HEADER DE NOVO PROTEIN 21-OCT-25 9YTQ TITLE COMPUTATIONALLY DESIGNED TETRAMER OF APO-HC4 (C1 SYMMETRY) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED TETRAMERIC HC4 PROTEIN.; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TETRAMER, COMPUTATIONALLY DESIGNED PROTEIN, DE NOVO PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR V.H.ENG,S.M.NAREHOOD,F.A.TEZCAN REVDAT 1 25-FEB-26 9YTQ 0 JRNL AUTH V.H.ENG,S.M.NAREHOOD,Y.LI,M.GASCON,A.M.HOFFNAGLE,A.A.SHIAU, JRNL AUTH 2 M.SEMONIS,M.T.GREEN,R.D.BRITT,F.A.TEZCAN JRNL TITL COMPUTATIONAL DESIGN OF A HIGHLY STABLE DICOPPER CATECHOL JRNL TITL 2 OXIDASE JRNL REF J.AM.CHEM.SOC. 2026 JRNL REFN ESSN 1520-5126 JRNL DOI 10.1021/JACS.5C18979 REMARK 2 REMARK 2 RESOLUTION. 4.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 4.340 REMARK 3 NUMBER OF PARTICLES : 108599 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 9YTQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000301337. 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 : TETRAMERIC HC4 CONSTRUCT 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 : 7.60 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA 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 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 B 16 CA - CB - CG ANGL. DEV. = 15.0 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 ALA A 25 56.44 -99.86 REMARK 500 LYS A 75 46.60 -85.04 REMARK 500 LYS B 75 47.17 -87.96 REMARK 500 ALA C 25 61.36 -105.28 REMARK 500 LYS C 75 47.05 -88.85 REMARK 500 LYS D 75 47.01 -89.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-73489 RELATED DB: EMDB REMARK 900 COMPUTATIONALLY DESIGNED TETRAMER OF APO-HC4 (C1 SYMMETRY) DBREF 9YTQ A 1 138 PDB 9YTQ 9YTQ 1 138 DBREF 9YTQ B 1 138 PDB 9YTQ 9YTQ 1 138 DBREF 9YTQ C 1 138 PDB 9YTQ 9YTQ 1 138 DBREF 9YTQ D 1 138 PDB 9YTQ 9YTQ 1 138 SEQRES 1 A 138 SER LYS THR ASP LYS LEU LEU GLU LEU ALA LYS LEU GLU SEQRES 2 A 138 LEU ILE LEU ASN PHE PHE LEU LEU ALA SER ASN ALA ASN SEQRES 3 A 138 ILE THR LYS GLU SER PHE LEU ILE ALA HIS LYS ALA TRP SEQRES 4 A 138 HIS LYS ALA LEU ASN LYS LEU TYR GLU ILE ASP LYS GLU SEQRES 5 A 138 LEU ALA LYS GLU TYR PHE TYR TYR MET HIS SER PHE SER SEQRES 6 A 138 ILE PRO TYR TYR GLU LYS LEU GLY PHE LYS ASP VAL ALA SEQRES 7 A 138 GLU TRP HIS LYS VAL MET VAL GLU TYR PHE LYS VAL GLY SEQRES 8 A 138 ASP LYS ASP GLU ALA LEU GLU LEU HIS ASN GLU GLY HIS SEQRES 9 A 138 LYS ALA LEU ARG ALA GLY ASP GLU GLU LYS PHE ALA ALA SEQRES 10 A 138 LEU LEU LYS LYS ALA ARG GLU LEU ILE GLU LYS ALA LYS SEQRES 11 A 138 SER ALA GLU ASN LEU TYR PHE GLN SEQRES 1 B 138 SER LYS THR ASP LYS LEU LEU GLU LEU ALA LYS LEU GLU SEQRES 2 B 138 LEU ILE LEU ASN PHE PHE LEU LEU ALA SER ASN ALA ASN SEQRES 3 B 138 ILE THR LYS GLU SER PHE LEU ILE ALA HIS LYS ALA TRP SEQRES 4 B 138 HIS LYS ALA LEU ASN LYS LEU TYR GLU ILE ASP LYS GLU SEQRES 5 B 138 LEU ALA LYS GLU TYR PHE TYR TYR MET HIS SER PHE SER SEQRES 6 B 138 ILE