[English] 日本語
Yorodumi
- PDB-4gzz: Crystal structures of bacterial RNA Polymerase paused elongation ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gzz
TitleCrystal structures of bacterial RNA Polymerase paused elongation complexes
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA transcript
  • non-template DNA
  • template DNA
KeywordsTRANSCRIPTION/DNA-RNA HYBRID / RNA Polymerase / transcription / paused transcription elongation complex / transcriptional pausing / DNA directed RNA transcription' / TRANSCRIPTION-DNA-RNA HYBRID complex
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / 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 / cytoplasm
Similarity search - Function
: / DNA-directed RNA polymerase subunit beta', hybrid domain / 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 subunit beta', hybrid domain / 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, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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 Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit alpha / 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 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2927 Å
AuthorsWeixlbaumer, A. / Leon, K. / Landick, R. / Darst, S.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Structural basis of transcriptional pausing in bacteria.
Authors: Weixlbaumer, A. / Leon, K. / Landick, R. / Darst, S.A.
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.version
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
N: non-template DNA
R: RNA transcript
T: template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,44411
Polymers395,2898
Non-polymers1553
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37460 Å2
ΔGint-196 kcal/mol
Surface area128850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)286.549, 286.549, 199.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

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

#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpoA, TTHA1664 / Production host: Thermus thermophilus (bacteria) / Strain (production host): HB8 / 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpoB, TTHA1813 / Production host: Thermus thermophilus (bacteria) / Strain (production host): HB8 / 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: 172378.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: genomic copy of rpoC replaced by a C-terminal 10His tagged version
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpoC, TTHA1812 / Production host: Thermus thermophilus (bacteria) / Strain (production host): HB8 / 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpoZ, TTHA1561 / Production host: Thermus thermophilus (bacteria) / Strain (production host): HB8 / References: UniProt: Q8RQE7, DNA-directed RNA polymerase

-
DNA chain , 2 types, 2 molecules NT

#5: DNA chain non-template DNA


Mass: 4000.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#7: DNA chain template DNA


Mass: 6696.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)

-
RNA chain , 1 types, 1 molecules R

#6: RNA chain RNA transcript


Mass: 5131.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)

-
Non-polymers , 2 types, 3 molecules

#8: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 5-7% PEG 3000, 0.1M MES pH 6.1-6.3, 0.3M LiCl, 10mM MgCl2, vapor diffusion, hanging drop, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.91956 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91956 Å / Relative weight: 1
ReflectionResolution: 4→45 Å / Num. all: 52138 / Num. obs: 51877 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.442 / Net I/σ(I): 4.9
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
4-4.074.8197.7
4.07-4.145.9199.7
4.14-4.226199.5
4.22-4.316199.4
4.31-4.46199.5
4.4-4.56199.5
4.5-4.626199.6
4.62-4.746199.4
4.74-4.886199.4
4.88-5.046199.70.947
5.04-5.226199.70.859
5.22-5.436199.50.806
5.43-5.676199.80.751
5.67-5.976199.70.663
5.97-6.355.9199.70.565
6.35-6.835.9199.80.495
6.83-7.525.8199.70.451
7.52-8.65.7199.80.43
8.6-10.815.6199.70.887
10.81-455.9199.80.719

-
Phasing

PhasingMethod: molecular replacement
Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.11data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O5I

