HEADER DE NOVO PROTEIN 16-MAR-20 6M6Z TITLE A DE NOVO DESIGNED TRANSMEMBRANE NANOPORE, TMH4C4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TMH4C4; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NANOPORE, DE NOVO DESIGN, MEMBRANE PROTEIN, DE NOVO PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR P.LU,C.XU,G.REGGIANO,Q.XU,F.DIMAIO,D.BAKER REVDAT 3 27-MAR-24 6M6Z 1 REMARK REVDAT 2 16-SEP-20 6M6Z 1 JRNL REVDAT 1 24-JUN-20 6M6Z 0 JRNL AUTH C.XU,P.LU,T.M.GAMAL EL-DIN,X.Y.PEI,M.C.JOHNSON,A.UYEDA, JRNL AUTH 2 M.J.BICK,Q.XU,D.JIANG,H.BAI,G.REGGIANO,Y.HSIA,T.J.BRUNETTE, JRNL AUTH 3 J.DOU,D.MA,E.M.LYNCH,S.E.BOYKEN,P.S.HUANG,L.STEWART, JRNL AUTH 4 F.DIMAIO,J.M.KOLLMAN,B.F.LUISI,T.MATSUURA,W.A.CATTERALL, JRNL AUTH 5 D.BAKER JRNL TITL COMPUTATIONAL DESIGN OF TRANSMEMBRANE PORES. JRNL REF NATURE V. 585 129 2020 JRNL REFN ESSN 1476-4687 JRNL PMID 32848250 JRNL DOI 10.1038/S41586-020-2646-5 REMARK 2 REMARK 2 RESOLUTION. 5.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION 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) : 5.900 REMARK 3 NUMBER OF PARTICLES : 64739 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6M6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016189. 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 : A DE NOVO DESIGNED REMARK 245 TRANSMEMBRANE NANOPORE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 6.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 5000.00 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: 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 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 ARG B 112 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG C 7 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG C 112 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG D 7 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30126 RELATED DB: EMDB REMARK 900 A DE NOVO DESIGNED TRANSMEMBRANE NANOPORE, TMH4C4 DBREF 6M6Z A 1 203 PDB 6M6Z 6M6Z 1 203 DBREF 6M6Z B 1 203 PDB 6M6Z 6M6Z 1 203 DBREF 6M6Z C 1 203 PDB 6M6Z 6M6Z 1 203 DBREF 6M6Z D 1 203 PDB 6M6Z 6M6Z 1 203 SEQRES 1 A 203 SER ALA GLU GLU LEU LEU ARG ARG SER ARG GLU TYR LEU SEQRES 2 A 203 LYS LYS VAL ALA LEU ILE GLN LEU VAL ILE ALA PHE VAL SEQRES 3 A 203 PHE LEU ILE LEU LEU ILE LEU LEU SER TRP ARG SER GLU SEQRES 4 A 203 GLU LEU ILE ARG GLU LEU GLU GLU LYS GLY ALA ALA SER SEQRES 5 A 203 GLU ALA GLU LEU ALA ARG MET LYS GLN GLN HIS MET THR SEQRES 6 A 203 ALA TYR LEU GLN ALA ALA LEU THR ALA TRP GLU ILE ILE SEQRES 7 A 203 SER LYS SER VAL ILE ALA LEU LEU LEU LEU GLN GLN ASN SEQRES 8 A 203 GLN LEU ASN LEU GLU LEU ASN THR ASP THR ASP LYS ASN SEQRES 9 A 203 VAL ALA GLU GLU LEU LEU ARG ARG SER ARG GLU TYR LEU SEQRES 10 A 203 LYS LYS VAL ALA LEU ILE GLN LEU VAL ILE ALA PHE VAL SEQRES 11 A 203 PHE LEU ILE LEU LEU ILE LEU LEU SER TRP ARG SER GLU SEQRES 12 A 203 GLU LEU ILE ARG GLU LEU GLU GLU LYS GLY ALA ALA SER SEQRES 13 A 203 GLU ALA GLU LEU ALA ARG MET LYS GLN GLN HIS MET THR SEQRES 14 A 203 ALA TYR LEU GLN ALA ALA LEU THR ALA TRP GLU ILE ILE SEQRES 15 A 203 SER LYS SER VAL ILE ALA LEU LEU LEU LEU GLN GLN ASN SEQRES 16 A 203 GLN LEU ASN LEU GLU LEU ARG HIS SEQRES 1 B 203 SER ALA GLU GLU LEU LEU ARG ARG SER ARG GLU TYR LEU SEQRES 2 B 203 LYS LYS VAL ALA LEU ILE GLN LEU VAL ILE ALA PHE VAL SEQRES 3 B 203 PHE LEU ILE LEU LEU ILE LEU LEU SER TRP ARG SER GLU SEQRES 4 B 203 GLU LEU ILE ARG GLU LEU GLU GLU LYS GLY ALA ALA SER SEQRES 5 B 203 GLU ALA GLU LEU ALA ARG MET LYS GLN GLN HIS MET THR