HEADER CHAPERONE 01-MAY-22 7XOO TITLE CRYO-EM STRUCTURE OF EMPTY RING SUBUNIT 2 (ER2) FROM GROEL-UGT1A TITLE 2 SINGLE EMPTY RING COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAPERONIN GROEL; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: 60 KDA CHAPERONIN,CHAPERONIN-60,CPN60,GROEL PROTEIN; COMPND 5 EC: 5.6.1.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: GROEL, GROL, MOPA, B4143, JW4103; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PKY206 KEYWDS CRYOGENIC ELECTRON MICROSCOPY, SINGLE-PARTICLE ANALYSIS, MOLECULAR KEYWDS 2 MOTION, STRUCTURE-FUNCTION RELATIONSHIP, FOCUS CLASSIFICATION, KEYWDS 3 SEPARATING HETEROGENEITY, GROEL, CHAPERONE, UNFOLDED PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.STAPLETON,J.TAKAGI,E.MIZOHATA REVDAT 1 03-MAY-23 7XOO 0 JRNL AUTH K.M.STAPLETON,T.MIZOBATA,N.MIYAZAKI,T.TAKATSUJI,T.KATO, JRNL AUTH 2 K.IWASAKI,D.M.STANDLEY,T.KAWAMURA,T.NAKANE,J.TAKAGI, JRNL AUTH 3 E.MIZOHATA JRNL TITL UNMASKING GROEL: STRUCTURE, DYNAMICS, AND SUBSTRATE BINDING JRNL TITL 2 REVEALED BY SINGLE-PARTICLE CRYO-EM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, RELION, CTFFIND, UCSF REMARK 3 CHIMERAX, PHENIX, RELION, RELION 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 : REAL 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) : 3.000 REMARK 3 NUMBER OF PARTICLES : 144509 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: D7 SYMMETRY EXPANDED PARTICLE SET REMARK 4 REMARK 4 7XOO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029125. 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 : GROEL-UGT1A SINGLE EMPTY RING REMARK 245 COMPLEX; EMPTY RING SUBUNIT 2 REMARK 245 (ER-2) OF GROEL; UDP- REMARK 245 GLUCURONOSYLTRANSFERASE 1A REMARK 245 (UGT1A) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 33.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : 3 UL OF 33 MG/ML GROEL-UGT1A REMARK 245 WAS PLACED ON HOLEY CARBON REMARK 245 QUANITIFOIL COPPER GRIDS (300 REMARK 245 MESH SIZE R1.2/1.3) AND BLOTTED REMARK 245 FOR 3 SECONDS (BLOT FORCE =1) REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : THE MODEL WAS BUILT IN THE REMARK 245 ADDITIONAL EM-MAP OF ER2 (MASKED); MODEL IS NOT BUILT REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2951 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 4000.00 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: B 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 LYS B 526 REMARK 465 ASN B 527 REMARK 465 ASP B 528 REMARK 465 ALA B 529 REMARK 465 ALA B 530 REMARK 465 ASP B 531 REMARK 465 LEU B 532 REMARK 465 GLY B 533 REMARK 465 ALA B 534 REMARK 465 ALA B 535 REMARK 465 GLY B 536 REMARK 465 GLY B 537 REMARK 465 MET B 538 REMARK 465 GLY B 539 REMARK 465 GLY B 540 REMARK 465 MET B 541 REMARK 465 GLY B 542 REMARK 465 GLY B 543 REMARK 465 MET B 544 REMARK 465 GLY B 545 REMARK 465 GLY B 546 REMARK 465 MET B 547 REMARK 465 MET B 548 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 B 152 51.20 -92.59 REMARK 500 SER B 217 77.02 -163.