HEADER MEMBRANE PROTEIN 03-APR-21 7EK2 TITLE CRYO-EM STRUCTURE OF VCCN1 IN LIPID NANODISC COMPND MOL_ID: 1; COMPND 2 MOLECULE: BESTROPHIN-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MALUS DOMESTICA; SOURCE 3 ORGANISM_COMMON: APPLE, PYRUS MALUS; SOURCE 4 ORGANISM_TAXID: 3750; SOURCE 5 GENE: DVH24_014265; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS ION CHANNEL, THYLAKOID, PHOTOSYNTHESIS, BESTROPHIN FAMILY, MEMBRANE KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.HAGINO,T.KATO,G.KASUYA,K.KOBAYASHI,T.KUSAKIZAKO,K.YAMASHITA, AUTHOR 2 T.NISHIZAWA,O.NUREKI REVDAT 3 05-JUN-24 7EK2 1 REMARK REVDAT 2 18-MAY-22 7EK2 1 JRNL REVDAT 1 06-APR-22 7EK2 0 JRNL AUTH T.HAGINO,T.KATO,G.KASUYA,K.KOBAYASHI,T.KUSAKIZAKO, JRNL AUTH 2 S.HAMAMOTO,T.SOBAJIMA,Y.FUJIWARA,K.YAMASHITA,H.KAWASAKI, JRNL AUTH 3 A.D.MATURANA,T.NISHIZAWA,O.NUREKI JRNL TITL CRYO-EM STRUCTURES OF THYLAKOID-LOCATED VOLTAGE-DEPENDENT JRNL TITL 2 CHLORIDE CHANNEL VCCN1. JRNL REF NAT COMMUN V. 13 2505 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35523970 JRNL DOI 10.1038/S41467-022-30292-W REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, CTFFIND, RELION, RELION, 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) : 2.700 REMARK 3 NUMBER OF PARTICLES : 345938 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 7EK2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021570. 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 : BESTROPHIN-LIKE PROTEIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL 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 : 2271 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS 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) : 4800.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C5). 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 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 350 BIOMT1 2 0.309017 -0.951057 0.000000 130.83770 REMARK 350 BIOMT2 2 0.951057 0.309017 0.000000 -20.72266 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.809017 -0.587785 0.000000 190.97720 REMARK 350 BIOMT2 3 0.587785 -0.809017 0.000000 97.30774 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.809017 0.587785 0.000000 97.30774 REMARK 350 BIOMT2 4 -0.587785 -0.809017 0.000000 190.97719 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.309017 0.951057 0.000000 -20.72266 REMARK 350 BIOMT2 5 -0.951057 0.309017 0.000000 130.83770 REMARK 350 BIOMT3 5 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 MET A 68 REMARK 465 PRO A 69 REMARK 465 ASN A 70 REMARK 465 PRO A 71 REMARK 465 SER A 72 REMARK 465 PRO A 73 REMARK 465 PRO A 74 REMARK 465 SER A 75 REMARK 465 SER A 76 REMARK 465 SER A 77 REMARK 465 ARG A 419 REMARK 465 ILE A 420 REMARK 465 GLN A 421 REMARK 465 SER A 422 REMARK 465 GLU A 423 REMARK 465 GLN A 424 REMARK 465 GLN A 425 REMARK 465 PHE A 426 REMARK 465 GLN A 427 REMARK 465 ASN A 428 REMARK 465 GLY A 429 REMARK 465 GLN A 430 REMARK 465 PRO A 431 REMARK 465 ARG A 432 REMARK 465 PRO A 433 REMARK 465 GLU A 434 REMARK 465 ASN A 435 REMARK 465 LEU A 436 REMARK 465 TYR A 437 REMARK 465 PHE A 438 REMARK 465 GLN A 439 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLN A 401 C GLN A 401 O 0.116 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 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 125 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 134 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 338 NE - CZ - NH1 ANGL. DEV. = 4.0 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 ASP A 110 -168.57 -103.48 REMARK 500 ARG A 118 46.93 -99.57 REMARK 500 HIS A 356 -130.77 52.