HEADER PROTEIN BINDING 17-JUL-19 6SAP TITLE STRUCTURE OF THE PUB DOMAIN FROM UBIQUITIN REGULATORY X DOMAIN PROTEIN TITLE 2 1 (UBXD1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBX DOMAIN-CONTAINING PROTEIN 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBX DOMAIN-CONTAINING PROTEIN 1; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE FIRST 4 RESIDUES REPRESENT A CLONING ARTIFACT. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBXN6, UBXD1, UBXDC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS UBXD1, PUB DOMAIN, P97, PROTEIN INTERACTION, NMR SOLUTION STRUCTURE, KEYWDS 2 PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.BEUCK,P.BAYER,M.BLUEGGEL REVDAT 3 19-JUN-24 6SAP 1 REMARK REVDAT 2 14-JUN-23 6SAP 1 REMARK REVDAT 1 25-DEC-19 6SAP 0 JRNL AUTH M.BLUEGGEL,J.VAN DEN BOOM,H.MEYER,P.BAYER,C.BEUCK JRNL TITL STRUCTURE OF THE PUB DOMAIN FROM UBIQUITIN REGULATORY X JRNL TITL 2 DOMAIN PROTEIN 1 (UBXD1) AND ITS INTERACTION WITH THE P97 JRNL TITL 3 AAA+ ATPASE. JRNL REF BIOMOLECULES V. 9 2019 JRNL REFN ESSN 2218-273X JRNL PMID 31847414 JRNL DOI 10.3390/BIOM9120876 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA 11.12.31 REMARK 3 AUTHORS : KRIEGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6SAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1292103376. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 900 UM [U-98% 13C; U-98% 15N] REMARK 210 UBXD1 PUB DOMAIN, 16 MM REMARK 210 POTASSIUM PHOSPHATE, 34 MM REMARK 210 SODIUM PHOSPHATE, 90 % H2O, 10 % REMARK 210 [U-99% 2H] D2O, 0.1 MM DSS, 90% REMARK 210 H2O/10% D2O; 500 UM [U-98% 13C; REMARK 210 U-98% 15N] UBXD1 PUB DOMAIN, 16 REMARK 210 MM POTASSIUM PHOSPHATE, 34 MM REMARK 210 SODIUM PHOSPHATE, 100 % [U-99% REMARK 210 2H] D2O, 0.1 MM DSS, 100% D2O; REMARK 210 700 UM [U-98% 15N] UBXD1 PUB REMARK 210 DOMAIN, 16 MM POTASSIUM REMARK 210 PHOSPHATE, 34 MM SODIUM REMARK 210 PHOSPHATE, 90 % H2O, 10 % [U-99% REMARK 210 2H] D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HNCO; 3D HN(CA)CO; 3D REMARK 210 H(CCO)NH; 3D C(CO)NH; 3D 1H-15N REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D HCCH- REMARK 210 COSY ALIPHATIC; 3D HCCH-TOCSY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D HISTIDIN H(C)N- REMARK 210 SOFAST-HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.5, CARA 1.6, UNIO 10, REMARK 210 CYANA 3.98.9 REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 20 GLU A 237 CG GLU A 237 CD 0.105 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 3 LEU A 228 CB - CG - CD2 ANGL. DEV. = -14.6 DEGREES REMARK 500 4 THR A 151 CA - C - N ANGL. DEV. = -14.3 DEGREES REMARK 500 4 ASP A 152 N - CA - CB ANGL. DEV. = -14.4 DEGREES REMARK 500 6 ASP A 152 N - CA - CB ANGL. DEV. = -13.5 DEGREES REMARK 500 6 GLU A 258 N - CA - CB ANGL. DEV. = -10.8 DEGREES REMARK 500 8 ASP A 152 N - CA - CB ANGL. DEV. = -11.9 DEGREES REMARK 500 10 ASP A 152 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 10 ARG A 255 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ASP A 152 N - CA - CB ANGL. DEV. = -14.0 DEGREES REMARK 500 16 ASP A 152 N - CA - CB ANGL. DEV. = -13.6 DEGREES REMARK 500 17 ASP A 152 N - CA - CB ANGL. DEV. = -14.2 DEGREES REMARK 500 18 ASP A 152 N - CA - CB ANGL. DEV. = -13.8 DEGREES REMARK 500 19 ASP A 152 N - CA - CB ANGL. DEV. = -13.5 DEGREES REMARK 500 20 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 20 LEU A 228 CB - CG - CD2 ANGL. DEV. = -14.3 DEGREES REMARK 500 20 GLU A 237 OE1 - CD - OE2 ANGL. DEV. = 15.8 DEGREES REMARK 500 20 GLU A 237 CG - CD - OE1 ANGL. DEV. = -48.1 