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33354 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF EMPTY RING SUBUNIT 2 (ER2) FROM GROEL-UGT1A REMARK 900 SINGLE EMPTY RING COMPLEX DBREF 7XOO B 2 548 UNP P0A6F5 CH60_ECOLI 2 548 SEQRES 1 B 547 ALA ALA LYS ASP VAL LYS PHE GLY ASN ASP ALA ARG VAL SEQRES 2 B 547 LYS MET LEU ARG GLY VAL ASN VAL LEU ALA ASP ALA VAL SEQRES 3 B 547 LYS VAL THR LEU GLY PRO LYS GLY ARG ASN VAL VAL LEU SEQRES 4 B 547 ASP LYS SER PHE GLY ALA PRO THR ILE THR LYS ASP GLY SEQRES 5 B 547 VAL SER VAL ALA ARG GLU ILE GLU LEU GLU ASP LYS PHE SEQRES 6 B 547 GLU ASN MET GLY ALA GLN MET VAL LYS GLU VAL ALA SER SEQRES 7 B 547 LYS ALA ASN ASP ALA ALA GLY ASP GLY THR THR THR ALA SEQRES 8 B 547 THR VAL LEU ALA GLN ALA ILE ILE THR GLU GLY LEU LYS SEQRES 9 B 547 ALA VAL ALA ALA GLY MET ASN PRO MET ASP LEU LYS ARG SEQRES 10 B 547 GLY ILE ASP LYS ALA VAL THR ALA ALA VAL GLU GLU LEU SEQRES 11 B 547 LYS ALA LEU SER VAL PRO CYS SER ASP SER LYS ALA ILE SEQRES 12 B 547 ALA GLN VAL GLY THR ILE SER ALA ASN SER ASP GLU THR SEQRES 13 B 547 VAL GLY LYS LEU ILE ALA GLU ALA MET ASP LYS VAL GLY SEQRES 14 B 547 LYS GLU GLY VAL ILE THR VAL GLU ASP GLY THR GLY LEU SEQRES 15 B 547 GLN ASP GLU LEU ASP VAL VAL GLU GLY MET GLN PHE ASP SEQRES 16 B 547 ARG GLY TYR LEU SER PRO TYR PHE ILE ASN LYS PRO GLU SEQRES 17 B 547 THR GLY ALA VAL GLU LEU GLU SER PRO PHE ILE LEU LEU SEQRES 18 B 547 ALA ASP LYS LYS ILE SER ASN ILE ARG GLU MET LEU PRO SEQRES 19 B 547 VAL LEU GLU ALA VAL ALA LYS ALA GLY LYS PRO LEU LEU SEQRES 20 B 547 ILE ILE ALA GLU ASP VAL GLU GLY GLU ALA LEU ALA THR SEQRES 21 B 547 LEU VAL VAL ASN THR MET ARG GLY ILE VAL LYS VAL ALA SEQRES 22 B 547 ALA VAL LYS ALA PRO GLY PHE GLY ASP ARG ARG LYS ALA SEQRES 23 B 547 MET LEU GLN ASP ILE ALA THR LEU THR GLY GLY THR VAL SEQRES 24 B 547 ILE SER GLU GLU ILE GLY MET GLU LEU GLU LYS ALA THR SEQRES 25 B 547 LEU GLU ASP LEU GLY GLN ALA LYS ARG VAL VAL ILE ASN SEQRES 26 B 547 LYS ASP THR THR THR ILE ILE ASP GLY VAL GLY GLU GLU SEQRES 27 B 547 ALA ALA ILE GLN GLY ARG VAL ALA GLN ILE ARG GLN GLN SEQRES 28 B 547 ILE GLU GLU ALA THR SER ASP TYR ASP ARG GLU LYS LEU SEQRES 29 B 547 GLN GLU ARG VAL ALA LYS LEU ALA GLY GLY VAL ALA VAL SEQRES 30 B 547 ILE LYS VAL GLY ALA ALA THR GLU VAL GLU MET LYS GLU SEQRES 31 B 547 LYS LYS ALA ARG