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PDBj>EM Navigator>Detail page - PDB-4v6p

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Structural characterization of mRNA-tRNA translocation intermediates (class 4b of the six classes)

by single particle reconstruction, at 13.5 A resolution

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Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4v6p
TitleStructural characterization of mRNA-tRNA translocation intermediates (class 4b of the six classes)
DescriptorProtein/RNA complex
KeywordsRIBOSOME, cryoelectron microscopy, molecular dynamics flexible fitting, ratchet-like rotation
AuthorsAgirrezabala, X., Liao, H., Schreiner, E., Fu, J., Ortiz-Meoz, R.F., Schulten, K., Green, R., Frank, J.
DateDeposition: 2011-12-08, Release: 2014-07-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-5364, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-5364, Image by UCSF CHIMERA

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EMDB-5364

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Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 109, Issue 16, Page 6094-9, Year 2012
TitleStructural characterization of mRNA-tRNA translocation intermediates.
AuthorsXabier Agirrezabala, Hstau Y Liao, Eduard Schreiner, Jie Fu, Rodrigo F Ortiz-Meoz, Klaus Schulten, Rachel Green, Joachim Frank
Structural Biology Unit, CIC-bioGUNE, Bizkaia Technology Park, Derio 48160, Basque Country, Spain.
KeywordsBinding Sites, Cryoelectron Microscopy, Crystallography, X-Ray, Escherichia coli (genetics), Macromolecular Substances (chemistry), Models, Molecular, Molecular Conformation, Protein Biosynthesis, RNA, Messenger (genetics), RNA, Transfer (genetics, 9014-25-9), Ribosomes (metabolism), Thermodynamics
LinksDOI: 10.1073/pnas.1201288109, PubMed: 22467828, PMC: PMC3340995
Components
ID 1 : 16S ribosomal RNA
Description16S ribosomal RNA
Typepolyribonucleotide
Formula weight499874.406 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksGenBank: 83754040, Sequence view
ID 2 : A site tRNA
DescriptionA site tRNA
Typepolyribonucleotide
Formula weight24644.932 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 3 : mRNA
DescriptionmRNA
Typepolyribonucleotide
Formula weight15036.825 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 4 : P site tRNA
DescriptionP site tRNA
Typepolyribonucleotide
Formula weight24832.918 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 5 : 30S ribosomal protein S2
Description30S ribosomal protein S2
Typepolypeptide(L)
Formula weight26650.475 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V0, Sequence view
ID 6 : 30S ribosomal protein S3
Description30S ribosomal protein S3
Typepolypeptide(L)
Formula weight25900.117 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V3, Sequence view
ID 7 : 30S ribosomal protein S4
Description30S ribosomal protein S4
Typepolypeptide(L)
Formula weight23383.002 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V8, Sequence view
ID 8 : 30S ribosomal protein S5
Description30S ribosomal protein S5
Typepolypeptide(L)
Formula weight17498.203 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7W1, Sequence view
ID 9 : 30S ribosomal protein S6
Description30S ribosomal protein S6
Typepolypeptide(L)
Formula weight15727.512 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02358, Sequence view
ID 10 : 30S ribosomal protein S7
Description30S ribosomal protein S7
Typepolypeptide(L)
Formula weight19923.959 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02359, Sequence view
ID 11 : 30S ribosomal protein S8
Description30S ribosomal protein S8
Typepolypeptide(L)
Formula weight14015.361 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7W7, Sequence view
ID 12 : 30S ribosomal protein S9
Description30S ribosomal protein S9
Typepolypeptide(L)
Formula weight14755.074 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7X3, Sequence view
ID 13 : 30S ribosomal protein S10
Description30S ribosomal protein S10
Typepolypeptide(L)
Formula weight11755.597 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R5, Sequence view
ID 14 : 30S ribosomal protein S11
Description30S ribosomal protein S11
Typepolypeptide(L)
Formula weight13739.778 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R9, Sequence view
ID 15 : 30S ribosomal protein S12
Description30S ribosomal protein S12
Typepolypeptide(L)
Formula weight13636.961 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7S3, Sequence view
ID 16 : 30S ribosomal protein S13
Description30S ribosomal protein S13
Typepolypeptide(L)
Formula weight12997.271 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7S9, Sequence view
ID 17 : 30S ribosomal protein S14
Description30S ribosomal protein S14
Typepolypeptide(L)
Formula weight11475.364 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG59, Sequence view
ID 18 : 30S ribosomal protein S15
Description30S ribosomal protein S15
Typepolypeptide(L)
Formula weight10188.687 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: Q8X9M2, Sequence view
ID 19 : 30S ribosomal protein S16
Description30S ribosomal protein S16
Typepolypeptide(L)
Formula weight9207.572 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7T3, Sequence view
ID 20 : 30S ribosomal protein S17
