HEADER TRANSLATION 10-JUL-15 5A7U TITLE SINGLE-PARTICLE CRYO-EM OF CO-TRANSLATIONAL FOLDED ADR1 DOMAIN INSIDE TITLE 2 THE E. COLI RIBOSOME EXIT TUNNEL. COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATORY PROTEIN ADR1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 130-158; COMPND 5 SYNONYM: ADR1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN FOLDING, TRANSLATION, RIBOSOME, ZINC FINGER, SECM, KEYWDS 2 TRANSLATIONAL ARREST PEPTIDE, CRYO-EM, SINGLE- MOLECULE STUDIES EXPDTA ELECTRON MICROSCOPY AUTHOR O.B.NILSSON,R.HEDMAN,J.MARINO,S.WICKLES,L.BISCHOFF,M.JOHANSSON, AUTHOR 2 A.MULLER-LUCKS,F.TROVATO,J.D.PUGLISI,E.O'BRIEN,R.BECKMANN,G.VON AUTHOR 3 HEIJNE REVDAT 4 08-MAY-24 5A7U 1 REMARK LINK REVDAT 3 23-AUG-17 5A7U 1 REMARK REVDAT 2 23-SEP-15 5A7U 1 JRNL REVDAT 1 16-SEP-15 5A7U 0 JRNL AUTH O.B.NILSSON,R.HEDMAN,J.MARINO,S.WICKLES,L.BISCHOFF, JRNL AUTH 2 M.JOHANSSON,A.MULLER-LUCKS,F.TROVATO,J.D.PUGLISI, JRNL AUTH 3 E.P.O'BRIEN,R.BECKMANN,G.VON HEIJNE JRNL TITL COTRANSLATIONAL PROTEIN FOLDING INSIDE THE RIBOSOME EXIT JRNL TITL 2 TUNNEL. JRNL REF CELL REP. V. 12 1533 2015 JRNL REFN ESSN 2211-1247 JRNL PMID 26321634 JRNL DOI 10.1016/J.CELREP.2015.07.065 REMARK 2 REMARK 2 RESOLUTION. 4.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2ADR 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 : METHOD--RIGID BODY REFINEMENT PROTOCOL--NMR REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 3.700 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.800 REMARK 3 NUMBER OF PARTICLES : 151900 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD REMARK 3 -3079. (DEPOSITION ID: 13581). REMARK 4 REMARK 4 5A7U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290064333. 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 : ADR1 DOMAIN COTRANSLATIONALLY REMARK 245 FOLDED INSIDE THE E. COLI REMARK 245 RIBOSOME EXIT TUNNEL REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : VITRIFICATION 1 -- CRYOGEN- REMARK 245 ETHANE, INSTRUMENT- FEI REMARK 245 VITROBOT MARK IV, REMARK 245 SAMPLE BUFFER : 20 MM HEPES PH 7.2 , 50 MM REMARK 245 KOAC, 5 MM MG OAC2, 0.03% DDM, REMARK 245 50 MICROM ZNCL2, 125 MM SUCROSE. REMARK 245 PH : 7.20 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 13-APR-15 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON II (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3200.00 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) : 500.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A 28 REMARK 465 ASN A 29 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 CYS A 11 SG 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 LYS A 1 CB - CA - C ANGL. DEV. = 20.0 DEGREES REMARK 500 TYR A 3 CB - CG - CD2 ANGL. DEV. = -4.2 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 PRO A 2 -1.47 -167.80 REMARK 500 TYR A 3 51.38 -112.53 REMARK 500 CYS A 8 17.08 -154.67 REMARK 500 ASN A 9 75.35 59.62 REMARK 500 THR A 13 -101.37 -104.20 REMARK 500 ILE A 25 -43.04 -139.08 REMARK 500 HIS A 26 -63.82 -98.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 1 PRO A 2 -124.61 REMARK 500 PRO A 2 TYR A 3 -141.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 3 0.16 SIDE CHAIN REMARK 500 ARG A 14 0.09 SIDE CHAIN REMARK 500 ARG A 15 0.12 SIDE CHAIN REMARK 500 ASP A 16 0.10 SIDE CHAIN REMARK 500 ARG A 20 0.15 SIDE CHAIN REMARK 500 GLN A 23 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CYS A 5 -10.12 REMARK 500 LEU A 7 12.97 REMARK 500 ARG A 10 -13.15 REMARK 500 ASP A 16 -11.79 REMARK 500 ALA A 22 -13.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 162 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 21 NE2 REMARK 620 2 HIS A 26 NE2 102.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 162 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-3079 RELATED DB: EMDB DBREF 5A7U A 1 29 UNP P07248 ADR1_YEAST 130 158 SEQRES 1 A 29 LYS PRO TYR PRO CYS GLY LEU CYS ASN ARG CYS PHE THR SEQRES 2 A 29 ARG ARG ASP LEU LEU ILE ARG HIS ALA GLN LYS ILE HIS SEQRES 3 A 29 SER GLY ASN HET ZN A 162 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ARG A 14 GLN A 23 1 10 LINK NE2 HIS A 21 ZN ZN A 162 1555 1555 1.89 LINK NE2 HIS A 26 ZN ZN A 162 1555 1555 1.86 SITE 1 AC1 4 CYS A 5 CYS A 8 HIS A 21 HIS A 26 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