DEGREES REMARK 500 20 GLU A 237 CG - CD - OE2 ANGL. DEV. = -49.0 DEGREES REMARK 500 20 ARG A 255 NE - CZ - NH1 ANGL. DEV. = 3.4 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 HIS A -2 -179.57 66.81 REMARK 500 1 MET A -1 135.94 67.28 REMARK 500 1 THR A 151 123.89 67.19 REMARK 500 1 ARG A 195 31.69 -75.81 REMARK 500 1 ARG A 207 -76.11 -122.79 REMARK 500 1 GLU A 212 -158.18 -72.86 REMARK 500 2 SER A 150 45.77 -145.75 REMARK 500 2 THR A 151 150.20 54.86 REMARK 500 2 ASN A 165 30.88 -71.14 REMARK 500 2 HIS A 188 77.27 -119.67 REMARK 500 2 ARG A 195 30.23 -72.18 REMARK 500 2 LEU A 211 -169.20 -124.76 REMARK 500 2 GLU A 212 -162.50 -71.79 REMARK 500 2 GLN A 233 78.94 -101.24 REMARK 500 3 SER A 150 55.07 -105.72 REMARK 500 3 ASN A 165 41.63 -73.39 REMARK 500 3 HIS A 188 77.10 -119.89 REMARK 500 3 ARG A 195 29.01 -70.16 REMARK 500 3 ILE A 208 -52.23 -126.68 REMARK 500 3 LEU A 211 -165.04 -125.43 REMARK 500 3 GLU A 212 -164.79 -69.37 REMARK 500 3 ALA A 263 48.95 -79.75 REMARK 500 4 HIS A -2 15.45 58.74 REMARK 500 4 SER A 150 44.31 -62.63 REMARK 500 4 PHE A 164 31.23 -87.27 REMARK 500 4 ASN A 165 38.71 -73.26 REMARK 500 4 HIS A 188 76.88 -119.00 REMARK 500 4 ARG A 195 30.87 -73.11 REMARK 500 4 ARG A 207 -73.58 -127.51 REMARK 500 4 GLU A 212 -155.54 -75.07 REMARK 500 4 GLU A 234 48.65 -83.60 REMARK 500 4 PRO A 236 92.94 -55.78 REMARK 500 5 PHE A 164 42.71 -98.54 REMARK 500 5 HIS A 188 77.41 -116.89 REMARK 500 5 GLN A 200 46.05 -74.79 REMARK 500 5 LEU A 211 -165.29 -126.14 REMARK 500 5 GLU A 212 -161.66 -65.66 REMARK 500 5 ALA A 262 30.75 -88.01 REMARK 500 5 ALA A 263 48.11 -73.21 REMARK 500 6 MET A -1 37.46 -93.63 REMARK 500 6 PHE A 164 34.08 -96.84 REMARK 500 6 HIS A 188 77.76 -115.49 REMARK 500 6 ARG A 195 26.74 -70.75 REMARK 500 6 GLN A 200 48.60 -75.74 REMARK 500 6 ILE A 208 -50.33 -123.02 REMARK 500 6 GLU A 212 -159.01 -67.80 REMARK 500 6 PRO A 236 77.73 -50.24 REMARK 500 7 ASN A 165 25.48 -71.23 REMARK 500 7 HIS A 188 67.85 -105.39 REMARK 500 7 GLU A 191 75.84 -102.16 REMARK 500 REMARK 500 THIS ENTRY HAS 145 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 151 ASP A 152 13 -149.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27977 RELATED DB: BMRB DBREF 6SAP A 150 264 UNP Q9BZV1 UBXN6_HUMAN 150 264 SEQADV 6SAP GLY A -4 UNP Q9BZV1 EXPRESSION TAG SEQADV 6SAP SER A -3 UNP Q9BZV1 EXPRESSION TAG SEQADV 6SAP HIS A -2 UNP Q9BZV1 EXPRESSION TAG SEQADV 6SAP MET A -1 UNP Q9BZV1 EXPRESSION TAG SEQRES 1 A 119 GLY SER HIS MET SER THR ASP PRO VAL ALA ALA SER ILE SEQRES 2 A 119 MET LYS ILE TYR THR PHE ASN LYS ASP GLN ASP ARG VAL SEQRES 3 A 119 LYS LEU GLY VAL ASP THR ILE ALA LYS TYR LEU ASP ASN SEQRES 4 A 119 ILE HIS LEU HIS PRO GLU GLU GLU LYS TYR ARG LYS ILE SEQRES 5 A 119 LYS LEU GLN ASN LYS VAL PHE GLN GLU ARG ILE ASN CYS SEQRES 6 A 119 LEU GLU GLY THR HIS GLU PHE PHE GLU ALA ILE GLY PHE SEQRES 7 A 119 GLN LYS VAL LEU LEU PRO ALA GLN ASP GLN GLU ASP PRO SEQRES 8 A 119 GLU GLU PHE TYR VAL LEU SER GLU THR THR LEU ALA GLN SEQRES 9 A 119 PRO GLN SER LEU GLU ARG HIS LYS GLU GLN LEU LEU ALA SEQRES 10 A 119 ALA GLU HELIX 1 AA1 PRO A 153 PHE A 164 1 12 HELIX 2 AA2 GLN A 168 LEU A 187 1 20 HELIX 3 AA3 GLU A 192 TYR A 194 1 3 HELIX 4 AA4 LYS A 202 CYS A 210 1 9 HELIX 5 AA5 THR A 214 ALA A 220 1 7 HELIX 6 AA6 GLU A 244 LEU A 247 1 4 HELIX 7 AA7 PRO A 250 LEU A 261 1 12 SHEET 1 AA1 3 LYS A 196 LYS A 198 0 SHEET 2 AA1 3 GLU A 238 LEU A 242 -1 O TYR A 240 N ILE A 197 SHEET 3 AA1 3 PHE A 223 LEU A 227 -1 N GLN A 224 O VAL A 241 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