Description30S ribosomal protein S17
Typepolypeptide(L)
Formula weight9593.296 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG63, Sequence view
ID 21 : 30S ribosomal protein S18
Description30S ribosomal protein S18
Typepolypeptide(L)
Formula weight8874.276 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7T7, Sequence view
ID 22 : 30S ribosomal protein S19
Description30S ribosomal protein S19
Typepolypeptide(L)
Formula weight10324.160 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7U3, Sequence view
ID 23 : 30S ribosomal protein S20
Description30S ribosomal protein S20
Typepolypeptide(L)
Formula weight9577.268 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7U7, Sequence view
ID 24 : 30S ribosomal protein S21
Description30S ribosomal protein S21
Typepolypeptide(L)
Formula weight8392.844 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P68679, Sequence view
ID 25 : 5S ribomosomal RNA
Description5S ribomosomal RNA
Typepolyribonucleotide
Formula weight38790.090 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksGenBank: 33357928, Sequence view
ID 26 : 23S ribomosomal RNA
Description23S ribomosomal RNA
Typepolyribonucleotide
Formula weight941813.562 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksGenBank: 33357927, Sequence view
ID 27 : 50S ribosomal protein L1
Description50S ribosomal protein L1
Typepolypeptide(L)
Formula weight24765.660 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:2285
Organism scientific: Sulfolobus acidocaldarius
LinksUniProt: P0A7L0, Sequence view
ID 28 : 50S ribosomal protein L2
Description50S ribosomal protein L2
Typepolypeptide(L)
Formula weight29792.424 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60422, Sequence view
ID 29 : 50S ribosomal protein L3
Description50S ribosomal protein L3
Typepolypeptide(L)
Formula weight22277.535 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60438, Sequence view
ID 30 : 50S ribosomal protein L4
Description50S ribosomal protein L4
Typepolypeptide(L)
Formula weight22121.566 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60723, Sequence view
ID 31 : 50S ribosomal protein L5
Description50S ribosomal protein L5
Typepolypeptide(L)
Formula weight20202.416 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P62399, Sequence view
ID 32 : 50S ribosomal protein L6
Description50S ribosomal protein L6
Typepolypeptide(L)
Formula weight18801.598 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG55, Sequence view
ID 33 : 50S ribosomal protein L9
Description50S ribosomal protein L9
Typepolypeptide(L)
Formula weight15789.020 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R1, Sequence view
ID 34 : 50S ribosomal protein L10
Description50S ribosomal protein L10
Typepolypeptide(L)
Formula weight17605.396 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:2285
Organism scientific: Sulfolobus acidocaldarius
LinksUniProt: P0A7J3, Sequence view
ID 35 : 50S ribosomal protein L11
Description50S ribosomal protein L11
Typepolypeptide(L)
Formula weight14763.165 Da
Number of molecules1
ID35
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7J7, Sequence view
ID 36 : 50S ribosomal protein L13
Description50S ribosomal protein L13
Typepolypeptide(L)
Formula weight16050.606 Da
Number of molecules1
ID36
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AA10, Sequence view
ID 37 : 50S ribosomal protein L14
Description50S ribosomal protein L14
Typepolypeptide(L)
Formula weight13565.067 Da
Number of molecules1
ID37
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY3, Sequence view
ID 38 : 50S ribosomal protein L15
Description50S ribosomal protein L15
Typepolypeptide(L)
Formula weight15008.471 Da
Number of molecules1
ID38
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02413, Sequence view
ID 39 : 50S ribosomal protein L16
Description50S ribosomal protein L16
Typepolypeptide(L)
Formula weight15312.269 Da
Number of molecules1
ID39
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY7, Sequence view
ID 40 : 50S ribosomal protein L17
Description50S ribosomal protein L17
Typepolypeptide(L)
Formula weight14393.657 Da
Number of molecules1
ID40
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG44, Sequence view
ID 41 : 50S ribosomal protein L18
Description50S ribosomal protein L18
Typepolypeptide(L)
Formula weight12794.668 Da
Number of molecules1
ID41
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0C018, Sequence view
ID 42 : 50S ribosomal protein L19
Description50S ribosomal protein L19
Typepolypeptide(L)
Formula weight13028.082 Da
Number of molecules1
ID42
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7K6, Sequence view
ID 43 : 50S ribosomal protein L20
Description50S ribosomal protein L20
Typepolypeptide(L)
Formula weight13396.828 Da
Number of molecules1
ID43
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L3, Sequence view
ID 44 : 50S ribosomal protein L21
Description50S ribosomal protein L21
Typepolypeptide(L)
Formula weight11586.374 Da
Number of molecules1
ID44
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG48, Sequence view
ID 45 : 50S ribosomal protein L22
Description50S ribosomal protein L22
Typepolypeptide(L)
Formula weight12253.359 Da
Number of molecules1
ID45
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P61175, Sequence view
