HEADER BIOSYNTHETIC PROTEIN 23-JUL-08 3DWU TITLE TRANSITION-STATE MODEL CONFORMATION OF THE SWITCH I REGION FITTED INTO TITLE 2 THE CRYO-EM MAP OF THE EEF2.80S.ALF4.GDP COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELONGATION FACTOR TU-B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SWITCH I REGION: UNP RESIDUES 21-66; COMPND 5 SYNONYM: EF-TU-B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS HB8; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8 / DSM 579; SOURCE 5 ATCC: 27634 KEYWDS TRANSITION STATE, CONSERVED SWITCH I, ANTIBIOTIC RESISTANCE, KEYWDS 2 ELONGATION FACTOR, GTP-BINDING, MEMBRANE, METHYLATION, NUCLEOTIDE- KEYWDS 3 BINDING, PHOSPHOPROTEIN, PROTEIN BIOSYNTHESIS, BIOSYNTHETIC PROTEIN EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR P.NISSEN,J.NYBORG,M.KJELDGAARD REVDAT 6 21-FEB-24 3DWU 1 REMARK REVDAT 5 18-JUL-18 3DWU 1 REMARK REVDAT 4 24-FEB-09 3DWU 1 VERSN REVDAT 3 02-SEP-08 3DWU 1 JRNL REVDAT 2 19-AUG-08 3DWU 1 REMARK REVDAT 1 12-AUG-08 3DWU 0 JRNL AUTH J.SENGUPTA,J.NILSSON,R.GURSKY,M.KJELDGAARD,P.NISSEN,J.FRANK JRNL TITL VISUALIZATION OF THE EEF2-80S RIBOSOME TRANSITION-STATE JRNL TITL 2 COMPLEX BY CRYO-ELECTRON MICROSCOPY. JRNL REF J.MOL.BIOL. V. 382 179 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18644383 JRNL DOI 10.1016/J.JMB.2008.07.004 REMARK 2 REMARK 2 RESOLUTION. 12.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : O, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3DNY REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--MANUAL REFINEMENT PROTOCOL--FITTED AS REMARK 3 RIGID BODY. CURRENT MODEL WAS ALIGNED TO THE HELIX A OF THE REMARK 3 FITTED EEF2 COORDINATES (PDB ENTRY 3DNY) WHICH IS LOCATED NEXT REMARK 3 TO THE SWITCH I SEQUENCE. THE COORDINATES FOR THIS ENTRY ARE REMARK 3 BASED ON MANUAL FITTING OF THE COORDINATES INTO CRYO-EM DENSITY REMARK 3 MAP. THEREFORE, AUTHORS DID NOT DEPOSIT STRUCTURE FACTORS. REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 2.820 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 12.60 REMARK 3 NUMBER OF PARTICLES : 28242 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: SINGLE PARTICLE RECONSTRUCTION, RESOLUTION REMARK 3 ESTIMATED: FSC CUT-OFF AT 0.15 REMARK 4 REMARK 4 3DWU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048588. 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 : EEF2.80S.ALF4.GDP COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : CRYOGEN ETHANE (93K), TWO-FACE REMARK 245 BLOTTING FOR 1 SECOND REMARK 245 SAMPLE BUFFER : 20 MM HEPES-NH3, 100 MM KCL, 20 REMARK 245 MM MGCL2 REMARK 245 PH : 7.20 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 TECNAI F20 REMARK 245 DETECTOR TYPE : NULL REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4500.00 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) : 1000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 49650 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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: 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AS2 RELATED DB: PDB REMARK 900 CURRENT MODEL OF THE CONSERVED SWITCH I REGION (OF EF-TU) USED TO REMARK 900 BUILT THIS STRUCTURE. REMARK 900 RELATED ID: 3DNY RELATED DB: PDB REMARK 