HEADER CHAPERONE 29-JUN-21 7R9H TITLE METHANOCOCCUS MARIPALUDIS CHAPERONIN, OPEN CONFORMATION 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAPERONIN; COMPND 3 CHAIN: J; COMPND 4 SYNONYM: MMCPN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCOCCUS MARIPALUDIS; SOURCE 3 ORGANISM_COMMON: METHANOCOCCUS DELTAE; SOURCE 4 ORGANISM_TAXID: 39152; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OPEN CONFORMATION, CHAPERONE EXPDTA ELECTRON MICROSCOPY AUTHOR Y.ZHAO,M.SCHMID,J.FRYDMAN,W.CHIU REVDAT 3 05-JUN-24 7R9H 1 REMARK REVDAT 2 25-AUG-21 7R9H 1 JRNL REVDAT 1 11-AUG-21 7R9H 0 JRNL AUTH Y.ZHAO,M.F.SCHMID,J.FRYDMAN,W.CHIU JRNL TITL CRYOEM REVEALS THE STOCHASTIC NATURE OF INDIVIDUAL ATP JRNL TITL 2 BINDING EVENTS IN A GROUP II CHAPERONIN. JRNL REF NAT COMMUN V. 12 4754 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34362932 JRNL DOI 10.1038/S41467-021-25099-0 REMARK 2 REMARK 2 RESOLUTION. 6.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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 : FLEXIBLE 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) : 6.300 REMARK 3 NUMBER OF PARTICLES : 3800 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7R9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257835. 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 : MMCPN 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 : 7.40 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 K2 SUMMIT (4K X 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: J 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: 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 OG SER J 333 OD1 ASP J 336 2.10 REMARK 500 OG1 THR J 156 O GLY J 487 2.16 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 J 20 -57.44 67.05 REMARK 500 LEU J 48 70.69 -104.84 REMARK 500 ASN J 59 74.29 -65.01 REMARK 500 ALA J 163 79.12 -156.61 REMARK 500 ALA J 166 54.20 -165.77 REMARK 500 VAL J 181 39.70 -98.61 REMARK 500 SER J 202 -178.01 -170.25 REMARK 500 ILE J 239 69.59 -100.01 REMARK 500 THR J 253 -34.86 -137.89 REMARK 500 LYS J 270 -62.05 -106.04 REMARK 500 GLN J 287 -73.38 -94.19 REMARK 500 LYS J 288 -175.28 -68.61 REMARK 500 ARG J 308 88.14 56.67 REMARK 500 ASP J 331 31.77 -94.61 REMARK 500 ASP J 339 96.30 -166.39 REMARK 500 SER J 349 66.96 62.67 REMARK 500 GLU J 358 77.50 -163.78 REMARK 500 HIS J 361 77.24 -161.15 REMARK 500 SER J 406 47.98 -91.62 REMARK 500 THR J 407 -36.82 -136.36 REMARK 500 SER J 423 -168.43 -73.14 REMARK 500 ARG J 425 37.66 -90.79 REMARK 500 ALA J 464 -74.79 -73.55 REMARK 500 SER J 465 -78.63 -116.67 REMARK 500 CYS J 470 22.72 -144.99 REMARK 500 ASP J 513 40.89 -160.05 REMARK 500 ASP J 514 113.44 -164.60 REMARK 500 LYS J 520 100.86 59.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-24324 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-24325 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-24326 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-24327 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-24328 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-24329 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-24330 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-24331 RELATED DB: EMDB DBREF 7R9H J 18 522 UNP Q877G8 Q877G8_METMI 18 522 SEQRES 1 J 505 ARG ASP ALA GLN ARG MET ASN ILE LEU ALA GLY ARG ILE SEQRES 2 J 505 ILE ALA GLU THR VAL ARG SER THR LEU GLY PRO LYS GLY SEQRES 3 J 505 MET ASP LYS MET LEU VAL ASP ASP LEU GLY ASP VAL VAL SEQRES 4 J 505 VAL THR ASN ASP GLY VAL THR ILE LEU ARG GLU MET SER SEQRES 5 J 505 VAL GLU HIS PRO ALA ALA LYS MET LEU ILE GLU VAL ALA SEQRES 6 J 505 LYS THR GLN GLU LYS GLU VAL GLY ASP GLY THR THR THR SEQRES 7 J 505 ALA VAL VAL VAL ALA GLY GLU LEU LEU ARG LYS ALA GLU SEQRES 8 J 505 GLU LEU LEU ASP GLN ASN VAL HIS