[English] 日本語
Yorodumi
- PDB-6uu6: E. coli sigma-S transcription initiation complex with a 4-nt RNA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uu6
TitleE. coli sigma-S transcription initiation complex with a 4-nt RNA and a UTP ("Old" crystal soaked with UTP, ddCTP, and dinucleotide ApG for 30 minutes)
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • (Synthetic DNA 50-mer (promoter ...) x 2
  • RNA 4-mer (dinucleotide ApG primed synthesis)
  • RNA polymerase sigma factor RpoS
KeywordsTRANSCRIPTION / TRANSFERASE/DNA/RNA / Transcription initiation / RNA polymerase / DNA promoter / transcription bubble / de novo RNA synthesis / DNA scrunching / sigma-S factor / TRANSFERASE-DNA-RNA complex
Function / homology
Function and homology information


sigma factor antagonist complex / RNA polymerase complex / response to stress / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex ...sigma factor antagonist complex / RNA polymerase complex / response to stress / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
RNA polymerase sigma factor RpoS / Sigma-70 factors family signature 1. / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 ...RNA polymerase sigma factor RpoS / Sigma-70 factors family signature 1. / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / RNA polymerase sigma factor RpoS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.201 Å
AuthorsZuo, Y. / De, S. / Steitz, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM22778 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Iscience / Year: 2020
Title: Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.
Authors: Zuo, Y. / De, S. / Feng, Y. / Steitz, T.A.
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_src_gen / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_asym / struct_conn / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end
Revision 2.1Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: DNA-directed RNA polymerase subunit alpha
BBB: DNA-directed RNA polymerase subunit alpha
CCC: DNA-directed RNA polymerase subunit beta
DDD: DNA-directed RNA polymerase subunit beta'
EEE: DNA-directed RNA polymerase subunit omega
FFF: RNA polymerase sigma factor RpoS
111: Synthetic DNA 50-mer (promoter non-template strand)
222: Synthetic DNA 50-mer (promoter template strand)
333: RNA 4-mer (dinucleotide ApG primed synthesis)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,63214
Polymers440,9689
Non-polymers6645
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.395, 154.105, 232.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules AAABBBCCCDDDEEE

#1: Protein DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 26899.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB, Z5560, ECs4910 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8V4, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 155366.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, tabB, b3988, JW3951 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8T7, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10118.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A800, DNA-directed RNA polymerase

-
Synthetic DNA 50-mer (promoter ... , 2 types, 2 molecules 111222

#6: DNA chain Synthetic DNA 50-mer (promoter non-template strand)


Mass: 15313.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain Synthetic DNA 50-mer (promoter template strand)


Mass: 15562.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein / RNA chain , 2 types, 2 molecules FFF333

#5: Protein RNA polymerase sigma factor RpoS / Sigma S / Sigma-38


Mass: 38777.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpoS, appR, katF, nur, otsX, sigS, b2741, JW5437 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13445
#8: RNA chain RNA 4-mer (dinucleotide ApG primed synthesis)


Mass: 1208.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 5 molecules

#9: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350, sodium chloride, HEPES / Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4.2→49.1 Å / Num. obs: 35121 / % possible obs: 99.1 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 7.53
Reflection shellResolution: 4.2→4.45 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 0.46 / Num. unique obs: 5349 / CC1/2: 0.114 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IPL