2o5i


Resolution: 4.2927→38.785 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.67 / σ(F): 1.96 / Phase error: 31.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2849 2070 5.02 %
Rwork0.2345 --
obs0.237 41266 99.01 %
all-41681 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 125.9191 Å2
Refinement stepCycle: LAST / Resolution: 4.2927→38.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23534 863 3 0 24400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524969
X-RAY DIFFRACTIONf_angle_d0.93433909
X-RAY DIFFRACTIONf_dihedral_angle_d16.3439678
X-RAY DIFFRACTIONf_chiral_restr0.0613835
X-RAY DIFFRACTIONf_plane_restr0.0054309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2927-4.39250.3641500.34632516X-RAY DIFFRACTION95
4.3925-4.50220.32911530.33172579X-RAY DIFFRACTION99
4.5022-4.62370.3351170.30422639X-RAY DIFFRACTION99
4.6237-4.75950.37251640.28612585X-RAY DIFFRACTION99
4.7595-4.91290.29511460.28452624X-RAY DIFFRACTION99
4.9129-5.08810.29781350.27362641X-RAY DIFFRACTION100
5.0881-5.29130.28881240.27612622X-RAY DIFFRACTION99
5.2913-5.53150.33721350.27462626X-RAY DIFFRACTION100
5.5315-5.82220.36691330.27162639X-RAY DIFFRACTION99
5.8222-6.18560.30491460.26032624X-RAY DIFFRACTION100
6.1856-6.6610.30881510.24182618X-RAY DIFFRACTION100
6.661-7.32730.27441430.21452649X-RAY DIFFRACTION100
7.3273-8.37820.25511260.18932598X-RAY DIFFRACTION99
8.3782-10.52070.23511240.18022648X-RAY DIFFRACTION99
10.5207-38.78670.25131230.21422588X-RAY DIFFRACTION98
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)
11.5699-0.44810.2751.2443-0.52461.6987-0.760.5218-0.81940.05550.17040.79520.2705-0.728-1.74980.3774-0.13410.12190.10510.70280.4208-166.498418.021868.3318
21.2254-0.19070.42921.95270.25611.3096-0.5483-0.19680.64320.08930.5629-0.6373-0.59280.43811.63371.17160.0973-0.61490.46520.40430.2829-131.819141.220282.4732
30.35120.13620.03220.5329-0.16910.1259-0.2261-0.38080.43090.45470.11790.079-0.5406-0.0105-0.02481.3647-0.0659-0.86551.05610.16990.9259-107.393328.5831111.8765
40.0384-0.0512-0.03910.12060.030.1118-0.496-0.02210.36980.67680.1451-0.33940.18160.2937-0.00191.0678-0.3482-0.291.40490.5921.6286-56.84386.1731116.7528
50.15320.1539-0.03480.21150.08960.4770.1954-0.4296-0.49340.4087-0.3011-0.20630.43490.42850.42641.33950.37910.63990.80270.7271.218-127.1923-22.065493.1461
60.1325-0.01270.02080.1764-0.11630.28090.2923-0.3412-0.22280.1371-0.0550.2532-0.02190.11540.41691.1220.0470.78530.95260.67881.1638-106.1131-17.358467.0582
70.15380.083-0.23950.1541-0.00770.4308-0.0759-0.4762-0.11180.27740.0517-0.21530.28170.34870.45151.32270.03810.56871.18350.54490.9278-150.07283.6108113.0662
80.03870.02740.00550.0390.02070.0391-0.05540.0735-0.15610.0436-0.06480.04350.00760.0201-0.01760.95170.13770.23350.83260.37860.4972-130.612216.910471.9573
90.02820.00970.00680.00410.00180.00190.0106-0.00780.00130.00240.0106-0.0043-0.0006-0.01760.00020.50530.06650.13170.3258-0.00190.5549-149.766634.749969.9858
100.0002-0.0008-0.0010.0054-0.00040.0039-0.03270.0659-0.0132-0.0244-0.0366-0.0008-0.0038-0.011801.01480.249-0.02520.8152-0.06290.646-113.951330.254293.4614
110.0014-00.00140.00110.00170.00260.01280.04560.017-0.06340.0028-0.0180.0068-0.038-01.03830.1894-0.33680.9217-0.03060.81-122.011525.631198.8068
120.0002-0.0019-0.00080.00350.00270.00150.014-0.02810.01020.0344-0.02860.0019-0.0206-0.0042-00.77920.3013-0.09131.10190.05890.8833-151.259412.802290.9153
130.0062-0.0014-0.00070.00030.00180.00360.02390.02020.01010.02590.04670.0087-0.01690.029501.14440.1688-0.16241.1616-0.22430.9612-138.324342.8575108.1553
140.0174-0.00580.01860.002-0.00640.01960.0144-0.0073-0.0102-0.01220.02140.0006-0.0113-0.0107-0.00010.78760.0677-0.02410.70490.13560.6429-126.766142.282998.0821
150.0166-0.00410.00970.0103-0.00760.0249-0.16450.1217-0.0011-0.0845-0.1465-0.34280.18770.3544-0.00044.2683-0.11040.29844.51090.03954.4632-100.065213.327482.1262
160.00990.0172-0.00550.0254-0.00740.01470.09590.0961-0.00330.016-0.01410.0119-0.07270.01560.00022.7974-0.2289-0.52742.4001-0.20072.3524-133.80178.047889.63
