HEADER PEPTIDE BINDING PROTEIN 29-DEC-20 7BEV TITLE NMR STRUCTURE OF AN OPTIMIZED VERSION OF THE FIRST TPR DOMAIN OF THE TITLE 2 HUMAN SPAG1 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERM-ASSOCIATED ANTIGEN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HSD-3.8,INFERTILITY-RELATED SPERM PROTEIN SPAG-1; COMPND 5 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: SPAG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HSP70, HSP90, EEVD, MD SIMULATION, RUVBL, R2TP, R2SP, CILIA, DYNEIN, KEYWDS 2 ASSEMBLY FACTOR, CHAPERONE, PEPTIDE BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.DERMOUCHE,M.E.CHAGOT,M.QUINTERNET REVDAT 3 31-JAN-24 7BEV 1 REMARK REVDAT 2 11-AUG-21 7BEV 1 JRNL REVDAT 1 31-MAR-21 7BEV 0 JRNL AUTH S.DERMOUCHE,M.E.CHAGOT,X.MANIVAL,M.QUINTERNET JRNL TITL OPTIMIZING THE FIRST TPR DOMAIN OF THE HUMAN SPAG1 PROTEIN JRNL TITL 2 PROVIDES INSIGHT INTO THE HSP70 AND HSP90 BINDING JRNL TITL 3 PROPERTIES. JRNL REF BIOCHEMISTRY V. 60 2349 2021 JRNL REFN ISSN 0006-2960 JRNL PMID 33739091 JRNL DOI 10.1021/ACS.BIOCHEM.1C00052 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7BEV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1292111826. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] SPAG1-TPR1, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HCCH-COSY; 2D NOESY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 3D HNHA; REMARK 210 3D HBHA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, TOPSPIN, CYANA 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 RESTRAINT 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: 7830 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 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 1 ARG A 234 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ARG A 248 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 ARG A 282 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 ARG A 321 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 ARG A 248 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 281 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 282 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 296 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 321 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG A 234 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 248 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 281 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 ARG A 282 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 ARG A 296 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 321 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 ARG A 296 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 234 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 248 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 ARG A 281 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 282 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 5 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ARG A 321 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 234 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 ARG A 248 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 282 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 6 ARG A 296 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 7 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 248 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 281 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 7 ARG A 282 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 7 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 7 ARG A 321 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 ARG A 281 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 282 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 8 ARG A 296 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG A 321 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 9 ARG A 248 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 296 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 321 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 10 ARG A 281 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 282 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 93 ANGLE DEVIATIONS. 