PRO TYR TYR GLU LYS LEU GLY PHE LYS ASP VAL ALA SEQRES 7 B 138 GLU TRP HIS LYS VAL MET VAL GLU TYR PHE LYS VAL GLY SEQRES 8 B 138 ASP LYS ASP GLU ALA LEU GLU LEU HIS ASN GLU GLY HIS SEQRES 9 B 138 LYS ALA LEU ARG ALA GLY ASP GLU GLU LYS PHE ALA ALA SEQRES 10 B 138 LEU LEU LYS LYS ALA ARG GLU LEU ILE GLU LYS ALA LYS SEQRES 11 B 138 SER ALA GLU ASN LEU TYR PHE GLN SEQRES 1 C 138 SER LYS THR ASP LYS LEU LEU GLU LEU ALA LYS LEU GLU SEQRES 2 C 138 LEU ILE LEU ASN PHE PHE LEU LEU ALA SER ASN ALA ASN SEQRES 3 C 138 ILE THR LYS GLU SER PHE LEU ILE ALA HIS LYS ALA TRP SEQRES 4 C 138 HIS LYS ALA LEU ASN LYS LEU TYR GLU ILE ASP LYS GLU SEQRES 5 C 138 LEU ALA LYS GLU TYR PHE TYR TYR MET HIS SER PHE SER SEQRES 6 C 138 ILE PRO TYR TYR GLU LYS LEU GLY PHE LYS ASP VAL ALA SEQRES 7 C 138 GLU TRP HIS LYS VAL MET VAL GLU TYR PHE LYS VAL GLY SEQRES 8 C 138 ASP LYS ASP GLU ALA LEU GLU LEU HIS ASN GLU GLY HIS SEQRES 9 C 138 LYS ALA LEU ARG ALA GLY ASP GLU GLU LYS PHE ALA ALA SEQRES 10 C 138 LEU LEU LYS LYS ALA ARG GLU LEU ILE GLU LYS ALA LYS SEQRES 11 C 138 SER ALA GLU ASN LEU TYR PHE GLN SEQRES 1 D 138 SER LYS THR ASP LYS LEU LEU GLU LEU ALA LYS LEU GLU SEQRES 2 D 138 LEU ILE LEU ASN PHE PHE LEU LEU ALA SER ASN ALA ASN SEQRES 3 D 138 ILE THR LYS GLU SER PHE LEU ILE ALA HIS LYS ALA TRP SEQRES 4 D 138 HIS LYS ALA LEU ASN LYS LEU TYR GLU ILE ASP LYS GLU SEQRES 5 D 138 LEU ALA LYS GLU TYR PHE TYR TYR MET HIS SER PHE SER SEQRES 6 D 138 ILE PRO TYR TYR GLU LYS LEU GLY PHE LYS ASP VAL ALA SEQRES 7 D 138 GLU TRP HIS LYS VAL MET VAL GLU TYR PHE LYS VAL GLY SEQRES 8 D 138 ASP LYS ASP GLU ALA LEU GLU LEU HIS ASN GLU GLY HIS SEQRES 9 D 138 LYS ALA LEU ARG ALA GLY ASP GLU GLU LYS PHE ALA ALA SEQRES 10 D 138 LEU LEU LYS LYS ALA ARG GLU LEU ILE GLU LYS ALA LYS SEQRES 11 D 138 SER ALA GLU ASN LEU TYR PHE GLN HELIX 1 AA1 LYS A 2 ALA A 25 1 24 HELIX 2 AA2 THR A 28 GLU A 48 1 21 HELIX 3 AA3 LYS A 51 SER A 65 1 15 HELIX 4 AA4 SER A 65 LEU A 72 1 8 HELIX 5 AA5 ASP A 76 GLY A 91 1 16 HELIX 6 AA6 LYS A 93 GLY A 110 1 18 HELIX 7 AA7 ASP A 111 GLN A 138 1 28 HELIX 8 AA8 LYS B 2 ALA B 25 1 24 HELIX 9 AA9 THR B 28 GLU B 48 1 21 HELIX 10 AB1 LYS B 51 SER B 65 1 15 HELIX 11 AB2 SER B 65 LEU B 72 1 8 HELIX 12 AB3 ASP B 76 GLY B 91 1 16 HELIX 13 AB4 LYS B 93 GLY B 110 1 18 HELIX 14 AB5 ASP B 111 GLN B 138 1 28 HELIX 15 AB6 LYS C 2 ALA C 25 1 24 HELIX 16 AB7 THR C 28 ASP C 50 1 23 HELIX 17 AB8 LYS C 51 SER C 65 1 15 HELIX 18 AB9 SER C 65 LEU C 72 1 8 HELIX 19 AC1 ASP C 76 GLY C 91 1 16 HELIX 20 AC2 LYS C 93 GLY C 110 1 18 HELIX 21 AC3 ASP C 111 GLN C 138 1 28 HELIX 22 AC4 LYS D 2 ALA D 25 1 24 HELIX 23 AC5 THR D 28 ASP D 50 1 23 HELIX 24 AC6 LYS D 51 SER D 65 1 15 HELIX 25 AC7 SER D 65 LEU D 72 1 8 HELIX 26 AC8 ASP D 76 GLY D 91 1 16 HELIX 27 AC9 ASP D 92 GLY D 110 1 19 HELIX 28 AD1 ASP D 111 GLN D 138 1 28 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 MASTER 142 0 0 28 0 0 0 6 4596 4 0 44 END