ID 46 : 50S ribosomal protein L23
Description50S ribosomal protein L23
Typepolypeptide(L)
Formula weight11222.160 Da
Number of molecules1
ID46
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADZ0, Sequence view
ID 47 : 50S ribosomal protein L24
Description50S ribosomal protein L24
Typepolypeptide(L)
Formula weight11208.054 Da
Number of molecules1
ID47
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60624, Sequence view
ID 48 : 50S ribosomal protein L25
Description50S ribosomal protein L25
Typepolypeptide(L)
Formula weight10713.465 Da
Number of molecules1
ID48
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P68919, Sequence view
ID 49 : 50S ribosomal protein L27
Description50S ribosomal protein L27
Typepolypeptide(L)
Formula weight9015.344 Da
Number of molecules1
ID49
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L8, Sequence view
ID 50 : 50S ribosomal protein L28
Description50S ribosomal protein L28
Typepolypeptide(L)
Formula weight8896.354 Da
Number of molecules1
ID50
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M2, Sequence view
ID 51 : 50S ribosomal protein L29
Description50S ribosomal protein L29
Typepolypeptide(L)
Formula weight7286.464 Da
Number of molecules1
ID51
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M6, Sequence view
ID 52 : 50S ribosomal protein L30
Description50S ribosomal protein L30
Typepolypeptide(L)
Formula weight6423.625 Da
Number of molecules1
ID52
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG51, Sequence view
ID 53 : 50S ribosomal protein L31
Description50S ribosomal protein L31
Typepolypeptide(L)
Formula weight7887.117 Da
Number of molecules1
ID53
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M9, Sequence view
ID 54 : 50S ribosomal protein L32
Description50S ribosomal protein L32
Typepolypeptide(L)
Formula weight6332.249 Da
Number of molecules1
ID54
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N4, Sequence view
ID 55 : 50S ribosomal protein L33
Description50S ribosomal protein L33
Typepolypeptide(L)
Formula weight6257.436 Da
Number of molecules1
ID55
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N9, Sequence view
ID 56 : 50S ribosomal protein L34
Description50S ribosomal protein L34
Typepolypeptide(L)
Formula weight5397.463 Da
Number of molecules1
ID56
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7P5, Sequence view
ID 57 : 50S ribosomal protein L35
Description50S ribosomal protein L35
Typepolypeptide(L)
Formula weight7181.835 Da
Number of molecules1
ID57
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7Q1, Sequence view
ID 58 : 50S ribosomal protein L36
Description50S ribosomal protein L36
Typepolypeptide(L)
Formula weight4377.390 Da
Number of molecules1
ID58
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7Q6, Sequence view
ID 59 : TRYPTOPHAN
DescriptionTRYPTOPHAN
Typenon-polymer
Formula weight204.225 Da
Number of molecules1
ID59
SourceMethod: Obtained synthetically
ID 60 : N-FORMYLMETHIONINE
DescriptionN-FORMYLMETHIONINE
Typenon-polymer
Formula weight177.221 Da
Number of molecules1
ID60
SourceMethod: Obtained synthetically
Sample
Assembly
Aggregation statePARTICLE
Mass-estimation Method2.8
Theoretical Mass2.8
NameTrp-tRNA-EFTu-GDP-kir-70S ribosome
Num components3
Entity assembly
Assembly-ID1
Detailswith A and P site tRNAs
Name70S ribosome
TypeRIBOSOME
Buffer
NameHiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration0.03 mg/ml
Sample support
Details200 mesh
Grid mesh size200
Vitrification
Cryogen nameNITROGEN
DetailsBlot for 6 seconds, plunge into liquid nitrogen (Vitrobot)
Humidity90
InstrumentVitrobot
Methodblot for 6 seconds
Temp80 Kelvin
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Date2011-05-01
Detailsautomated data collection system AutoEMation (CCD mag. 100000x)
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose25 e/A**2
Illumination modeFLOODBEAM
Lens
ModeBRIGHTFIELD
MagnificationCalibrated: 58269 X, Nominal: 59000 X
CsNominal: 2.26 mm
Nominal defocusMax: 4000 nm, Min: 1200 nm
Energy filternone
Specimen holder
Specimen holderModel: OTHER, Type: cartridge
Temperature80.7 Kelvin
Recording temperatureMaximum: 80.7, Minimum: 80.7
Detector
TypeTVIPS TemCam-F415 (CCD)
Processing
2D projection selection
Number of particles21000
Software nameMDFF
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
Actual pixel size1.5 A/pix
CTF correction methodVolumes were CTF-corrected in defocus groups
Magnification calibration50000
Number of particles21000
Resolution13.5 A
Resolution methodFSC at 0.5 cut-off
SoftwareSPIDER
3D fitting
Refinement ProtocolMolecular Dynamics based flexible fitting
Refinement SpaceREAL
Software nameMDFF
Target criteriaRMSD, cross correlation
3D fitting list
3D Fitting ID1
PDB entry ID2I2U
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms57562
Ligand atoms24
Nucleic acid atoms37350
Protein atoms20188
Download
PDB format
Allpdb4v6p.ent.gz
pdb4v6p.ent (uncompressed file)
Header onlypdb4v6p.ent.gz
mmCIF format
mmCIF4v6p.cif.gz
XML format
All4v6p.xml.gz
No-atom4v6p-noatom.xml.gz
Ext-atom4v6p-extatom.xml.gz
Movie files
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movie #2
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movie #3
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