[English] 日本語
Yorodumi
- PDB-5ipl: SigmaS-transcription initiation complex with 4-nt nascent RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ipl
TitleSigmaS-transcription initiation complex with 4-nt nascent RNA
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • RNA polymerase sigma factor RpoS
  • nascent RNA 4-mer
  • synthetic nontemplate strand DNA (50-MER)
  • synthetic template strand DNA (50-MER)
KeywordsTRANSCRIPTION / TRANSFERASE/DNA/RNA / Transcription initiation / RNA polymerase / general stress sigma factor / pyrophosphate release / TRANSFERASE-DNA-RNA complex
Function / homology
Function and homology information


bacterial-type RNA polymerase core enzyme binding / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / sigma factor activity / bacterial-type flagellum-dependent cell motility ...bacterial-type RNA polymerase core enzyme binding / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / sigma factor activity / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
RNA polymerase sigma factor RpoS / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit ...RNA polymerase sigma factor RpoS / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Sigma-70 factors family signature 1. / RNA Polymerase Alpha Subunit; Chain A, domain 2 / 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 / Gyrase A; domain 2 / 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, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHATE / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsLiu, B. / Zuo, Y. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structures of E. coli sigma S-transcription initiation complexes provide new insights into polymerase mechanism.
Authors: Liu, B. / Zuo, Y. / Steitz, T.A.
History
DepositionMar 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoS
1: synthetic nontemplate strand DNA (50-MER)
2: synthetic template strand DNA (50-MER)
3: nascent RNA 4-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,55514
Polymers441,2019
Non-polymers3535
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53210 Å2
ΔGint-261 kcal/mol
Surface area143510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.710, 152.671, 226.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 6 - 232 / Label seq-ID: 13 - 239

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

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

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


Mass: 26899.572 Da / Num. of mol.: 2 / Fragment: UNP residues 1-235
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 / Polymerase / 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, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8V2, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / 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 / Polymerase / 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

-
DNA chain , 2 types, 2 molecules 12

#6: DNA chain synthetic nontemplate strand DNA (50-MER)


Mass: 15329.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain synthetic template strand DNA (50-MER)


Mass: 15547.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein / RNA chain , 2 types, 2 molecules F3

#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 (E. coli) / Gene: rpoS, appR, katF, nur, otsX, sigS, b2741, JW5437 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13445
#8: RNA chain nascent RNA 4-mer