170.03480.0143-0.00010.01760.01530.02150.1144-0.0368-0.0056-0.10770.1108-0.0212-0.23080.05760.00032.9413-0.24690.61322.6840.41612.7615-135.53599.114793.4024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' ) or (chain 'B' ) or (chain 'C' and resseq 1:17) or (chain 'C' and resseq 394:700) or (chain 'C' and resseq 833:997) or (chain 'D' and resseq 783:1069)A7 - 229
2X-RAY DIFFRACTION1(chain 'A' ) or (chain 'B' ) or (chain 'C' and resseq 1:17) or (chain 'C' and resseq 394:700) or (chain 'C' and resseq 833:997) or (chain 'D' and resseq 783:1069)B7 - 229
3X-RAY DIFFRACTION1(chain 'A' ) or (chain 'B' ) or (chain 'C' and resseq 1:17) or (chain 'C' and resseq 394:700) or (chain 'C' and resseq 833:997) or (chain 'D' and resseq 783:1069)C1 - 17
4X-RAY DIFFRACTION1(chain 'A' ) or (chain 'B' ) or (chain 'C' and resseq 1:17) or (chain 'C' and resseq 394:700) or (chain 'C' and resseq 833:997) or (chain 'D' and resseq 783:1069)C394 - 700
5X-RAY DIFFRACTION1(chain 'A' ) or (chain 'B' ) or (chain 'C' and resseq 1:17) or (chain 'C' and resseq 394:700) or (chain 'C' and resseq 833:997) or (chain 'D' and resseq 783:1069)C833 - 997
6X-RAY DIFFRACTION1(chain 'A' ) or (chain 'B' ) or (chain 'C' and resseq 1:17) or (chain 'C' and resseq 394:700) or (chain 'C' and resseq 833:997) or (chain 'D' and resseq 783:1069)D783 - 1069
7X-RAY DIFFRACTION2(chain 'C' and resseq 1006:1071) or (chain 'D' and resseq 621:778) or (chain 'D' and resseq 1103:1432) or (chain 'D' and resseq 1473:1499) or (chain 'E' )C1006 - 1071
8X-RAY DIFFRACTION2(chain 'C' and resseq 1006:1071) or (chain 'D' and resseq 621:778) or (chain 'D' and resseq 1103:1432) or (chain 'D' and resseq 1473:1499) or (chain 'E' )D621 - 778
9X-RAY DIFFRACTION2(chain 'C' and resseq 1006:1071) or (chain 'D' and resseq 621:778) or (chain 'D' and resseq 1103:1432) or (chain 'D' and resseq 1473:1499) or (chain 'E' )D1103 - 1432
10X-RAY DIFFRACTION2(chain 'C' and resseq 1006:1071) or (chain 'D' and resseq 621:778) or (chain 'D' and resseq 1103:1432) or (chain 'D' and resseq 1473:1499) or (chain 'E' )D1473 - 1499
11X-RAY DIFFRACTION2(chain 'C' and resseq 1006:1071) or (chain 'D' and resseq 621:778) or (chain 'D' and resseq 1103:1432) or (chain 'D' and resseq 1473:1499) or (chain 'E' )E2 - 94
12X-RAY DIFFRACTION3(chain 'C' and resseq 1083:1112) or (chain 'D' and resseq 2:131) or (chain 'D' and resseq 455:605) or (chain 'D' and resseq 1444:1468)C1083 - 1112
13X-RAY DIFFRACTION3(chain 'C' and resseq 1083:1112) or (chain 'D' and resseq 2:131) or (chain 'D' and resseq 455:605) or (chain 'D' and resseq 1444:1468)D2 - 131
14X-RAY DIFFRACTION3(chain 'C' and resseq 1083:1112) or (chain 'D' and resseq 2:131) or (chain 'D' and resseq 455:605) or (chain 'D' and resseq 1444:1468)D455 - 605
15X-RAY DIFFRACTION3(chain 'C' and resseq 1083:1112) or (chain 'D' and resseq 2:131) or (chain 'D' and resseq 455:605) or (chain 'D' and resseq 1444:1468)D1444 - 1468
16X-RAY DIFFRACTION4(chain 'D' and resseq 132:454)D132 - 454
17X-RAY DIFFRACTION5(chain 'C' and resseq 18:142) or (chain 'C' and resseq 332:393)C18 - 142
18X-RAY DIFFRACTION5(chain 'C' and resseq 18:142) or (chain 'C' and resseq 332:393)C332 - 393
19X-RAY DIFFRACTION6(chain 'C' and resseq 143:331)C143 - 331
20X-RAY DIFFRACTION7(chain 'C' and resseq 701:832)C701 - 832
21X-RAY DIFFRACTION8(chain 'D' and resseq 1070:1102)D0
22X-RAY DIFFRACTION9(chain 'D' and resseq 779:782)D779 - 782
23X-RAY DIFFRACTION10(chain 'D' and resseq 1433:1443)D0
24X-RAY DIFFRACTION11(chain 'D' and resseq 606:620)D606 - 620
25X-RAY DIFFRACTION12(chain 'C' and resseq 998:1005)C998 - 1005
26X-RAY DIFFRACTION13(chain 'C' and resseq 1072:1082)C0
27X-RAY DIFFRACTION14(chain 'D' and resseq 1469:1472)D0
28X-RAY DIFFRACTION15(chain 'N' ) or (chain 'T' and resseq 1:13)N0
29X-RAY DIFFRACTION16chain 'R'R21 - 29
30X-RAY DIFFRACTION17chain 'T' and resseq 14:22T14 - 22

+
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