[English] 日本語
Yorodumi
- PDB-6kqd: Thermus thermophilus initial transcription complex comprising sig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kqd
TitleThermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 3 nt
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*GP*G)-3')
  • DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G*)-3')
  • RNA (5'-R(*GP*GP*A)-3')
  • RNA polymerase sigma factor SigA
KeywordsTRANSCRIPTION / Thermus thermophilus / RNA polymerase / initiation transcription complex / 3nt RNA
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
: / DNA-directed RNA polymerase subunit beta', hybrid domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit ...: / DNA-directed RNA polymerase subunit beta', hybrid domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / Beta Complex / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZhang, Y. / Li, L. / Ebright, R.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Authors: Li, L. / Molodtsov, V. / Lin, W. / Ebright, R.H. / Zhang, Y.
History
DepositionAug 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_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 SigA
G: DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*GP*G)-3')
H: DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G*)-3')
I: RNA (5'-R(*GP*GP*A)-3')
K: DNA-directed RNA polymerase subunit alpha
L: DNA-directed RNA polymerase subunit alpha
M: DNA-directed RNA polymerase subunit beta
N: DNA-directed RNA polymerase subunit beta'
O: DNA-directed RNA polymerase subunit omega
P: RNA polymerase sigma factor SigA
Q: DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*GP*G)-3')
R: DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G*)-3')
S: RNA (5'-R(*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)890,49731
Polymers889,37018
Non-polymers1,12613
Water1,928107
1
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 SigA
G: DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*GP*G)-3')
H: DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G*)-3')
I: RNA (5'-R(*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,26016
Polymers444,6859
Non-polymers5757
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53770 Å2
ΔGint-237 kcal/mol
Surface area141950 Å2
MethodPISA
2
K: DNA-directed RNA polymerase subunit alpha
L: DNA-directed RNA polymerase subunit alpha
M: DNA-directed RNA polymerase subunit beta
N: DNA-directed RNA polymerase subunit beta'
O: DNA-directed RNA polymerase subunit omega
P: RNA polymerase sigma factor SigA
Q: DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*GP*G)-3')
R: DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G*)-3')
S: RNA (5'-R(*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,23615
Polymers444,6859
Non-polymers5516
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53950 Å2
ΔGint-232 kcal/mol
Surface area141310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.501, 104.044, 297.441
Angle α, β, γ (deg.)90.000, 98.500, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABKLCMDNEO

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


Mass: 35056.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHR6, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 125436.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE8, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11533.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE7, DNA-directed RNA polymerase

-
DNA chain , 2 types, 4 molecules GQHR

#6: DNA chain DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*GP*G)-3')


Mass: 6440.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G*)-3')


Mass: 8421.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein / RNA chain , 2 types, 4 molecules FPIS

#5: Protein RNA polymerase sigma factor SigA


Mass: 50769.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: sigA, TTHA0532 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SKW1
#8: RNA chain RNA (5'-R(*GP*GP*A)-3')


Mass: 974.660 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 120 molecules

#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#10: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#11: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Magnesium chloride, 0.2 M Potassium chloride, 0.1 M Tris-HCl pH 8.0, 10% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.3→45 Å / Num. obs: 155222 / % possible obs: 91.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.092 / Χ2: 1.006 / Net I/σ(I): 7.1 / Num. measured all: 433949
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.3-3.362.70.5179320.901193.6
3.36-3.422.70.44577760.881193.3
3.42-3.482.70.38879310.897193.4
3.48-3.552.70.33578190.914193.1
3.55-3.632.80.28278300.954193.2
3.63-3.722.80.23678640.958192.9
3.72-3.812.80.19777640.955192.6
3.81-3.912.80.16677860.944192.7
3.91-4.032.80.13378550.982192.5
4.03-4.162.80.10977900.99192.3
4.16-4.312.80.09577441.009191.9
4.31-4.482.80.08177271.016191.8
4.48-4.682.80.07377301.043191.4
4.68-4.932.80.0777521.069191.3
4.93-5.242.80.07276981.018190.8
5.24-5.642.80.07676611.128190.4
5.64-6.212.90.07776921.15190
6.21-7.12.80.05976131.087189.3
7.1-8.942.80.0475911.071188.6
8.94-452.90.03276671.121187

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G7H

4g7h


Resolution: 3.3→44.351 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.02
RfactorNum. reflection% reflection
Rfree0.2499 1337 0.86 %
Rwork0.2067 --
obs0.207 154582 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 218.5 Å2 / Biso mean: 83.0623 Å2 / Biso min: 18.36 Å2
Refinement stepCycle: final / Resolution: 3.3→44.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55228 1770 55 107 57160
Biso mean--97.03 58.93 -
Num. residues----7060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.41790.31231330.28821536492
3.4179-3.55470.28561380.26711556793
3.5547-3.71640.34861370.25451553793
3.7164-3.91220.26521350.23131539593
3.9122-4.15720.27381350.20551545892
4.1572-4.47790.2521340.18991532492
4.4779-4.9280.23861350.17751530491
4.928-5.63980.22211330.19191522691
5.6398-7.10090.24461310.20991514490
7.1009-44.3510.19471260.17441492687

+
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