HEADER CHAPERONE 22-AUG-19 6U3R TITLE SOLUTION NMR STRUCTURE OF THE DNAJB6B DELTAST VARIANT (ALIGNED ON THE TITLE 2 J DOMAIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNAJ HOMOLOG SUBFAMILY B MEMBER 6,DNAJ HOMOLOG SUBFAMILY B COMPND 3 MEMBER 6; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: HHDJ1,HEAT SHOCK PROTEIN J2,HSJ-2,MRJ,MSJ-1,HHDJ1,HEAT SHOCK COMPND 6 PROTEIN J2,HSJ-2,MRJ,MSJ-1; 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: DNAJB6, HSJ2, MRJ, MSJ1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HSP40, ANTI-AGGREGATION, AMYLOID, CHAPERONE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.K.KARAMANOS,G.M.CLORE REVDAT 5 14-JUN-23 6U3R 1 REMARK REVDAT 4 25-DEC-19 6U3R 1 REMARK REVDAT 3 06-NOV-19 6U3R 1 JRNL REVDAT 2 23-OCT-19 6U3R 1 JRNL REVDAT 1 09-OCT-19 6U3R 0 JRNL AUTH T.K.KARAMANOS,V.TUGARINOV,G.M.CLORE JRNL TITL UNRAVELING THE STRUCTURE AND DYNAMICS OF THE HUMAN DNAJB6B JRNL TITL 2 CHAPERONE BY NMR REVEALS INSIGHTS INTO HSP40-MEDIATED JRNL TITL 3 PROTEOSTASIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 116 21529 2019 JRNL REFN ESSN 1091-6490 JRNL PMID 31591220 JRNL DOI 10.1073/PNAS.1914999116 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CS-ROSETTA REMARK 3 AUTHORS : SHEN, VERNON, BAKER AND BAX REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6U3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243839. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.7; 7 REMARK 210 IONIC STRENGTH : 87; 145 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2E-04 M [U-13C; U-15N; U-2H] REMARK 210 DNAJB6B DELTAST VARIANT. THIS REMARK 210 VARIANT IS MISSING RESIDUES 132- REMARK 210 183 IN COMPARISON TO THE FULL- REMARK 210 LENGTH DNAJB6B, 5E-05 M SODIUM REMARK 210 CHLORIDE, 0.02 % W/V SODIUM REMARK 210 AZIDE, 0.02 M SODIUM PHOSPHATE, REMARK 210 90% H2O/10% D2O; 2E-04 M [ILV- REMARK 210 CH3; U-13C; U-15N; U-2H] DNAJB6B REMARK 210 DELTAST VARIANT. THIS VARIANT IS REMARK 210 MISSING RESIDUES 132-183 IN REMARK 210 COMPARISON TO THE FULL-LENGTH REMARK 210 DNAJB6B, 0.05 M SODIUM CHLORIDE, REMARK 210 0.02 % W/V SODIUM AZIDE, 0.02 M REMARK 210 SODIUM PHOSPHATE, 100% D2O; 2E- REMARK 210 04 M [ILV-CH3; U-15N; U-2H] REMARK 210 DNAJB6B DELTAST VARIANT. THIS REMARK 210 VARIANT IS MISSING RESIDUES 132- REMARK 210 183 IN COMPARISON TO THE FULL- REMARK 210 LENGTH DNAJB6B, 0.05 M SODIUM REMARK 210 CHLORIDE, 0.02 % W/V SODIUM REMARK 210 AZIDE, 0.02 M SODIUM PHOSPHATE, REMARK 210 100% D2O; 2E-04 M [U-13C; U-15N] REMARK 210 DNAJB6B DELTAST VARIANT. THIS REMARK 210 VARIANT IS MISSING RESIDUES 132- REMARK 210 183 IN COMPARISON TO THE FULL- REMARK 210 LENGTH DNAJB6B, 0.05 M SODIUM REMARK 210 CHLORIDE, 0.02 % W/V SODIUM REMARK 210 AZIDE, 0.02 M SODIUM PHOSPHATE, REMARK 210 90% H2O/10% D2O; 