5ipl


Resolution: 4.201→49.077 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.851 / SU B: 713.838 / SU ML: 3.475 / Cross valid method: FREE R-VALUE / ESU R Free: 1.557
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.389 1678 4.799 %0
Rwork0.3425 ---
all0.345 ---
obs-34963 98.872 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 251.227 Å2
Baniso -1Baniso -2Baniso -3
1-0.154 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.094 Å2
Refinement stepCycle: LAST / Resolution: 4.201→49.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27579 1396 51 0 29026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01329595
X-RAY DIFFRACTIONr_bond_other_d0.0010.01727663
X-RAY DIFFRACTIONr_angle_refined_deg1.451.61940264
X-RAY DIFFRACTIONr_angle_other_deg1.0171.61964120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71453511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.68121.7261582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54155173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.19315263
X-RAY DIFFRACTIONr_chiral_restr0.0670.23883
X-RAY DIFFRACTIONr_gen_planes_refined0.0380.0232224
X-RAY DIFFRACTIONr_gen_planes_other0.0350.026071
X-RAY DIFFRACTIONr_nbd_refined0.2280.36875
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2390.329460
X-RAY DIFFRACTIONr_nbtor_refined0.1570.52963
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2680.5967
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.160.561
X-RAY DIFFRACTIONr_metal_ion_refined0.2060.52
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.350.354
X-RAY DIFFRACTIONr_nbd_other0.4010.397
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3860.58
X-RAY DIFFRACTIONr_mcbond_it5.84120.48414062
X-RAY DIFFRACTIONr_mcbond_other5.84120.48414061
X-RAY DIFFRACTIONr_mcangle_it10.39934.55517567
X-RAY DIFFRACTIONr_mcangle_other10.39834.55517568
X-RAY DIFFRACTIONr_scbond_it4.3521.0515533
X-RAY DIFFRACTIONr_scbond_other4.3521.05115534
X-RAY DIFFRACTIONr_scangle_it8.08935.35422697
X-RAY DIFFRACTIONr_scangle_other8.08935.35522698
X-RAY DIFFRACTIONr_lrange_it23.899287.733107628
X-RAY DIFFRACTIONr_lrange_other23.899287.732107629
X-RAY DIFFRACTIONr_ncsr_local_group_10.1330.056383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
4.201-4.310.521140.53522630.53525760.5180.51192.27480.529
4.31-4.4270.4951270.49823640.49824920.2840.2399.95990.492
4.427-4.5540.4521160.42822930.4324130.4230.43899.83420.426
4.554-4.6930.4161280.39122370.39223660.5320.54799.95770.391
4.693-4.8450.452990.39121860.39422870.5450.54299.91260.39
4.845-5.0140.3951230.38820810.38822050.4560.49199.95460.39
5.014-5.2010.421960.39220560.39321520.5220.5481000.396
5.201-5.4110.417970.39419580.39620560.5020.53999.95140.396
5.411-5.6480.396880.40719050.40720010.4960.51699.60020.41
5.648-5.920.499800.43718150.4419120.5190.50399.11090.439
5.92-6.2350.497910.42117120.42518090.5810.56499.66830.42
6.235-6.6070.462600.37916570.38117280.6240.69399.36340.373
6.607-7.0540.415840.31315390.31816340.7130.7799.32680.291
7.054-7.6060.311840.26114240.26415150.7880.81599.5380.24
7.606-8.3120.369680.23113460.23814220.820.87899.43740.211
8.312-9.260.27680.20212150.20612910.8940.92599.38030.191
9.26-10.6290.329480.21310750.21811440.8730.92498.16430.205
10.629-12.8680.267370.2259330.22710060.9360.92996.42150.226
12.868-17.6030.36480.3297350.3317940.8550.85998.61460.332
17.603-49.0770.474220.5014910.4995260.6090.67897.52850.603
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.27331.0051-0.71842.0129-0.19641.90550.1149-0.93220.50690.37050.1713-0.32960.34140.3846-0.28610.14460.1033-0.11870.2415-0.1860.165541.529-5.1164.509
24.1328-0.391-1.447.45152.60363.92060.19591.04240.0288-0.95740.20070.5919-0.062-1.064-0.39660.187-0.0719-0.08550.77270.45020.518818.145-1.554-40.158
36.2082-1.2683-0.8865.19072.01035.45660.04060.52030.6763-0.56860.1508-0.04870.05420.1996-0.19130.3319-0.07190.12960.3640.35020.615754.571.773-57.522
413.3474.9418-2.06486.39172.04336.877-0.28980.45350.764-0.54690.1346-0.2293-0.5107-0.02380.15530.9620.39380.13020.81850.11660.694471.796-30.504-29.68
59.5253-4.2729-4.59677.755-5.456512.10971.02211.36581.6254-0.9153-0.1595-0.5736-0.4734-1.167-0.86261.7134-0.1082-0.02430.7816-0.35681.94150.92732.007-18.335
615.9369-3.674-2.44413.7545-2.63493.95290.19950.34910.01980.01580.17650.3753-0.4068-0.264-0.3761.8167-0.14980.05581.0431-0.61381.689534.26430.80810.934