SEQRES 6 B 203 ALA TYR LEU GLN ALA ALA LEU THR ALA TRP GLU ILE ILE SEQRES 7 B 203 SER LYS SER VAL ILE ALA LEU LEU LEU LEU GLN GLN ASN SEQRES 8 B 203 GLN LEU ASN LEU GLU LEU ASN THR ASP THR ASP LYS ASN SEQRES 9 B 203 VAL ALA GLU GLU LEU LEU ARG ARG SER ARG GLU TYR LEU SEQRES 10 B 203 LYS LYS VAL ALA LEU ILE GLN LEU VAL ILE ALA PHE VAL SEQRES 11 B 203 PHE LEU ILE LEU LEU ILE LEU LEU SER TRP ARG SER GLU SEQRES 12 B 203 GLU LEU ILE ARG GLU LEU GLU GLU LYS GLY ALA ALA SER SEQRES 13 B 203 GLU ALA GLU LEU ALA ARG MET LYS GLN GLN HIS MET THR SEQRES 14 B 203 ALA TYR LEU GLN ALA ALA LEU THR ALA TRP GLU ILE ILE SEQRES 15 B 203 SER LYS SER VAL ILE ALA LEU LEU LEU LEU GLN GLN ASN SEQRES 16 B 203 GLN LEU ASN LEU GLU LEU ARG HIS SEQRES 1 C 203 SER ALA GLU GLU LEU LEU ARG ARG SER ARG GLU TYR LEU SEQRES 2 C 203 LYS LYS VAL ALA LEU ILE GLN LEU VAL ILE ALA PHE VAL SEQRES 3 C 203 PHE LEU ILE LEU LEU ILE LEU LEU SER TRP ARG SER GLU SEQRES 4 C 203 GLU LEU ILE ARG GLU LEU GLU GLU LYS GLY ALA ALA SER SEQRES 5 C 203 GLU ALA GLU LEU ALA ARG MET LYS GLN GLN HIS MET THR SEQRES 6 C 203 ALA TYR LEU GLN ALA ALA LEU THR ALA TRP GLU ILE ILE SEQRES 7 C 203 SER LYS SER VAL ILE ALA LEU LEU LEU LEU GLN GLN ASN SEQRES 8 C 203 GLN LEU ASN LEU GLU LEU ASN THR ASP THR ASP LYS ASN SEQRES 9 C 203 VAL ALA GLU GLU LEU LEU ARG ARG SER ARG GLU TYR LEU SEQRES 10 C 203 LYS LYS VAL ALA LEU ILE GLN LEU VAL ILE ALA PHE VAL SEQRES 11 C 203 PHE LEU ILE LEU LEU ILE LEU LEU SER TRP ARG SER GLU SEQRES 12 C 203 GLU LEU ILE ARG GLU LEU GLU GLU LYS GLY ALA ALA SER SEQRES 13 C 203 GLU ALA GLU LEU ALA ARG MET LYS GLN GLN HIS MET THR SEQRES 14 C 203 ALA TYR LEU GLN ALA ALA LEU THR ALA TRP GLU ILE ILE SEQRES 15 C 203 SER LYS SER VAL ILE ALA LEU LEU LEU LEU GLN GLN ASN SEQRES 16 C 203 GLN LEU ASN LEU GLU LEU ARG HIS SEQRES 1 D 203 SER ALA GLU GLU LEU LEU ARG ARG SER ARG GLU TYR LEU SEQRES 2 D 203 LYS LYS VAL ALA LEU ILE GLN LEU VAL ILE ALA PHE VAL SEQRES 3 D 203 PHE LEU ILE LEU LEU ILE LEU LEU SER TRP ARG SER GLU SEQRES 4 D 203 GLU LEU ILE ARG GLU LEU GLU GLU LYS GLY ALA ALA SER SEQRES 5 D 203 GLU ALA GLU LEU ALA ARG MET LYS GLN GLN HIS MET THR SEQRES 6 D 203 ALA TYR LEU GLN ALA ALA LEU THR ALA TRP GLU ILE ILE SEQRES 7 D 203 SER LYS SER VAL ILE ALA LEU LEU LEU LEU GLN GLN ASN SEQRES 8 D 203 GLN LEU ASN LEU GLU LEU ASN THR ASP THR ASP LYS ASN SEQRES 9 D 203 VAL ALA GLU GLU LEU LEU ARG ARG SER ARG GLU TYR LEU SEQRES 10 D 203 LYS LYS VAL ALA LEU ILE GLN LEU VAL ILE ALA PHE VAL SEQRES 11 D 203 PHE LEU ILE LEU LEU ILE LEU LEU SER TRP ARG SER GLU SEQRES 12 D 203 GLU LEU ILE ARG GLU LEU GLU GLU LYS GLY ALA ALA SER SEQRES 13 D 203 GLU ALA GLU LEU ALA ARG MET LYS GLN GLN HIS MET THR SEQRES 14 D 203 ALA TYR LEU GLN ALA ALA LEU THR ALA TRP GLU ILE ILE SEQRES 15 D 203 SER LYS SER VAL ILE ALA LEU LEU LEU LEU GLN GLN ASN SEQRES 16 D 203 GLN LEU ASN LEU GLU LEU ARG HIS HELIX 1 AA1 SER A 1 GLY A 49 1 49 HELIX 2 AA2 SER A 52 ASN A 98 1 47 HELIX 3 AA3 ASP A 102 GLY A 153 1 52 HELIX 4 AA4 SER A 156 ARG A 202 1 47 HELIX 5 AA5 ALA B 2 GLY B 49 1 48 HELIX 6 AA6 SER B 52 ASN B 98 1 47 HELIX 7 AA7 ASP B 102 GLY B 153 1 52 HELIX 8 AA8 SER B 156 ARG B 202 1 47 HELIX 9 AA9 ALA C 2 GLY C 49 1 48 HELIX 10 AB1 SER C 52 ASN C 98 1 47 HELIX 11 AB2 ASP C 102 GLY C 153 1 52 HELIX 12 AB3 SER C 156 ARG C 202 1 47 HELIX 13 AB4 ALA D 2 GLY D 49 1 48 HELIX 14 AB5 SER D 52 ASN D 98 1 47 HELIX 15 AB6 ASP D 102 GLY D 153 1 52 HELIX 16 AB7 SER D 156 ARG D 202 1 47 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