HEADER STRUCTURAL PROTEIN 16-APR-20 6YQF TITLE CRYSTAL STRUCTURE OF THE SYCE2-TEX12 DELTA-CTIP COMPLEX IN A 4:4 TITLE 2 ASSEMBLY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTONEMAL COMPLEX CENTRAL ELEMENT PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CENTRAL ELEMENT SYNAPTONEMAL COMPLEX PROTEIN 1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TESTIS-EXPRESSED PROTEIN 12; COMPND 8 CHAIN: C, D; COMPND 9 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: SYCE2, CESC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: TEX12; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SYNAPTONEMAL COMPLEX MEIOSIS RECOMBINATION COILED-COIL SELF-ASSEMBLY KEYWDS 2 SYCE2 TEX12 STRUCTURAL PROTEIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.DUNCE,O.R.DAVIES REVDAT 3 24-JAN-24 6YQF 1 REMARK REVDAT 2 15-SEP-21 6YQF 1 JRNL REVDAT 1 28-APR-21 6YQF 0 JRNL AUTH J.M.DUNCE,L.J.SALMON,O.R.DAVIES JRNL TITL STRUCTURAL BASIS OF MEIOTIC CHROMOSOME SYNAPTIC ELONGATION JRNL TITL 2 THROUGH HIERARCHICAL FIBROUS ASSEMBLY OF SYCE2-TEX12. JRNL REF NAT.STRUCT.MOL.BIOL. V. 28 681 2021 JRNL REFN ESSN 1545-9985 JRNL PMID 34373646 JRNL DOI 10.1038/S41594-021-00636-Z REMARK 2 REMARK 2 RESOLUTION. 3.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 3.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 64.1 REMARK 3 NUMBER OF REFLECTIONS : 4053 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.329 REMARK 3 R VALUE (WORKING SET) : 0.327 REMARK 3 FREE R VALUE : 0.367 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 202 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 47.4500 - 3.3300 0.64 3851 202 0.3266 0.3672 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.399 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.276 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.52 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 : 0.001 2447 REMARK 3 ANGLE : 0.272 3274 REMARK 3 CHIRALITY : 0.031 378 REMARK 3 PLANARITY : 0.001 419 REMARK 3 DIHEDRAL : 8.353 962 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 6YQF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9688 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE, STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4098 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.327 REMARK 200 RESOLUTION RANGE LOW (A) : 47.452 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 64.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 27.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 6R17 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, 65% MPD, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 21.33500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.84000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.33500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.84000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A 54 REMARK 465 SER A 55 REMARK 465 MET A 56 REMARK 465 HIS A 151 REMARK 465 SER A 152 REMARK 465 VAL A 153 REMARK 465 GLU A 154 REMARK 465 THR A 155 REMARK 465 VAL A 156 REMARK 465 TYR A 157 REMARK 465 LYS A 158 REMARK 465 ASP A 159 REMARK 465 LEU A 160 REMARK 465 CYS A 161 REMARK 465 LEU A 162 REMARK 465 GLN A 163 REMARK 465 PRO A 164 REMARK 465 GLU A 165 REMARK 465 GLY B 54 REMARK 465 SER B 55 REMARK 465 MET B 56 REMARK 465 GLY B 57 REMARK 465 LEU B 58 REMARK 465 TYR B 59 REMARK 465 PHE B 60 REMARK 465 HIS B 151 REMARK 465 SER B 152 REMARK 465 VAL B 153 REMARK 465 GLU B 154 REMARK 465 THR B 155 REMARK 465 VAL B 156 REMARK 465 TYR B 157 REMARK 465 LYS B 158 REMARK 465 ASP B 159 REMARK 465 LEU B 160 REMARK 465 CYS B 161 REMARK 465 LEU B 162 REMARK 465 GLN B 163 REMARK 465 PRO B 164 REMARK 465 GLU B 165 REMARK 465 GLY C 45 REMARK 465 SER C 46 REMARK 465 MET C 47 REMARK 