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 ASP A 224 78.27 -107.17 REMARK 500 1 ASN A 257 53.72 -98.63 REMARK 500 2 ASN A 257 51.51 -95.38 REMARK 500 2 PRO A 273 96.53 -59.82 REMARK 500 2 ASN A 290 17.39 56.62 REMARK 500 2 LYS A 291 36.99 -83.24 REMARK 500 2 SER A 326 46.58 -79.80 REMARK 500 3 ASN A 257 48.97 -95.93 REMARK 500 3 PRO A 273 99.27 -61.63 REMARK 500 3 LYS A 291 34.38 -90.08 REMARK 500 3 ASN A 309 103.46 -56.75 REMARK 500 4 ASN A 257 54.10 -91.32 REMARK 500 4 PRO A 273 96.21 -66.74 REMARK 500 4 LYS A 291 37.70 -92.74 REMARK 500 5 ASP A 224 73.81 -103.22 REMARK 500 5 PRO A 273 96.15 -61.31 REMARK 500 5 ASN A 290 19.11 57.31 REMARK 500 5 LYS A 291 32.40 -88.77 REMARK 500 5 ASN A 309 93.24 -69.26 REMARK 500 6 ASN A 257 51.82 -94.76 REMARK 500 6 PRO A 273 96.07 -58.79 REMARK 500 6 SER A 326 48.91 -82.15 REMARK 500 7 ASN A 257 49.60 -103.45 REMARK 500 7 PRO A 273 90.36 -66.34 REMARK 500 7 ASN A 290 15.36 59.24 REMARK 500 7 LYS A 291 31.47 -85.41 REMARK 500 7 ASN A 309 99.09 -58.14 REMARK 500 7 SER A 326 35.31 -88.89 REMARK 500 8 ASN A 257 57.82 -97.12 REMARK 500 8 PRO A 273 94.77 -66.29 REMARK 500 8 LYS A 291 34.99 -92.92 REMARK 500 8 ASN A 309 96.87 -64.36 REMARK 500 8 SER A 326 44.30 -76.89 REMARK 500 9 ASN A 257 51.07 -96.94 REMARK 500 9 PRO A 273 79.10 -64.71 REMARK 500 9 ASN A 309 98.13 -63.70 REMARK 500 10 ASN A 257 49.81 -97.58 REMARK 500 10 PRO A 273 99.49 -67.95 REMARK 500 10 ASN A 290 19.72 59.12 REMARK 500 10 LYS A 291 34.64 -85.95 REMARK 500 10 ASN A 309 104.73 -59.78 REMARK 500 11 ASN A 257 51.21 -98.28 REMARK 500 11 PRO A 273 83.51 -65.01 REMARK 500 11 LYS A 291 33.78 -93.31 REMARK 500 12 ASN A 257 54.44 -106.16 REMARK 500 12 PRO A 273 92.96 -69.76 REMARK 500 12 LYS A 291 35.58 -82.18 REMARK 500 13 ASN A 257 49.11 -86.98 REMARK 500 13 PRO A 273 96.22 -59.39 REMARK 500 13 LYS A 291 35.25 -95.12 REMARK 500 REMARK 500 THIS ENTRY HAS 78 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 ARG A 296 0.09 SIDE CHAIN REMARK 500 9 TYR A 245 0.07 SIDE CHAIN REMARK 500 13 TYR A 286 0.07 SIDE CHAIN REMARK 500 14 ARG A 321 0.07 SIDE CHAIN REMARK 500 15 TYR A 286 0.09 SIDE CHAIN REMARK 500 17 TYR A 245 0.07 SIDE CHAIN REMARK 500 18 TYR A 245 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34586 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF AN OPTIMIZED VERSION OF THE FIRST TPR DOMAIN OF REMARK 900 THE HUMAN SPAG1 PROTEIN DBREF 7BEV A 206 327 UNP Q07617 SPAG1_HUMAN 206 327 SEQADV 7BEV GLY A 202 UNP Q07617 EXPRESSION TAG SEQADV 7BEV PRO A 203 UNP Q07617 EXPRESSION TAG SEQADV 7BEV HIS A 204 UNP Q07617 EXPRESSION TAG SEQADV 7BEV MET A 205 UNP Q07617 EXPRESSION TAG SEQADV 7BEV TYR A 207 UNP Q07617 PHE 207 CONFLICT SEQADV 7BEV TYR A 252 UNP Q07617 GLU 252 CONFLICT SEQADV 7BEV GLU A 262 UNP Q07617 PHE 262 CONFLICT SEQADV 7BEV ALA A 285 UNP Q07617 THR 285 CONFLICT SEQADV 7BEV ARG A 296 UNP Q07617 THR 296 CONFLICT SEQADV 7BEV LYS A 300 UNP Q07617 SER 300 CONFLICT SEQADV 7BEV LYS A 304 UNP Q07617 ASP 304 CONFLICT SEQRES 1 A 126 GLY PRO HIS MET ASP TYR LEU ALA THR ARG GLU LYS GLU SEQRES 2 A 126 LYS GLY ASN GLU ALA PHE ASN SER GLY ASP TYR GLU GLU SEQRES 3 A 126 ALA VAL MET TYR TYR THR ARG SER ILE SER ALA LEU PRO SEQRES 4 A 126 THR VAL VAL ALA TYR ASN ASN ARG ALA GLN ALA TYR ILE SEQRES 5 A 126 LYS LEU GLN ASN TRP ASN SER ALA GLU GLN ASP CYS GLU SEQRES 6 A 126 LYS VAL LEU GLU LEU GLU PRO GLY ASN VAL LYS ALA LEU SEQRES 7 A 126 LEU ARG ARG ALA THR ALA TYR LYS HIS GLN ASN LYS LEU SEQRES 8 A 126 ARG GLU ALA ARG GLU ASP LEU LYS LYS VAL LEU LYS VAL SEQRES 9 A 126 GLU PRO ASP ASN ASP LEU ALA LYS LYS THR LEU SER GLU SEQRES 10 A 126 VAL GLU ARG ASP LEU LYS ASN SER GLU HELIX 1 AA1 HIS A 204 GLY A 223 1 20 HELIX 2 AA2 ASP A 224 LEU A 239 1 16 HELIX 3 AA3 THR A 241 LEU A 255 1 15 HELIX 4 AA4 ASN A 257 GLU A 272 1 16 HELIX 5 AA5 ASN A 275 GLN A 289 1 15 HELIX 6 AA6 LYS A 291 LYS A 304 1 14 HELIX 7 AA7 ASN A 309 SER A 326 1 18 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