VAL GLU ASP ALA LEU HIS ALA THR ARG SEQRES 32 B 547 ALA ALA VAL GLU GLU GLY VAL VAL ALA GLY GLY GLY VAL SEQRES 33 B 547 ALA LEU ILE ARG VAL ALA SER LYS LEU ALA ASP LEU ARG SEQRES 34 B 547 GLY GLN ASN GLU ASP GLN ASN VAL GLY ILE LYS VAL ALA SEQRES 35 B 547 LEU ARG ALA MET GLU ALA PRO LEU ARG GLN ILE VAL LEU SEQRES 36 B 547 ASN CYS GLY GLU GLU PRO SER VAL VAL ALA ASN THR VAL SEQRES 37 B 547 LYS GLY GLY ASP GLY ASN TYR GLY TYR ASN ALA ALA THR SEQRES 38 B 547 GLU GLU TYR GLY ASN MET ILE ASP MET GLY ILE LEU ASP SEQRES 39 B 547 PRO THR LYS VAL THR ARG SER ALA LEU GLN TYR ALA ALA SEQRES 40 B 547 SER VAL ALA GLY LEU MET ILE THR THR GLU CYS MET VAL SEQRES 41 B 547 THR ASP LEU PRO LYS ASN ASP ALA ALA ASP LEU GLY ALA SEQRES 42 B 547 ALA GLY GLY MET GLY GLY MET GLY GLY MET GLY GLY MET SEQRES 43 B 547 MET HELIX 1 AA1 GLY B 9 VAL B 29 1 21 HELIX 2 AA2 ASP B 52 ILE B 60 1 9 HELIX 3 AA3 ASP B 64 GLY B 86 1 23 HELIX 4 AA4 GLY B 88 ALA B 109 1 22 HELIX 5 AA5 ASN B 112 SER B 135 1 24 HELIX 6 AA6 ASP B 140 ALA B 152 1 13 HELIX 7 AA7 ASP B 155 GLY B 170 1 16 HELIX 8 AA8 SER B 201 ILE B 205 5 5 HELIX 9 AA9 MET B 233 GLY B 244 1 12 HELIX 10 AB1 GLY B 256 ARG B 268 1 13 HELIX 11 AB2 GLY B 282 GLY B 297 1 16 HELIX 12 AB3 GLU B 338 GLU B 355 1 18 HELIX 13 AB4 SER B 358 GLY B 375 1 18 HELIX 14 AB5 THR B 385 GLU B 409 1 25 HELIX 15 AB6 GLY B 416 ALA B 427 1 12 HELIX 16 AB7 ASN B 433 GLY B 459 1 27 HELIX 17 AB8 GLU B 461 GLY B 472 1 12 HELIX 18 AB9 MET B 488 GLY B 492 1 5 HELIX 19 AC1 THR B 497 THR B 516 1 20 SHEET 1 AA1 2 LYS B 4 PHE B 8 0 SHEET 2 AA1 2 CYS B 519 ASP B 523 -1 O THR B 522 N ASP B 5 SHEET 1 AA2 2 VAL B 38 LEU B 40 0 SHEET 2 AA2 2 THR B 48 THR B 50 -1 O THR B 48 N LEU B 40 SHEET 1 AA3 3 VAL B 174 ASP B 179 0 SHEET 2 AA3 3 VAL B 376 VAL B 381 1 O ILE B 379 N THR B 176 SHEET 3 AA3 3 GLU B 186 VAL B 190 -1 N VAL B 190 O VAL B 376 SHEET 1 AA4 4 MET B 193 PHE B 195 0 SHEET 2 AA4 4 THR B 330 GLY B 335 -1 O ILE B 332 N MET B 193 SHEET 3 AA4 4 GLY B 318 ILE B 325 -1 N ARG B 322 O ILE B 333 SHEET 4 AA4 4 VAL B 213 LEU B 215 -1 N VAL B 213 O ILE B 325 SHEET 1 AA5 6 MET B 193 PHE B 195 0 SHEET 2 AA5 6 THR B 330 GLY B 335 -1 O ILE B 332 N MET B 193 SHEET 3 AA5 6 GLY B 318 ILE B 325 -1 N ARG B 322 O ILE B 333 SHEET 4 AA5 6 PHE B 219 LEU B 222 -1 N ILE B 220 O GLY B 318 SHEET 5 AA5 6 LEU B 247 ALA B 251 1 O LEU B 248 N PHE B 219 SHEET 6 AA5 6 VAL B 273 LYS B 277 1 O VAL B 276 N ILE B 249 SHEET 1 AA6 2 VAL B 411 ALA B 413 0 SHEET 2 AA6 2 LEU B 494 PRO B 496 -1 O ASP B 495 N VAL B 412 SHEET 1 AA7 2 TYR B 476 ASN B 479 0 SHEET 2 AA7 2 GLU B 484 ASN B 487 -1 O GLU B 484 N ASN B 479 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