HEADER PROTEIN BINDING 11-OCT-23 8WQI TITLE LOCAL REFINEMENT OF FEM1B BOUND WITH THE C-DEGRON OF CUX1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN FEM-1 HOMOLOG B; COMPND 3 CHAIN: D; COMPND 4 SYNONYM: FEM1B,FEM1-BETA,FEM-1-LIKE DEATH RECEPTOR-BINDING PROTEIN COMPND 5 ALPHA,FEM-1-LIKE IN APOPTOTIC PATHWAY PROTEIN ALPHA,F1A-ALPHA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN CASP; COMPND 9 CHAIN: G; COMPND 10 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: FEM1B, F1AA, KIAA0396; 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: CUX1, CUTL1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E3 UBIQUITIN LIGASE, PRO/C-DEGRON, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR X.CHEN,K.ZHANG,C.XU REVDAT 2 08-MAY-24 8WQI 1 JRNL REVDAT 1 03-APR-24 8WQI 0 JRNL AUTH X.CHEN,A.RAIFF,S.LI,Q.GUO,J.ZHANG,H.ZHOU,R.T.TIMMS,X.YAO, JRNL AUTH 2 S.J.ELLEDGE,I.KOREN,K.ZHANG,C.XU JRNL TITL MECHANISM OF PSI-PRO/C-DEGRON RECOGNITION BY THE CRL2 FEM1B JRNL TITL 2 UBIQUITIN LIGASE. JRNL REF NAT COMMUN V. 15 3558 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38670995 JRNL DOI 10.1038/S41467-024-47890-5 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.500 REMARK 3 NUMBER OF PARTICLES : 206765 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8WQI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 13-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300041772. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : LOCAL REFINEMENT OF FEM1B BOUND REMARK 245 WITH THE C-DEGRON OF CUX1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 5.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 8112 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2900.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5760.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, G 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 GLY G -31 REMARK 465 GLY G -30 REMARK 465 GLY G -29 REMARK 465 SER G -28 REMARK 465 GLY G -27 REMARK 465 GLY G -26 REMARK 465 GLY G -25 REMARK 465 SER G -24 REMARK 465 GLU G -13 REMARK 465 ASN G -12 REMARK 465 ASP G -11 REMARK 465 ASN G -10 REMARK 465 GLY G -9 REMARK 465 ALA G -8 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP D 406 CG OD1 OD2 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 OD2 ASP D 548 OG1 THR D 551 2.19 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 LEU D 50 CA - CB - CG ANGL. DEV. = 14.6 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 GLN D 41 -66.56 -91.51 REMARK 500 LEU D 50 47.79 -94.12 REMARK 500 GLN D 72 93.10 -69.51 REMARK 500 ASP D 82 -134.96 58.75 REMARK 500 THR D 156 153.88 -45.18 REMARK 500 ALA D 188 49.69 -141.66 REMARK 500 ALA D 212 171.10 62.77 REMARK 500 ASP D 245 163.78 64.73 REMARK 500 ASN D 262 57.64 -98.66 REMARK 500 GLU D 265 -72.36 -67.76 REMARK 500 ASP D 288 46.33 -92.17 REMARK 500 ASN D 289 29.31 -144.13 REMARK 500 TYR D 302 51.01 -91.19 REMARK 500 GLU D 307 178.12 61.65 REMARK 500 ARG D 318 46.00 -82.81 REMARK 500 GLN D 319 -4.66 -142.07 REMARK 500 GLU D 359 75.71 -100.05 REMARK 500 LYS D 376 47.19 -90.69 REMARK 500 THR D 381 51.40 -94.28 REMARK 500 LEU D 398 -75.03 -77.78 REMARK 500 ASN D 399 -1.04 -152.04 REMARK 500 ASP D 430 2.69 -68.05 REMARK 500 ASP D 478 71.31 57.35 REMARK 500 CYS D 507 113.35 -167.43 REMARK 500 PRO D 545 44.30 -91.83 REMARK 500 ASP D 548 35.38 -99.22 REMARK 500 ASN D 611 66.74 60.