 21 ZN ZN B 102 1555 1555 2.28 LINK SG CYS B 27 ZN ZN B 101 1555 1555 2.30 LINK SG CYS B 30 ZN ZN B 101 1555 1555 2.27 LINK NE2 HIS B 36 ZN ZN B 102 1555 1555 1.91 LINK ND1 HIS B 39 ZN ZN B 102 1555 1555 2.04 SITE 1 AC1 4 CYS A 4 CYS A 7 CYS A 27 CYS A 30 SITE 1 AC2 4 CYS A 18 CYS A 21 HIS A 36 HIS A 39 SITE 1 AC3 4 CYS B 4 CYS B 7 CYS B 27 CYS B 30 SITE 1 AC4 4 CYS B 18 CYS B 21 HIS B 36 HIS B 39 CRYST1 29.085 43.822 67.219 90.00 90.00 90.00 P 21 21 21 8 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 0.034382 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014877 0.00000