2E-04 M [U-15N; REMARK 210 U-2H] DNAJB6B DELTAST VARIANT. REMARK 210 THIS VARIANT IS MISSING RESIDUES REMARK 210 132-183 IN COMPARISON TO THE REMARK 210 FULL-LENGTH DNAJB6B, 0.05 M REMARK 210 SODIUM CHLORIDE, 0.02 % W/V REMARK 210 SODIUM AZIDE, 0.02 M SODIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 2E- REMARK 210 04 M [U-15N;U-2H] DNAJB6B REMARK 210 DELTAST VARIANT. THIS VARIANT IS REMARK 210 MISSING RESIDUES 132-183 IN REMARK 210 COMPARISON TO THE FULL-LENGTH REMARK 210 DNAJB6B, 0.1 M SODIUM CHLORIDE, REMARK 210 0.02 % W/V SODIUM AZIDE, 0.02 M REMARK 210 SODIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O; 2E-04 M [U-15N;U-2H] REMARK 210 DNAJB6B DELTAST VARIANT. THIS REMARK 210 VARIANT IS MISSING RESIDUES 132- REMARK 210 183 IN COMPARISON TO THE FULL- REMARK 210 LENGTH DNAJB6B, 0.05 M SODIUM REMARK 210 CHLORIDE, 0.02 % W/V SODIUM REMARK 210 AZIDE, 2E-05 M SODIUM PHOSPHATE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N TROSY; 3D HNCACB; 3D REMARK 210 HNCO; 2D 1H-13C HMQC; 2D 1H-13C REMARK 210 HMQC CONSTANT TIME; 3D HMCMCBCA; REMARK 210 3D HMCM(CBCA)CO; 3D HHN NOESY- REMARK 210 TROSY; 3D HHC NOESY-HMQC; 3D HHC REMARK 210 HMQC-NOESY; 3D HCC HMQC-NOESY- REMARK 210 HMQC; 2D HN PRE; 2D HN ARTSY PF1; REMARK 210 2D HN ARTSY PEGHEX REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS, NMRPIPE, REMARK 210 NMRDRAW, X-PLOR NIH, CS-ROSETTA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 10 PRO A 130 C ARG A 131 N 0.141 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 10 PRO A 130 CA - C - N ANGL. DEV. = 22.1 DEGREES REMARK 500 10 PRO A 130 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 10 ARG A 131 C - N - CA ANGL. DEV. = -22.4 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 ASN A 39 57.46 -102.00 REMARK 500 1 LEU A 74 107.22 -52.85 REMARK 500 1 PHE A 90 50.66 -113.73 REMARK 500 2 HIS A 83 57.77 -162.14 REMARK 500 2 GLU A 89 59.84 -148.58 REMARK 500 2 PHE A 90 30.85 -95.18 REMARK 500 2 PRO A 130 -169.55 -79.26 REMARK 500 2 LYS A 138 -63.18 -96.04 REMARK 500 3 ASN A 39 53.98 -150.60 REMARK 500 3 LEU A 74 107.20 -53.03 REMARK 500 3 PHE A 90 51.67 -115.87 REMARK 500 3 GLU A 117 44.66 -106.94 REMARK 500 3 ARG A 131 157.60 68.18 REMARK 500 3 LYS A 138 -60.17 -96.14 REMARK 500 4 ASN A 39 55.22 -150.11 REMARK 500 4 LEU A 74 109.46 -51.50 REMARK 500 4 HIS A 83 43.69 -151.53 REMARK 500 4 GLU A 89 52.34 -119.99 REMARK 500 4 GLU A 117 56.11 -103.91 REMARK 500 4 PRO A 130 -150.53 -79.84 REMARK 500 5 TRP A 31 32.42 -98.94 REMARK 500 5 GLU A 72 58.01 -119.89 REMARK 500 5 HIS A 83 57.78 -163.36 REMARK 500 5 GLU A 89 54.50 -141.43 REMARK 500 6 GLU A 72 55.63 -117.70 REMARK 500 6 HIS A 83 57.13 -163.63 REMARK 500 6 GLU A 89 58.72 -149.05 REMARK 500 6 GLU A 121 40.98 -103.63 REMARK 500 6 