RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase III / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / positive regulation of innate immune response / RNA polymerase III complex ...RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase III / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / positive regulation of innate immune response / RNA polymerase III complex / positive regulation of interferon-beta production / DNA-directed 5'-3' RNA polymerase activity / single-stranded DNA binding / defense response to virus / innate immune response / DNA-templated transcription / nucleoplasm / cytosol Similarity search - Function
Helix Hairpins - #1450 / RNA polymerase III Rpc82, C -terminal / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase III subunit RPC82 / DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 helix-turn-helix domain / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Helix Hairpins - #1450 / RNA polymerase III Rpc82, C -terminal / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase III subunit RPC82 / DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 helix-turn-helix domain / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
DNA-DIRECTEDRNAPOLYMERASEIIISUBUNITRPC3 / RNA POLYMERASE III SUBUNIT C3 / DNA-DIRECTED RNA POLYMERASE III SUBUNIT C / RNA POLYMERASE III 62 ...RNA POLYMERASE III SUBUNIT C3 / DNA-DIRECTED RNA POLYMERASE III SUBUNIT C / RNA POLYMERASE III 62 KDA SUBUNIT / RPC62 / HRPC62
Mass: 60692.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9BUI4
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.98 Å / Relative weight: 1
Reflection
Resolution: 2.8→45 Å / Num. obs: 19023 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5.26 % / Biso Wilson estimate: 74.74 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1
Reflection shell
Resolution: 2.8→2.9 Å / Redundancy: 5.19 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 98.2
-
Processing
Software
Name
Version
Classification
BUSTER
2.9.1
refinement
XDS
datareduction
SCALEPACK
datascaling
SHELXD
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.8→43.13 Å / SU R Cruickshank DPI: 0.428 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.398 / SU Rfree Blow DPI: 0.265 / SU Rfree Cruickshank DPI: 0.274
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2298
943
4.96 %
RANDOM
Rwork
0.1884
-
-
-
obs
0.1905
18071
99.52 %
-
Displacement parameters
Biso mean: 101.77 Å2
Baniso -1
Baniso -2
Baniso -3
1-
15.2132 Å2
0 Å2
-6.6746 Å2
2-
-
2.4813 Å2
0 Å2
3-
-
-
-17.6945 Å2
Refine analyze
Luzzati coordinate error obs: 0.553 Å
Refinement step
Cycle: LAST / Resolution: 2.8→43.13 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3436
0
0
13
3449
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
3480
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.11
4690
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1277
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
94
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
494
HARMONIC
5
X-RAY DIFFRACTION
t_it
3480
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.25
X-RAY DIFFRACTION
t_other_torsion
20.91
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
470
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
4036
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.8→2.95 Å / Total num. of bins used: 10
Rfactor
Num. reflection
% reflection
Rfree
0.2632
132
4.86 %
Rwork
0.2154
2586
-
all
0.2177
2718
-
obs
-
-
99.52 %
Refinement TLS params.
Method: refined / Origin x: 47.0892 Å / Origin y: -1.4398 Å / Origin z: 30.3491 Å
11
12
13
21
22
23
31
32
33
T
-0.2954 Å2
0.0916 Å2
0.1513 Å2
-
-0.3579 Å2
-0.0637 Å2
-
-
0.0648 Å2
L
3.4282 °2
0.1952 °2
-0.5106 °2
-
1.7799 °2
-0.5853 °2
-
-
1.3194 °2
S
0.142 Å °
0.1542 Å °
-0.1981 Å °
-0.1182 Å °
-0.1945 Å °
0.2478 Å °
0.1897 Å °
0.3874 Å °
0.0525 Å °
Refinement TLS group
Selection details: CHAIN A
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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