900 THE FITTED EEF2 STRUCTURE INTO THE CRYO-EM MAP EMD-5015 REMARK 900 RELATED ID: 1N0U RELATED DB: PDB REMARK 900 EEF2 CRYSTAL STRUCTURE USED FOR FITTING IN ENTRY 3DNY REMARK 900 RELATED ID: EMD-5015 RELATED DB: EMDB REMARK 900 CRYO-EM MAP FOR EEF2.80S.ALF4-.GDP COMPLEX DBREF 3DWU A 20 65 UNP P60339 EFTU2_THET8 21 66 SEQRES 1 A 46 VAL ASP HIS GLY LYS THR THR LEU THR ALA ALA LEU THR SEQRES 2 A 46 PHE VAL THR ALA ALA GLU ASN PRO ASN VAL GLU VAL LYS SEQRES 3 A 46 ASP TYR GLY ASP ILE ASP LYS ALA PRO GLU GLU ARG ALA SEQRES 4 A 46 ARG GLY ILE THR ILE ASN THR 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 ATOM 1 CA VAL A 20 -16.058 41.883 -65.323 1.00 12.42 C ATOM 2 CA ASP A 21 -13.057 44.078 -66.242 1.00 15.26 C ATOM 3 CA HIS A 22 -14.559 45.495 -69.430 1.00 6.08 C ATOM 4 CA GLY A 23 -14.278 49.058 -68.227 1.00 13.93 C ATOM 5 CA LYS A 24 -17.313 50.295 -66.277 1.00 6.88 C ATOM 6 CA THR A 25 -15.404 52.005 -63.436 1.00 7.64 C ATOM 7 CA THR A 26 -12.850 53.546 -65.804 1.00 17.70 C ATOM 8 CA LEU A 27 -15.722 55.007 -67.831 1.00 17.81 C ATOM 9 CA THR A 28 -17.549 56.252 -64.745 1.00 11.01 C ATOM 10 CA ALA A 29 -14.342 58.044 -63.761 1.00 16.54 C ATOM 11 CA ALA A 30 -13.791 59.360 -67.261 1.00 18.09 C ATOM 12 CA LEU A 31 -17.348 60.732 -67.225 1.00 13.08 C ATOM 13 CA THR A 32 -16.755 62.914 -64.152 1.00 12.33 C ATOM 14 CA PHE A 33 -13.524 64.399 -65.545 1.00 29.13 C ATOM 15 CA VAL A 34 -14.869 65.106 -69.007 1.00 20.88 C ATOM 16 CA THR A 35 -17.963 66.988 -67.840 1.00 10.22 C ATOM 17 CA ALA A 36 -16.049 68.854 -65.146 1.00 18.26 C ATOM 18 CA ALA A 37 -14.133 70.650 -67.896 1.00 26.23 C ATOM 19 CA GLU A 38 -17.516 72.074 -68.961 1.00 28.22 C ATOM 20 CA ASN A 39 -18.947 72.410 -65.579 1.00 29.95 C ATOM 21 CA PRO A 40 -17.157 73.547 -62.390 1.00 37.07 C ATOM 22 CA ASN A 41 -19.896 72.143 -60.167 1.00 33.33 C ATOM 23 CA VAL A 42 -18.579 68.828 -61.005 1.00 24.62 C ATOM 24 CA GLU A 43 -16.186 67.253 -58.726 1.00 14.34 C ATOM 25 CA VAL A 44 -12.704 67.135 -60.267 1.00 21.03 C ATOM 26 CA LYS A 45 -9.881 65.194 -58.657 1.00 25.24 C ATOM 27 CA ASP A 46 -6.667 66.040 -60.649 1.00 24.87 C ATOM 28 CA TYR A 47 -4.304 67.343 -57.976 1.00 16.40 C ATOM 29 CA GLY A 48 -1.178 65.387 -57.085 1.00 9.29 C ATOM 30 CA ASP A 49 -2.490 64.910 -53.546 1.00 15.50 C ATOM 31 CA ILE A 50 -5.338 62.839 -55.006 1.00 22.82 C ATOM 32 CA ASP A 51 -3.018 60.983 -57.390 1.00 15.67 C ATOM 33 CA LYS A 52 -0.412 60.349 -54.543 1.00 23.57 C ATOM 34 CA ALA A 53 -2.780 57.712 -53.146 1.00 2.91 C ATOM 35 CA PRO A 54 -2.412 55.484 -56.185 1.00 13.14 C ATOM 36 CA GLU A 55 1.386 55.526 -55.825 1.00 26.64 C ATOM 37 CA GLU A 56 0.695 52.209 -54.010 1.00 16.34 C ATOM 38 CA ARG A 57 -1.072 50.775 -57.023 1.00 22.55 C ATOM 39 CA ALA A 58 -3.936 48.650 -58.008 1.00 19.85 C ATOM 40 CA ARG A 59 -6.404 48.246 -60.926 1.00 23.03 C ATOM 41 CA GLY A 60 -9.061 47.853 -58.162 1.00 19.74 C ATOM 42 CA ILE A 61 -12.068 45.122 -58.124 1.00 16.41 C ATOM 43 CA THR A 62 -15.125 47.467 -57.893 1.00 12.37 C ATOM 44 CA ILE A 63 -17.063 45.822 -55.115 1.00 20.14 C ATOM 45 CA ASN A 64 -20.048 47.812 -54.021 1.00 16.77 C ATOM 46 CA THR A 65 -22.159 49.967 -56.197 1.00 9.03 C TER 47 THR A 65 MASTER 111 0 0 0 0 0 0 6 46 1 0 4 END