Mass: 1440.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 5 molecules

#9: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: PEG3350, sodium chloride, HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 14, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.6→126.632 Å / Num. obs: 50952 / % possible obs: 99.6 % / Redundancy: 5.1 % / Net I/σ(I): 9.87
Reflection shellHighest resolution: 3.6 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→126.63 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 164.132 / SU ML: 0.951 / Cross valid method: THROUGHOUT / ESU R Free: 0.791 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29326 2560 4.8 %RANDOM
Rwork0.2471 ---
obs0.24936 50952 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 203.582 Å2
Baniso -1Baniso -2Baniso -3
1--11.21 Å20 Å20 Å2
2--7.49 Å20 Å2
3---3.72 Å2
Refinement stepCycle: LAST / Resolution: 3.6→126.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26167 1452 13 0 27632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01928186
X-RAY DIFFRACTIONr_bond_other_d0.0020.0226896
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9338366
X-RAY DIFFRACTIONr_angle_other_deg0.843361889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75853320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.19323.9981263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73154920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.57615255
X-RAY DIFFRACTIONr_chiral_restr0.0770.24288
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.02130843
X-RAY DIFFRACTIONr_gen_planes_other0.020.026159
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.19516.4313301
X-RAY DIFFRACTIONr_mcbond_other6.19416.4313300
X-RAY DIFFRACTIONr_mcangle_it10.01327.72416614
X-RAY DIFFRACTIONr_mcangle_other10.01327.72416615
X-RAY DIFFRACTIONr_scbond_it6.6817.21114885
X-RAY DIFFRACTIONr_scbond_other6.67317.21114876
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.81228.85121740
X-RAY DIFFRACTIONr_long_range_B_refined16.49142.944127594
X-RAY DIFFRACTIONr_long_range_B_other16.49142.944127582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27680 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.531 182 -
Rwork0.535 3742 -
obs--99.64 %
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)
15.09990.5297-2.17054.024-0.48058.555-0.1284-0.4508-0.7686-0.0663-0.0163-0.66150.32540.85170.14470.960.2852-0.15810.22250.10240.86652.101-18.5883.849
210.72911.4128-0.51812.30620.90311.3550.0893-0.3026-0.66820.10640.1732-0.10940.6653-0.0131-0.26251.30710.0536-0.06740.21820.380.7625-31.885-32.5946.98
39.83914.51470.4745.3906-3.31474.08940.5205-0.7417-0.26910.4056-0.4386-0.55790.06140.458-0.0821.23640.1119-0.16671.063-0.20851.455430.5932.6820.451
44.2915-0.06180.52291.25980.0421.3222-0.1724-0.53450.38420.4620.1882-0.0461-0.03950.08-0.01581.01430.1469-0.08770.1122-0.06490.0429-29.518.125-0.437
52.813-0.39480.14173.755-0.23633.0863-0.05810.72750.1922-0.46550.1716-0.53310.03450.8152-0.11350.8008-0.02250.06380.439-0.08640.2352-17.4252.334-42.272
62.83891.02121.66971.1150.48046.25910.1526-0.398-0.96670.3017-0.07160.3330.3824-2.117-0.0811.7545-0.15850.1680.7580.06291.2034-59.651-30.422-4.501
73.0514-0.6915-2.42157.15196.41146.90120.1397-0.1303-0.54660.37870.442-1.0670.21520.2324-0.58171.77680.232-0.25870.8465-0.33461.2506-31.2-47.974-51.243
89.9646-1.08944.28732.106-0.06693.6153-0.11110.075-0.2607-0.32840.04081.0981-0.057-0.92660.07030.996-0.12760.13280.56750.03680.8537-76.5-3.935-18.392
96.58412.0931.71235.6349-1.50086.61380.02290.4443-1.1529-0.45180.1312-0.00310.76160.2765-0.15410.69920.16450.01570.1314-0.01170.291-70.32229.583-29.845
104.44540.1571.89815.90011.9437.990.0377-0.22710.74710.3628-0.00650.0198-0.9868-0.0001-0.03121.0490.13690.11630.24270.06450.2004-74.0762.752-27.683
117.70731.7247-1.09811.1910.38230.71550.48990.59611.1161-0.0556-0.2948-0.1254-0.4457-0.3989-0.19511.6020.0451-0.12360.98560.27671.9222-28.51550.17-52.952
123.6165-0.04460.24822.1359-0.04881.54240.04210.1765-0.0402-0.329-0.08020.8838-0.0543-0.31590.03821.2857-0.0697-0.20120.2497-0.16650.468-63.128-2.352-55.471
132.83-1.35564.69614.97092.028112.02840.2084-0.6914-1.01350.3499-0.182.15840.82-1.6494-0.02830.8368-0.03320.02820.23770.04381.0174-39.235-2.117-25.25
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 51
2X-RAY DIFFRACTION1A179 - 235
3X-RAY DIFFRACTION1B6 - 51
4X-RAY DIFFRACTION1B179 - 233
5X-RAY DIFFRACTION2A52 - 178
6X-RAY DIFFRACTION3B52 - 178
7X-RAY DIFFRACTION4C3 - 28
8X-RAY DIFFRACTION4C146 - 152
9X-RAY DIFFRACTION4C445 - 455
10X-RAY DIFFRACTION4C517 - 831
11X-RAY DIFFRACTION4C1057 - 1241
12X-RAY DIFFRACTION4D501 - 790
13X-RAY DIFFRACTION5C1242 - 1320
14X-RAY DIFFRACTION5D343 - 500
15X-RAY DIFFRACTION5D791 - 942
16X-RAY DIFFRACTION5D1132 - 1153
17X-RAY DIFFRACTION5D1213 - 1317
18X-RAY DIFFRACTION5D1345 - 1376
19X-RAY DIFFRACTION5D1502 - 1503
20X-RAY DIFFRACTION5E2 - 80
21X-RAY DIFFRACTION5F220 - 244
22X-RAY DIFFRACTION6C832 - 891
23X-RAY DIFFRACTION6C912 - 1056
24X-RAY DIFFRACTION7C892 - 911
25X-RAY DIFFRACTION7F245 - 329
26X-RAY DIFFRACTION8C29 - 145
27X-RAY DIFFRACTION8C456 - 516
28X-RAY DIFFRACTION9C153 - 226
29X-RAY DIFFRACTION9C337 - 444
30X-RAY DIFFRACTION9143 - 50
31X-RAY DIFFRACTION10C227 - 336
32X-RAY DIFFRACTION11D1154 - 1212
33X-RAY DIFFRACTION12C1321 - 1342
34X-RAY DIFFRACTION12D15 - 342
35X-RAY DIFFRACTION12D1318 - 1344
36X-RAY DIFFRACTION12D1501
37X-RAY DIFFRACTION12F53 - 219
38X-RAY DIFFRACTION12127 - 42
39X-RAY DIFFRACTION12222 - 36
40X-RAY DIFFRACTION12151 - 59
41X-RAY DIFFRACTION1224 - 12
42X-RAY DIFFRACTION13213 - 21
43X-RAY DIFFRACTION13314 - 17

+
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