PRO THR ILE VAL VAL SEQRES 9 J 505 LYS GLY TYR GLN ALA ALA ALA GLN LYS ALA GLN GLU LEU SEQRES 10 J 505 LEU LYS THR ILE ALA CYS GLU VAL GLY ALA GLN ASP LYS SEQRES 11 J 505 GLU ILE LEU THR LYS ILE ALA MET THR SER ILE THR GLY SEQRES 12 J 505 LYS GLY ALA GLU LYS ALA LYS GLU LYS LEU ALA GLU ILE SEQRES 13 J 505 ILE VAL GLU ALA VAL SER ALA VAL VAL ASP ASP GLU GLY SEQRES 14 J 505 LYS VAL ASP LYS ASP LEU ILE LYS ILE GLU LYS LYS SER SEQRES 15 J 505 GLY ALA SER ILE ASP ASP THR GLU LEU ILE LYS GLY VAL SEQRES 16 J 505 LEU VAL ASP LYS GLU ARG VAL SER ALA GLN MET PRO LYS SEQRES 17 J 505 LYS VAL THR ASP ALA LYS ILE ALA LEU LEU ASN CYS ALA SEQRES 18 J 505 ILE GLU ILE LYS GLU THR GLU THR ASP ALA GLU ILE ARG SEQRES 19 J 505 ILE THR ASP PRO ALA LYS LEU MET GLU PHE ILE GLU GLN SEQRES 20 J 505 GLU GLU LYS MET LEU LYS ASP MET VAL ALA GLU ILE LYS SEQRES 21 J 505 ALA SER GLY ALA ASN VAL LEU PHE CYS GLN LYS GLY ILE SEQRES 22 J 505 ASP ASP LEU ALA GLN HIS TYR LEU ALA LYS GLU GLY ILE SEQRES 23 J 505 VAL ALA ALA ARG ARG VAL LYS LYS SER ASP MET GLU LYS SEQRES 24 J 505 LEU ALA LYS ALA THR GLY ALA ASN VAL ILE THR ASN ILE SEQRES 25 J 505 LYS ASP LEU SER ALA GLN ASP LEU GLY ASP ALA GLY LEU SEQRES 26 J 505 VAL GLU GLU ARG LYS ILE SER GLY ASP SER MET ILE PHE SEQRES 27 J 505 VAL GLU GLU CYS LYS HIS PRO LYS ALA VAL THR MET LEU SEQRES 28 J 505 ILE ARG GLY THR THR GLU HIS VAL ILE GLU GLU VAL ALA SEQRES 29 J 505 ARG ALA VAL ASP ASP ALA VAL GLY VAL VAL GLY CYS THR SEQRES 30 J 505 ILE GLU ASP GLY ARG ILE VAL SER GLY GLY GLY SER THR SEQRES 31 J 505 GLU VAL GLU LEU SER MET LYS LEU ARG GLU TYR ALA GLU SEQRES 32 J 505 GLY ILE SER GLY ARG GLU GLN LEU ALA VAL ARG ALA PHE SEQRES 33 J 505 ALA ASP ALA LEU GLU VAL ILE PRO ARG THR LEU ALA GLU SEQRES 34 J 505 ASN ALA GLY LEU ASP ALA ILE GLU ILE LEU VAL LYS VAL SEQRES 35 J 505 ARG ALA ALA HIS ALA SER ASN GLY ASN LYS CYS ALA GLY SEQRES 36 J 505 LEU ASN VAL PHE THR GLY ALA VAL GLU ASP MET CYS GLU SEQRES 37 J 505 ASN GLY VAL VAL GLU PRO LEU ARG VAL LYS THR GLN ALA SEQRES 38 J 505 ILE GLN SER ALA ALA GLU SER THR GLU MET LEU LEU ARG SEQRES 39 J 505 ILE ASP ASP VAL ILE ALA ALA GLU LYS LEU ARG HELIX 1 AA1 ALA J 20 LEU J 26 1 7 HELIX 2 AA2 ALA J 27 ARG J 29 5 3 HELIX 3 AA3 ILE J 30 VAL J 35 1 6 HELIX 4 AA4 THR J 63 GLU J 67 5 5 HELIX 5 AA5 PRO J 73 GLY J 90 1 18 HELIX 6 AA6 THR J 93 ASP J 112 1 20 HELIX 7 AA7 HIS J 116 ALA J 139 1 24 HELIX 8 AA8 ILE J 149 THR J 159 1 11 HELIX 9 AA9 GLY J 160 GLY J 162 5 3 HELIX 10 AB1 ALA J 166 SER J 179 1 14 HELIX 11 AB2 ASP J 189 ILE J 193 5 5 HELIX 12 AB3 SER J 202 THR J 206 5 5 HELIX 13 AB4 ASP J 254 ALA J 256 5 3 HELIX 14 AB5 LYS J 257 GLY J 280 1 24 HELIX 15 AB6 LEU J 293 GLY J 302 1 10 HELIX 16 AB7 SER J 312 GLY J 322 1 11 HELIX 17 AB8 ASN J 328 LEU J 332 5 5 HELIX 18 AB9 THR J 373 GLY J 398 1 26 HELIX 19 AC1 THR J 407 ILE J 422 1 16 HELIX 20 AC2 GLU J 426 ALA J 436 1 11 HELIX 21 AC3 GLU J 438 ALA J 448 1 11 HELIX 22 AC4 VAL J 457 ALA J 462 1 6 HELIX 23 AC5 MET J 483 GLY J 487 1 5 HELIX 24 AC6 LEU J 492 THR J 506 1 15 HELIX 25 AC7 THR J 506 ARG J 511 1 6 SHEET 1 AA1 3 CYS J 140 GLU J 141 0 SHEET 2 AA1 3 ARG J 399 SER J 402 -1 O ILE J 400 N CYS J 140 SHEET 3 AA1 3 VAL J 489 PRO J 491 -1 O GLU J 490 N VAL J 401 SHEET 1 AA2 2 GLU J 196 LYS J 197 0 SHEET 2 AA2 2 LEU J 368 ILE J 369 1 O ILE J 369 N GLU J 196 SHEET 1 AA3 4 GLY J 211 VAL J 214 0 SHEET 2 AA3 4 MET J 353 GLU J 357 -1 O ILE J 354 N VAL J 214 SHEET 3 AA3 4 ALA J 340 ARG J 346 -1 N ARG J 346 O MET J 353 SHEET 4 AA3 4 LYS J 226 ALA J 230 -1 N ALA J 230 O ALA J 340 SHEET 1 AA4 2 LEU J 234 LEU J 235 0 SHEET 2 AA4 2 VAL J 325 ILE J 326 1 O ILE J 326 N LEU J 234 SHEET 1 AA5 2 ALA J 471 LEU J 473 0 SHEET 2 AA5 2 VAL J 480 ASP J 482 -1 O GLU J 481 N GLY J 472 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