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37746 RELATED DB: EMDB REMARK 900 LOCAL REFINEMENT OF FEM1B BOUND WITH THE C-DEGRON OF CUX1 DBREF 8WQI D 1 627 UNP Q9UK73 FEM1B_HUMAN 1 627 DBREF 8WQI G -23 -1 UNP Q13948 CASP_HUMAN 656 678 SEQADV 8WQI GLY G -31 UNP Q13948 EXPRESSION TAG SEQADV 8WQI GLY G -30 UNP Q13948 EXPRESSION TAG SEQADV 8WQI GLY G -29 UNP Q13948 EXPRESSION TAG SEQADV 8WQI SER G -28 UNP Q13948 EXPRESSION TAG SEQADV 8WQI GLY G -27 UNP Q13948 EXPRESSION TAG SEQADV 8WQI GLY G -26 UNP Q13948 EXPRESSION TAG SEQADV 8WQI GLY G -25 UNP Q13948 EXPRESSION TAG SEQADV 8WQI SER G -24 UNP Q13948 EXPRESSION TAG SEQRES 1 D 627 MET GLU GLY LEU ALA GLY TYR VAL TYR LYS ALA ALA SER SEQRES 2 D 627 GLU GLY LYS VAL LEU THR LEU ALA ALA LEU LEU LEU ASN SEQRES 3 D 627 ARG SER GLU SER ASP ILE ARG TYR LEU LEU GLY TYR VAL SEQRES 4 D 627 SER GLN GLN GLY GLY GLN ARG SER THR PRO LEU ILE ILE SEQRES 5 D 627 ALA ALA ARG ASN GLY HIS ALA LYS VAL VAL ARG LEU LEU SEQRES 6 D 627 LEU GLU HIS TYR ARG VAL GLN THR GLN GLN THR GLY THR SEQRES 7 D 627 VAL ARG PHE ASP GLY TYR VAL ILE ASP GLY ALA THR ALA SEQRES 8 D 627 LEU TRP CYS ALA ALA GLY ALA GLY HIS PHE GLU VAL VAL SEQRES 9 D 627 LYS LEU LEU VAL SER HIS GLY ALA ASN VAL ASN HIS THR SEQRES 10 D 627 THR VAL THR ASN SER THR PRO LEU ARG ALA ALA CYS PHE SEQRES 11 D 627 ASP GLY ARG LEU ASP ILE VAL LYS TYR LEU VAL GLU ASN SEQRES 12 D 627 ASN ALA ASN ILE SER ILE ALA ASN LYS TYR ASP ASN THR SEQRES 13 D 627 CYS LEU MET ILE ALA ALA TYR LYS GLY HIS THR ASP VAL SEQRES 14 D 627 VAL ARG TYR LEU LEU GLU GLN ARG ALA ASP PRO ASN ALA SEQRES 15 D 627 LYS ALA HIS CYS GLY ALA THR ALA LEU HIS PHE ALA ALA SEQRES 16 D 627 GLU ALA GLY HIS ILE ASP ILE VAL LYS GLU LEU ILE LYS SEQRES 17 D 627 TRP ARG ALA ALA ILE VAL VAL ASN GLY HIS GLY MET THR SEQRES 18 D 627 PRO LEU LYS VAL ALA ALA GLU SER CYS LYS ALA ASP VAL SEQRES 19 D 627 VAL GLU LEU LEU LEU SER HIS ALA ASP CYS ASP ARG ARG SEQRES 20 D 627 SER ARG ILE GLU ALA LEU GLU LEU LEU GLY ALA SER PHE SEQRES 21 D 627 ALA ASN ASP ARG GLU ASN TYR ASP ILE ILE LYS THR TYR SEQRES 22 D 627 HIS TYR LEU TYR LEU ALA MET LEU GLU ARG PHE GLN ASP SEQRES 23 D 627 GLY ASP ASN ILE LEU GLU LYS GLU VAL LEU PRO PRO ILE SEQRES 24 D 627 HIS ALA TYR GLY ASN ARG THR GLU CYS ARG ASN PRO GLN SEQRES 25 D 627 GLU LEU GLU SER ILE ARG GLN ASP ARG ASP ALA LEU HIS SEQRES 26 D 627 MET GLU GLY LEU ILE VAL ARG GLU ARG ILE LEU GLY ALA SEQRES 27 D 627 ASP ASN ILE ASP VAL SER HIS PRO ILE ILE TYR ARG GLY SEQRES 28 D 627 ALA VAL TYR ALA ASP ASN MET GLU PHE GLU GLN CYS ILE SEQRES 29 D 627 LYS LEU TRP