712.00363.81233.35737.0654.48263.56030.093-0.8985-0.30391.25750.38610.70320.6801-0.0259-0.47921.24040.08210.31051.86250.21961.8249-28.517-3.3232.445
85.67460.73251.40150.2627-0.05836.65550.7588-0.1178-0.57280.4069-0.1823-0.23710.16731.9091-0.57661.27110.06460.04461.0549-0.28251.481686.7121.695-51.778
91.14971.03354.7361.07694.449320.09860.0076-0.2224-0.05230.2097-0.39240.49250.6595-0.5460.38480.9475-0.14280.23752.4411-0.1252.544576.81821.011-29.558
100.44521.31410.36915.60891.47410.4411-0.51040.39140.3260.1060.52351.3212-0.15040.0477-0.01312.66880.04540.25752.5630.51953.203835.04548.906-42.864
117.9756-1.3638-3.06515.56783.08923.1256-0.2263-0.66660.8703-1.28190.2547-0.9749-0.58541.1614-0.02840.52980.2078-0.14281.47680.32211.333479.1612.776-16.258
123.62272.54160.07247.2126-2.71715.45590.0143-0.3458-1.6420.3645-0.121-0.06830.27170.33620.10671.42690.07630.18141.14580.21471.424673.94-62.771-30.924
130.17980.4980.07142.72260.17840.07980.5785-0.3899-0.25071.0717-0.6298-1.92950.41130.15470.05132.6874-0.2063-0.02523.56380.27122.550972.99326.43414.004
147.04040.41961.10282.76650.1495.1760.3417-0.17880.77990.06880.3494-0.17940.1221-0.7397-0.69111.25480.26770.11331.0417-0.07661.76710.40117.7686.852
156.27894.83739.96353.73117.68315.88210.25520.4359-0.5570.12060.2952-0.44030.37240.5227-0.55042.0705-0.26670.32041.8570.03372.366428.831-48.208-53.636
168.5775-6.3022-5.3257.67656.30496.5851-0.01890.8398-4.1676-0.2446-0.73241.39220.36110.59060.75130.89790.30040.01991.167-0.81533.144423.923-29.142-3.592
174.8841-0.7099-0.16024.103-0.83710.22510.10410.83130.2155-0.2184-0.02170.19350.1097-0.2653-0.08240.5431-0.33780.10241.6199-0.06230.9689-3.464-6.602-12.238
1810.353-0.33760.20122.8870.31591.1689-0.0595-0.21870.51240.6123-0.0267-0.21080.4548-0.18260.08611.888-0.08220.04171.93410.0381.823628.467-52.926-30.099
191.9772-2.2156-7.376312.11927.546828.46020.1269-0.44310.2393.1361-0.3191-1.8176-0.20531.5820.19211.4132-0.2847-0.07712.5897-0.44562.539643.1393.483-24.007
207.19882.01143.19141.09672.13655.11160.0248-0.19561.3285-0.82940.51450.2286-1.49160.5703-0.53932.5103-0.47880.23082.4061-0.27873.390781.36730.748-51.55
210.0727-0.0157-0.01870.08190.00190.0618-0.15560.1281-0.3157-0.3469-0.04470.25130.09970.30270.20032.65860.0936-0.04222.5919-0.04812.147548.812-20.964-43.101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLCCC1 - 28
2X-RAY DIFFRACTION1ALLCCC146 - 152
3X-RAY DIFFRACTION1ALLCCC445 - 455
4X-RAY DIFFRACTION1ALLCCC517 - 832
5X-RAY DIFFRACTION1ALLCCC1056 - 1241
6X-RAY DIFFRACTION1ALLDDD767 - 790
7X-RAY DIFFRACTION1ALLDDD1504
8X-RAY DIFFRACTION1ALL333501
9X-RAY DIFFRACTION2ALLCCC1242 - 1321
10X-RAY DIFFRACTION2ALLDDD343 - 500
11X-RAY DIFFRACTION2ALLDDD791 - 943
12X-RAY DIFFRACTION2ALLDDD1129 - 1153
13X-RAY DIFFRACTION2ALLDDD1213 - 1317
14X-RAY DIFFRACTION2ALLDDD1345 - 1407
15X-RAY DIFFRACTION2ALLDDD1502 - 1503
16X-RAY DIFFRACTION2ALLEEE2 - 91
17X-RAY DIFFRACTION3ALLCCC1322 - 1342
18X-RAY DIFFRACTION3ALLDDD1 - 342
19X-RAY DIFFRACTION3ALLDDD1318 - 1344
20X-RAY DIFFRACTION3ALLDDD1501
21X-RAY DIFFRACTION3ALLFFF218 - 226
22X-RAY DIFFRACTION3ALLFFF232 - 241
23X-RAY DIFFRACTION4ALLCCC153 - 226
24X-RAY DIFFRACTION4ALLCCC337 - 444
25X-RAY DIFFRACTION4ALL11145 - 52
26X-RAY DIFFRACTION5ALLCCC833 - 891
27X-RAY DIFFRACTION5ALLCCC912 - 936
28X-RAY DIFFRACTION5ALLCCC1040 - 1055
29X-RAY DIFFRACTION6ALLAAA52 - 178
30X-RAY DIFFRACTION7ALLBBB52 - 178
31X-RAY DIFFRACTION8ALLFFF53 - 166
32X-RAY DIFFRACTION8ALL11137 - 44
33X-RAY DIFFRACTION9ALLFFF167 - 217
34X-RAY DIFFRACTION9ALL22222 - 26
35X-RAY DIFFRACTION10ALLFFF242 - 329
36X-RAY DIFFRACTION10ALLCCC892 - 911
37X-RAY DIFFRACTION11ALLCCC29 - 145
38X-RAY DIFFRACTION11ALLCCC456 - 516
39X-RAY DIFFRACTION12ALLCCC227 - 336
40X-RAY DIFFRACTION13ALLCCC937 - 1039
41X-RAY DIFFRACTION14ALLAAA1 - 51
42X-RAY DIFFRACTION14ALLAAA179 - 235
43X-RAY DIFFRACTION14ALLBBB1 - 51
44X-RAY DIFFRACTION14ALLBBB179 - 235
45X-RAY DIFFRACTION15ALLDDD1154 - 1212
46X-RAY DIFFRACTION16ALLDDD637 - 766
47X-RAY DIFFRACTION17ALLDDD501 - 636
48X-RAY DIFFRACTION18ALLDDD944 - 1128
49X-RAY DIFFRACTION19ALLFFF227 - 231
50X-RAY DIFFRACTION19ALL22211 - 21
51X-RAY DIFFRACTION19ALL33315 - 18
52X-RAY DIFFRACTION20ALL11120 - 36
53X-RAY DIFFRACTION20ALL22227 - 43
54X-RAY DIFFRACTION21ALL11153 - 59
55X-RAY DIFFRACTION21ALL2223 - 10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more