LYS A 138 -63.95 -98.14 REMARK 500 7 PRO A 130 -148.64 -79.94 REMARK 500 7 ARG A 131 90.96 -51.05 REMARK 500 8 TRP A 31 32.42 -98.94 REMARK 500 8 GLU A 72 58.01 -119.89 REMARK 500 8 HIS A 83 57.78 -163.36 REMARK 500 8 GLU A 89 54.50 -141.43 REMARK 500 8 PRO A 130 -156.57 -76.58 REMARK 500 8 ARG A 131 -27.72 66.24 REMARK 500 9 HIS A 83 57.47 -162.87 REMARK 500 9 GLU A 89 59.79 -146.44 REMARK 500 9 PHE A 90 31.05 -94.60 REMARK 500 9 ARG A 131 178.83 52.78 REMARK 500 9 LYS A 174 -60.18 -94.97 REMARK 500 10 TRP A 31 31.68 -99.77 REMARK 500 10 PHE A 90 41.25 -142.74 REMARK 500 10 GLU A 117 40.62 -109.82 REMARK 500 10 ARG A 131 158.46 72.76 REMARK 500 10 LEU A 185 52.60 -110.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 6 PRO A 130 -10.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30655 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF THE DNAJB6B DELTAST VARIANT (ALIGNED ON REMARK 900 THE J DOMAIN). DBREF 6U3R A 2 128 UNP O75190 DNJB6_HUMAN 1 127 DBREF 6U3R A 133 190 UNP O75190 DNJB6_HUMAN 184 241 SEQADV 6U3R GLY A 1 UNP O75190 EXPRESSION TAG SEQADV 6U3R GLY A 129 UNP O75190 LINKER SEQADV 6U3R PRO A 130 UNP O75190 LINKER SEQADV 6U3R ARG A 131 UNP O75190 LINKER SEQADV 6U3R GLY A 132 UNP O75190 LINKER SEQRES 1 A 190 GLY MET VAL ASP TYR TYR GLU VAL LEU GLY VAL GLN ARG SEQRES 2 A 190 HIS ALA SER PRO GLU ASP ILE LYS LYS ALA TYR ARG LYS SEQRES 3 A 190 LEU ALA LEU LYS TRP HIS PRO ASP LYS ASN PRO GLU ASN SEQRES 4 A 190 LYS GLU GLU ALA GLU ARG LYS PHE LYS GLN VAL ALA GLU SEQRES 5 A 190 ALA TYR GLU VAL LEU SER ASP ALA LYS LYS ARG ASP ILE SEQRES 6 A 190 TYR ASP LYS TYR GLY LYS GLU GLY LEU ASN GLY GLY GLY SEQRES 7 A 190 GLY GLY GLY SER HIS PHE ASP SER PRO PHE GLU PHE GLY SEQRES 8 A 190 PHE THR PHE ARG ASN PRO ASP ASP VAL PHE ARG GLU PHE SEQRES 9 A 190 PHE GLY GLY ARG ASP PRO PHE SER PHE ASP PHE PHE GLU SEQRES 10 A 190 ASP PRO PHE GLU ASP PHE PHE GLY ASN ARG ARG GLY PRO SEQRES 11 A 190 ARG GLY GLY MET GLY ASN PHE LYS SER ILE SER THR SER SEQRES 12 A 190 THR LYS MET VAL ASN GLY ARG LYS ILE THR THR LYS ARG SEQRES 13 A 190 ILE VAL GLU ASN GLY GLN GLU ARG VAL GLU VAL GLU GLU SEQRES 14 A 190 ASP GLY GLN LEU LYS SER LEU THR ILE ASN GLY LYS GLU SEQRES 15 A 190 GLN LEU LEU ARG LEU ASP ASN LYS HELIX 1 AA1 ASP A 4 LEU A 9 1 6 HELIX 2 AA2 PRO A 17 TRP A 31 1 15 HELIX 3 AA3 PRO A 33 LYS A 35 1 3 HELIX 4 AA4 LYS A 40 SER A 58 1 19 HELIX 5 AA5 ALA A 60 TYR A 69 1 10 HELIX 6 AA6 PRO A 97 PHE A 105 1 9 SHEET 1 AA1 5 LYS A 138 VAL A 147 0 SHEET 2 AA1 5 ARG A 150 GLU A 159 -1 O ILE A 152 N LYS A 145 SHEET 3 AA1 5 GLN A 162 GLU A 169 -1 O GLU A 168 N THR A 153 SHEET 4 AA1 5 GLN A 172 ILE A 178 -1 O GLN A 172 N GLU A 169 SHEET 5 AA1 5 LYS A 181 GLU A 182 -1 O LYS A 181 N ILE A 178 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