LEU HIS ALA LEU HIS LEU ARG GLN LYS GLY SEQRES 30 D 627 ASN ARG ASN THR HIS LYS ASP LEU LEU ARG PHE ALA GLN SEQRES 31 D 627 VAL PHE SER GLN MET ILE HIS LEU ASN GLU THR VAL LYS SEQRES 32 D 627 ALA PRO ASP ILE GLU CYS VAL LEU ARG CYS SER VAL LEU SEQRES 33 D 627 GLU ILE GLU GLN SER MET ASN ARG VAL LYS ASN ILE SER SEQRES 34 D 627 ASP ALA ASP VAL HIS ASN ALA MET ASP ASN TYR GLU CYS SEQRES 35 D 627 ASN LEU TYR THR PHE LEU TYR LEU VAL CYS ILE SER THR SEQRES 36 D 627 LYS THR GLN CYS SER GLU GLU ASP GLN CYS LYS ILE ASN SEQRES 37 D 627 LYS GLN ILE TYR ASN LEU ILE HIS LEU ASP PRO ARG THR SEQRES 38 D 627 ARG GLU GLY PHE THR LEU LEU HIS LEU ALA VAL ASN SER SEQRES 39 D 627 ASN THR PRO VAL ASP ASP PHE HIS THR ASN ASP VAL CYS SEQRES 40 D 627 SER PHE PRO ASN ALA LEU VAL THR LYS LEU LEU LEU ASP SEQRES 41 D 627 CYS GLY ALA GLU VAL ASN ALA VAL ASP ASN GLU GLY ASN SEQRES 42 D 627 SER ALA LEU HIS ILE ILE VAL GLN TYR ASN ARG PRO ILE SEQRES 43 D 627 SER ASP PHE LEU THR LEU HIS SER ILE ILE ILE SER LEU SEQRES 44 D 627 VAL GLU ALA GLY ALA HIS THR ASP MET THR ASN LYS GLN SEQRES 45 D 627 ASN LYS THR PRO LEU ASP LYS SER THR THR GLY VAL SER SEQRES 46 D 627 GLU ILE LEU LEU LYS THR GLN MET LYS MET SER LEU LYS SEQRES 47 D 627 CYS LEU ALA ALA ARG ALA VAL ARG ALA ASN ASP ILE ASN SEQRES 48 D 627 TYR GLN ASP GLN ILE PRO ARG THR LEU GLU GLU PHE VAL SEQRES 49 D 627 GLY PHE HIS SEQRES 1 G 31 GLY GLY GLY SER GLY GLY GLY SER LYS PHE ALA ASP HIS SEQRES 2 G 31 LEU HIS LYS PHE HIS GLU ASN ASP ASN GLY ALA ALA ALA SEQRES 3 G 31 GLY ASP LEU TRP GLN HELIX 1 AA1 LEU D 4 GLU D 14 1 11 HELIX 2 AA2 VAL D 17 LEU D 24 1 8 HELIX 3 AA3 SER D 28 GLY D 37 1 10 HELIX 4 AA4 THR D 48 ASN D 56 1 9 HELIX 5 AA5 HIS D 58 LEU D 66 1 9 HELIX 6 AA6 THR D 90 GLY D 99 1 10 HELIX 7 AA7 HIS D 100 LEU D 106 1 7 HELIX 8 AA8 THR D 123 GLY D 132 1 10 HELIX 9 AA9 ARG D 133 ASN D 143 1 11 HELIX 10 AB1 THR D 156 LYS D 164 1 9 HELIX 11 AB2 HIS D 166 GLN D 176 1 11 HELIX 12 AB3 THR D 189 GLY D 198 1 10 HELIX 13 AB4 HIS D 199 TRP D 209 1 11 HELIX 14 AB5 THR D 221 SER D 229 1 9 HELIX 15 AB6 LYS D 231 LEU D 239 1 9 HELIX 16 AB7 SER D 240 ALA D 242 5 3 HELIX 17 AB8 CYS D 244 PHE D 260 1 17 HELIX 18 AB9 ILE D 269 PHE D 284 1 16 HELIX 19 AC1 ASN D 310 SER D 316 1 7 HELIX 20 AC2 ASP D 320 GLY D 337 1 18 HELIX 21 AC3 VAL D 343 ASN D 357 1 15 HELIX 22 AC4 GLU D 359 LYS D 376 1 18 HELIX 23 AC5 LYS D 383 ASN D 399 1 17 HELIX 24 AC6 LYS D 403 ASN D 427 1 25 HELIX 25 AC7 ASP D 432 LYS D 456 1 25 HELIX 26 AC8 SER D 460 ASP D 478 1 19 HELIX 27 AC9 LEU D 488 ASN D 493 1 6 HELIX 28 AD1 ASN D 511 ASP D 520 1 10 HELIX 29 AD2 SER D 534 GLN D 541 1 8 HELIX 30 AD3 PHE D 549 SER D 554 1 6 HELIX 31 AD4 THR D 575 SER D 580 5 6 HELIX 32 AD5 GLY D 583 GLN D 592 1 10 HELIX 33 AD6 SER D 596 ASN D 608 1 13 HELIX 34 AD7 PRO D 617 HIS D 627 1 11 HELIX 35 AD8 ALA G -21 HIS G -14 5 8 CISPEP 1 PHE D 509 PRO D 510 0 4.42 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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