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-31166 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF VCCN1 IN LIPID NANODISC REMARK 999 REMARK 999 SEQUENCE REMARK 999 SER 207 IS THE NATURAL MUTATION, WHICH APPEARED IN THE SEQUENCE REMARK 999 AMPLIFIED FROM THE CDNA LIBRARY. DBREF1 7EK2 A 69 433 UNP A0A498JCY7_MALDO DBREF2 7EK2 A A0A498JCY7 69 433 SEQADV 7EK2 MET A 68 UNP A0A498JCY INITIATING METHIONINE SEQADV 7EK2 SER A 207 UNP A0A498JCY ALA 207 CONFLICT SEQADV 7EK2 GLU A 434 UNP A0A498JCY EXPRESSION TAG SEQADV 7EK2 ASN A 435 UNP A0A498JCY EXPRESSION TAG SEQADV 7EK2 LEU A 436 UNP A0A498JCY EXPRESSION TAG SEQADV 7EK2 TYR A 437 UNP A0A498JCY EXPRESSION TAG SEQADV 7EK2 PHE A 438 UNP A0A498JCY EXPRESSION TAG SEQADV 7EK2 GLN A 439 UNP A0A498JCY EXPRESSION TAG SEQRES 1 A 372 MET PRO ASN PRO SER PRO PRO SER SER SER SER PRO VAL SEQRES 2 A 372 GLN THR LEU ILE SER ILE LEU ARG ILE ILE PRO ASP TRP SEQRES 3 A 372 SER ASP ARG THR GLN GLU ARG GLY MET ARG GLN HIS ARG SEQRES 4 A 372 THR LEU TYR ASP HIS GLU LYS TRP MET HIS HIS ARG SER SEQRES 5 A 372 SER TYR ARG HIS LEU ARG HIS LEU LEU SER SER LEU SER SEQRES 6 A 372 SER ARG VAL ILE LEU SER LEU ILE PRO PRO VAL ILE ALA SEQRES 7 A 372 PHE THR LEU VAL ALA VAL VAL ILE ALA SER TYR ASN THR SEQRES 8 A 372 ALA VAL ALA LEU ASP LEU LEU PRO GLY ILE PHE PRO LEU SEQRES 9 A 372 LEU ARG SER SER SER LEU PRO TYR GLN LEU THR ALA PRO SEQRES 10 A 372 ALA LEU ALA LEU LEU LEU VAL PHE ARG THR GLU ALA SER SEQRES 11 A 372 TYR SER ARG PHE GLU GLU GLY ARG LYS SER TRP THR GLU SEQRES 12 A 372 VAL ILE ALA GLY ALA ASN ASP PHE ALA ARG GLN ILE ILE SEQRES 13 A 372 SER SER VAL GLU THR SER GLY ASP ALA GLN LEU LYS LYS SEQRES 14 A 372 ALA LEU LEU GLN TYR ILE VAL ALA PHE PRO VAL ALA LEU SEQRES 15 A 372 LYS CYS HIS VAL ILE TYR GLY SER ASP ILE ALA ARG ASP SEQRES 16 A 372 LEU GLN ASN LEU LEU GLU VAL ASP ASP LEU LEU VAL VAL SEQRES 17 A 372 LEU ASN SER LYS HIS ARG PRO GLY CYS ILE ILE GLN PHE SEQRES 18 A 372 ILE SER ARG SER LEU GLN LEU LEU LYS LEU GLU GLU SER SEQRES 19 A 372 ARG ARG ILE MET LEU GLN SER LYS ILE SER CYS PHE HIS SEQRES 20 A 372 GLU GLY ILE GLY ILE CYS GLU GLN LEU ILE GLY THR PRO SEQRES 21 A 372 ILE PRO LEU SER TYR THR ARG LEU THR SER ARG PHE LEU SEQRES 22 A 372 VAL LEU TRP HIS LEU THR LEU PRO ILE ILE LEU TRP ASP SEQRES 23 A 372 ASP CYS HIS TRP ILE VAL VAL PRO ALA THR PHE ILE SER SEQRES 24 A 372 ALA ALA SER LEU PHE CYS ILE GLU GLN VAL GLY VAL LEU SEQRES 25 A 372 ILE GLU GLU PRO PHE PRO MET LEU ALA LEU ASP ASP LEU SEQRES 26 A 372 CYS ASN SER VAL ARG ASN ASN VAL GLN GLU ALA LEU ALA SEQRES 27 A 372 SER GLU LYS LEU ILE ARG ALA ARG LEU ALA ALA LYS GLY SEQRES 28 A 372 ARG ILE GLN SER GLU GLN GLN PHE GLN ASN GLY GLN PRO SEQRES 29 A 372 ARG PRO GLU ASN LEU TYR PHE GLN HELIX 1 AA1 VAL A 80 ARG A 88 1 9 HELIX 2 AA2 ILE A 89 GLY A 101 1 13 HELIX 3 AA3 ASP A 110 ARG A 118 1 9 HELIX 4 AA4 TYR A 121 SER A 129 1 9 HELIX 5 AA5 SER A 133 LEU A 139 1 7 HELIX 6 AA6 LEU A 139 LEU A 162 1 24 HELIX 7 AA7 SER A 176 VAL A 226 1 51 HELIX 8 AA8 THR A 228 GLY A 230 5 3 HELIX 9 AA9 ASP A 231 ILE A 254 1 24 HELIX 10 AB1 ASP A 258 LEU A 263 1 6 HELIX 11 AB2 GLU A 268 ASN A 277 1 10 HELIX 12 AB3 HIS A 280 LEU A 296 1 17 HELIX 13 AB4 GLU A 299 SER A 308 1 10 HELIX 14 AB5 ILE A 310 THR A 326 1 17 HELIX 15 AB6 PRO A 329 HIS A 356 1 28 HELIX 16 AB7 ILE A 358 ILE A 380 1 23 HELIX 17 AB8 PRO A 383 LEU A 387 5 5 HELIX 18 AB9 ALA A 388 GLY A 418 1 31 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 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.309017 -0.951057 0.000000 130.83771 MTRIX2 2 0.951057 0.309017 0.000000 -20.72266 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 -0.809017 -0.587785 0.000000 190.97720 MTRIX2 3 0.587785 -0.809017 0.000000 97.30775 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 MTRIX1 4 -0.809017 0.587785 0.000000 97.30775 MTRIX2 4 -0.587785 -0.809017 0.000000 190.97720 MTRIX3 4 0.000000 0.000000 1.000000 0.00000 MTRIX1 5 0.309017 0.951057 0.000000 -20.72266 MTRIX2 5 -0.951057 0.309017 0.000000 130.83771 MTRIX3 5 0.000000 0.000000 1.000000 0.00000