HEADER SIGNALING PROTEIN 01-NOV-17 5YPG TITLE P62/SQSTM1 ZZ DOMAIN WITH LEU-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(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) 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 5YPG 1 REMARK REVDAT 2 03-OCT-18 5YPG 1 TITLE REVDAT 1 29-AUG-18 5YPG 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. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 4630 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 464 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 27.0067 - 3.1698 0.96 1421 158 0.2226 0.2769 REMARK 3 2 3.1698 - 2.5166 0.99 1391 155 0.2579 0.3169 REMARK 3 3 2.5166 - 2.1986 0.99 1354 151 0.2523 0.3175 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.190 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 : 0.005 792 REMARK 3 ANGLE : 0.592 1050 REMARK 3 CHIRALITY : 0.042 114 REMARK 3 PLANARITY : 0.003 140 REMARK 3 DIHEDRAL : 12.881 468 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 5YPG 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_1300005679. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-17 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) : 1.0 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 : 4633 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.199 REMARK 200 RESOLUTION RANGE LOW (A) : 27.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MGCL2, SODIUM CACODYLATE, VAPOR REMARK 280 DIFFUSION, 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 14.26700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.07550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.13950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.07550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.26700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.13950 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: 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 HE2 HIS A 36 ZN ZN A 102 1.14 REMARK 500 HG CYS B 21 ZN ZN B 101 1.49 REMARK 500 O GLY A 13 H SER A 46 1.56 REMARK 500 OG1 THR B 14 O HOH B 201 1.98 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 110.3 REMARK 620 3 CYS A 27 SG 114.8 109.9 REMARK 620 4 CYS A 30 SG 91.5 112.9 116.4 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 121.9 REMARK 620 3 HIS A 36 NE2 107.5 99.6 REMARK 620 4 HIS A 39 ND1 113.1 101.4 112.6 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 4 SG REMARK 620 2 CYS B 7 SG 108.6 REMARK 620 3 CYS B 27 SG 114.2 110.0 REMARK 620 4 CYS B 30 SG 98.9 113.5 111.2 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 18 SG REMARK 620 2 CYS B 21 SG 122.0 REMARK 620 3 HIS B 36 NE2 118.5 102.5 REMARK 620 4 HIS B 39 ND1 109.4 106.4 94.2 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 LEU (-3 POSITION) IS SYNTHETIC RESIDUE GENERATED BY SPECIAL ENZYME DBREF 5YPG A -2 1 UNP P11021 GRP78_HUMAN 19 22 DBREF 5YPG A 2 56 UNP Q13501 SQSTM_HUMAN 126 180 DBREF 5YPG B -2 1 UNP P11021 GRP78_HUMAN 19 22 DBREF 5YPG B 2 56 UNP Q13501 SQSTM_HUMAN 126 180 SEQADV 5YPG LEU A -3 UNP P11021 SEE SEQUENCE DETAILS SEQADV 5YPG LEU B -3 UNP P11021 SEE SEQUENCE DETAILS SEQRES 1 A 60 LEU 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 LEU 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 *10(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 SER A 46 N GLY A 13 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 GLY B 13 O SER B 46 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 2.31 LINK SG CYS A 7 ZN ZN A 101 1555 1555 2.32 LINK SG CYS A 18 ZN ZN A 102 1555 1555 2.26 LINK SG CYS A 21 ZN ZN A 102 1555 1555 2.27 LINK SG CYS A 27 ZN ZN A 101 1555 1555 2.32 LINK SG CYS A 30 ZN ZN A 101 1555 1555 2.29 LINK NE2 HIS A 36 ZN ZN A 102 1555 1555 1.99 LINK ND1 HIS A 39 ZN ZN A 102 1555 1555 2.02 LINK SG CYS B 4 ZN ZN B 102 1555 1555 2.34 LINK SG CYS B 7 ZN ZN B 102 1555 1555 2.34 LINK SG CYS B 18 ZN ZN B 101 1555 1555 2.29 LINK SG CYS B 21 ZN ZN B 101 1555 1555 2.27 LINK SG CYS B 27 ZN ZN B 102 1555 1555 2.24 LINK SG CYS B 30 ZN ZN B 102 1555 1555 2.31 LINK NE2 HIS B 36 ZN ZN B 101 1555 1555 2.00 LINK ND1 HIS B 39 ZN ZN B 101 1555 1555 2.06 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 18 CYS B 21 HIS B 36 HIS B 39 SITE 1 AC4 4 CYS B 4 CYS B 7 CYS B 27 CYS B 30 CRYST1 28.534 44.279 68.151 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 0.035046 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022584 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014673 0.00000