465 GLY C 48 REMARK 465 LYS C 49 REMARK 465 ASP C 50 REMARK 465 GLN C 112 REMARK 465 ARG C 113 REMARK 465 GLY D 45 REMARK 465 SER D 46 REMARK 465 MET D 47 REMARK 465 GLY D 48 REMARK 465 LYS D 49 REMARK 465 ASP D 50 REMARK 465 GLU D 51 REMARK 465 ALA D 52 REMARK 465 LEU D 53 REMARK 465 GLU D 54 REMARK 465 LYS D 55 REMARK 465 ASP D 56 REMARK 465 LEU D 57 REMARK 465 GLU D 108 REMARK 465 PHE D 109 REMARK 465 LEU D 110 REMARK 465 ARG D 111 REMARK 465 GLN D 112 REMARK 465 ARG D 113 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6R17 RELATED DB: PDB REMARK 900 6R17 CONTAINS THE SAME PROTEIN AS A 2:2 COMPLEX DBREF 6YQF A 57 165 UNP Q6PIF2 SYCE2_HUMAN 57 165 DBREF 6YQF B 57 165 UNP Q6PIF2 SYCE2_HUMAN 57 165 DBREF 6YQF C 49 113 UNP Q9BXU0 TEX12_HUMAN 49 113 DBREF 6YQF D 49 113 UNP Q9BXU0 TEX12_HUMAN 49 113 SEQADV 6YQF GLY A 54 UNP Q6PIF2 EXPRESSION TAG SEQADV 6YQF SER A 55 UNP Q6PIF2 EXPRESSION TAG SEQADV 6YQF MET A 56 UNP Q6PIF2 EXPRESSION TAG SEQADV 6YQF GLY B 54 UNP Q6PIF2 EXPRESSION TAG SEQADV 6YQF SER B 55 UNP Q6PIF2 EXPRESSION TAG SEQADV 6YQF MET B 56 UNP Q6PIF2 EXPRESSION TAG SEQADV 6YQF GLY C 45 UNP Q9BXU0 EXPRESSION TAG SEQADV 6YQF SER C 46 UNP Q9BXU0 EXPRESSION TAG SEQADV 6YQF MET C 47 UNP Q9BXU0 EXPRESSION TAG SEQADV 6YQF GLY C 48 UNP Q9BXU0 EXPRESSION TAG SEQADV 6YQF GLY D 45 UNP Q9BXU0 EXPRESSION TAG SEQADV 6YQF SER D 46 UNP Q9BXU0 EXPRESSION TAG SEQADV 6YQF MET D 47 UNP Q9BXU0 EXPRESSION TAG SEQADV 6YQF GLY D 48 UNP Q9BXU0 EXPRESSION TAG SEQRES 1 A 112 GLY SER MET GLY LEU TYR PHE SER SER LEU ASP SER SER SEQRES 2 A 112 ILE ASP ILE LEU GLN LYS ARG ALA GLN GLU LEU ILE GLU SEQRES 3 A 112 ASN ILE ASN LYS SER ARG GLN LYS ASP HIS ALA LEU MET SEQRES 4 A 112 THR ASN PHE ARG ASN SER LEU LYS THR LYS VAL SER ASP SEQRES 5 A 112 LEU THR GLU LYS LEU GLU GLU ARG ILE TYR GLN ILE TYR SEQRES 6 A 112 ASN ASP HIS ASN LYS ILE ILE GLN GLU LYS LEU GLN GLU SEQRES 7 A 112 PHE THR GLN LYS MET ALA LYS ILE SER HIS LEU GLU THR SEQRES 8 A 112 GLU LEU LYS GLN VAL CYS HIS SER VAL GLU THR VAL TYR SEQRES 9 A 112 LYS ASP LEU CYS LEU GLN PRO GLU SEQRES 1 B 112 GLY SER MET GLY LEU TYR PHE SER SER LEU ASP SER SER SEQRES 2 B 112 ILE ASP ILE LEU GLN LYS ARG ALA GLN GLU LEU ILE GLU SEQRES 3 B 112 ASN ILE ASN LYS SER ARG GLN LYS ASP HIS ALA LEU MET SEQRES 4 B 112 THR ASN PHE ARG ASN SER LEU LYS THR LYS VAL SER ASP SEQRES 5 B 112 LEU THR GLU LYS LEU GLU GLU ARG ILE TYR GLN ILE TYR SEQRES 6 B 112 ASN ASP HIS ASN LYS ILE ILE GLN GLU LYS LEU GLN GLU SEQRES 7 B 112 PHE THR GLN LYS MET ALA LYS ILE SER HIS LEU GLU THR SEQRES 8 B 112 GLU LEU LYS GLN VAL CYS HIS SER VAL GLU THR VAL TYR SEQRES 9 B 112 LYS ASP LEU CYS LEU GLN PRO GLU SEQRES 1 C 69 GLY SER MET GLY LYS ASP GLU ALA LEU GLU LYS ASP LEU SEQRES 2 C 69 ASN ASP VAL SER LYS GLU ILE ASN LEU MET LEU SER THR SEQRES 3 C 69 TYR ALA LYS LEU LEU SER GLU ARG ALA ALA VAL ASP ALA SEQRES 4 C 69 SER TYR ILE ASP GLU ILE ASP GLU LEU PHE LYS GLU ALA SEQRES 5 C 69 ASN ALA ILE GLU ASN PHE LEU ILE GLN LYS ARG GLU PHE SEQRES 6 C 69 LEU ARG GLN ARG SEQRES 1 D 69 GLY SER MET GLY LYS ASP GLU ALA LEU GLU LYS ASP LEU SEQRES 2 D 69 ASN ASP VAL SER LYS GLU ILE ASN LEU MET LEU SER THR SEQRES 3 D 69 TYR ALA LYS LEU LEU SER GLU ARG ALA ALA VAL ASP ALA SEQRES 4 D 69 SER TYR ILE ASP GLU ILE ASP GLU LEU PHE LYS GLU ALA SEQRES 5 D 69 ASN ALA ILE GLU ASN PHE LEU ILE GLN LYS ARG GLU PHE SEQRES 6 D 69 LEU ARG GLN ARG HELIX 1 AA1 GLY A 57 CYS A 150 1 94 HELIX 2 AA2 SER B 62 CYS B 150 1 89 HELIX 3 AA3 ALA C 52 ARG C 111 1 60 HELIX 4 AA4 ASP D 59 ARG D 107 1 49 CRYST1 42.670 59.680 156.490 90.00 90.00 90.00 P 21 21 2 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 0.023436 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016756 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006390 0.00000