[English] 日本語
Yorodumi
- PDB-4i3h: A three-gate structure of topoisomerase IV from Streptococcus pne... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i3h
TitleA three-gate structure of topoisomerase IV from Streptococcus pneumoniae
Components
  • DNA (5'-D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*AP*AP*TP*CP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*AP*TP*TP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*CP*CP*GP*CP*CP*TP*TP*TP*G)-3')
  • Topoisomerase IV subunit B, DNA topoisomerase 4 subunit A chimera
KeywordsISOMERASE/DNA / DNA unwinding / supercoiling / ISOMERASE-DNA complex
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / Rossmann fold - #670 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / Rossmann fold - #670 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Toprim domain profile. / TOPRIM domain / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA topoisomerase 4 subunit A / DNA topoisomerase 4 subunit B / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsLaponogov, I. / Veselkov, D.A. / Pan, X.-S. / Crevel, I. / Fisher, L.M. / Sanderson, M.R.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.
Authors: Laponogov, I. / Veselkov, D.A. / Crevel, I.M. / Pan, X.S. / Fisher, L.M. / Sanderson, M.R.
History
DepositionNov 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Dec 4, 2013Group: Database references
Revision 1.3Jul 26, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.4Sep 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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
E: DNA (5'-D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*AP*AP*TP*CP*AP*GP*G)-3')
F: DNA (5'-D(*CP*CP*TP*GP*AP*TP*TP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*CP*CP*GP*CP*CP*TP*TP*TP*G)-3')
A: Topoisomerase IV subunit B, DNA topoisomerase 4 subunit A chimera
B: Topoisomerase IV subunit B, DNA topoisomerase 4 subunit A chimera
G: DNA (5'-D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*AP*AP*TP*CP*AP*GP*G)-3')
H: DNA (5'-D(*CP*CP*TP*GP*AP*TP*TP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*CP*CP*GP*CP*CP*TP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,5569
Polymers298,4836
Non-polymers733
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.600, 160.600, 280.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsAsymmetric unit consists of one biological dimer formed by two chains: A and B

-
Components

#1: DNA chain DNA (5'-D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*AP*AP*TP*CP*AP*GP*G)-3')


Mass: 10525.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: V-site DNA
#2: DNA chain DNA (5'-D(*CP*CP*TP*GP*AP*TP*TP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*CP*CP*GP*CP*CP*TP*TP*TP*G)-3')


Mass: 10391.674 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: V-site DNA
#3: Protein Topoisomerase IV subunit B, DNA topoisomerase 4 subunit A chimera


Mass: 128323.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: parE, parC / Production host: Escherichia coli (E. coli)
References: UniProt: Q3HZ71, UniProt: D6ZLV0, UniProt: Q59961*PLUS, Isomerases; Other isomerases; Sole sub-subclass for isomerases that do not belong in the other subclasses, EC: 5.99.1.3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 4% isopropanol, 50 mM sodium citrate, 600 nL + 400 nL (protein + precipitant) drop ratio, VAPOR DIFFUSION, SITTING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 23, 2012
RadiationMonochromator: Single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.7→72.19 Å / Num. all: 39884 / Num. obs: 39884 / % possible obs: 99.75 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 12.11 % / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 3.1256
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 11.46 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.71 / % possible all: 100

-
Processing

Software
NameVersionClassification
GDEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RAE,1EI1

3rae

1ei1


Resolution: 3.7→71.823 Å / SU ML: 0.87 / σ(F): 1.34 / Phase error: 21.92 / Stereochemistry target values: ML
Details: The second DNA dimer (chains E&F) has two alternative orientations related by crystallographic symmetry.
RfactorNum. reflection% reflection
Rfree0.2485 2006 5.04 %
Rwork0.1855 --
obs0.1886 39825 99.69 %
all-39884 -
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.569 Å2 / ksol: 0.262 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.8718 Å20 Å2-0 Å2
2--7.8718 Å2-0 Å2
3----12.19 Å2
Refinement stepCycle: LAST / Resolution: 3.7→71.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14849 1374 3 2 16228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916631
X-RAY DIFFRACTIONf_angle_d1.39622931
X-RAY DIFFRACTIONf_dihedral_angle_d18.9035783
X-RAY DIFFRACTIONf_chiral_restr0.0872700
X-RAY DIFFRACTIONf_plane_restr0.0052783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.79250.2421490.18182649X-RAY DIFFRACTION100
3.7925-3.89510.24461390.17912672X-RAY DIFFRACTION100
3.8951-4.00970.2381540.1682636X-RAY DIFFRACTION100
4.0097-4.13910.23861290.16352683X-RAY DIFFRACTION100
4.1391-4.2870.23291350.15592655X-RAY DIFFRACTION100
4.287-4.45860.24421530.14682681X-RAY DIFFRACTION100
4.4586-4.66150.19231270.13982670X-RAY DIFFRACTION100
4.6615-4.90720.24781490.14682689X-RAY DIFFRACTION100
4.9072-5.21460.21141380.1642642X-RAY DIFFRACTION98
5.2146-5.61710.2691540.17732688X-RAY DIFFRACTION100
5.6171-6.18210.26281340.19722730X-RAY DIFFRACTION100
6.1821-7.07590.28411470.19572738X-RAY DIFFRACTION100
7.0759-8.91230.24521470.18232792X-RAY DIFFRACTION100
8.9123-71.83610.27291510.2552894X-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)
11.9102-0.8765-3.36981.35932.69848.64720.1163-0.59970.22490.1219-0.0393-0.1923-0.58140.301-0.01360.3896-0.0099-0.32580.54820.10880.393972.2768-48.804971.2692
21.21870.58180.75050.44610.27751.6576-0.0587-0.22790.19320.1034-0.32490.0425-0.56380.1070.07010.9625-0.3042-0.20031.1693-0.27110.321159.4517-36.001394.8546
30.4189-0.8910.58725.3937-1.66580.8717-0.3092-0.84750.11510.25550.33420.4664-0.1033-0.5034-0.05330.270.0859-0.02450.70170.33070.649267.6939-38.027639.2041
40.26550.3311-0.3140.4743-0.25110.67940.21390.01610.5123-0.09890.0602-0.3441-0.27430.0441-0.11010.22410.03240.18230.33290.24060.636870.8759-21.539530.0523
52.5508-0.23561.02292.31260.0882.0103-0.0428-0.31940.0409-0.2095-0.33010.6463-0.2484-0.61050.25350.34440.2303-0.16660.5201-0.05010.443855.4384-49.532950.0803
67.1572-1.3092-5.63341.15151.2614.4885-0.1283-1.3294-0.50020.36550.18490.39980.42130.2875-0.11780.7361-0.0063-0.34720.740.19650.592171.33-53.332383.9828
71.18411.17280.35573.22011.05612.4764-0.25080.2645-0.375-0.03050.23310.1792-0.0477-0.13020.01830.47890.2377-0.13880.636-0.16810.714955.5355-73.976422.8384
82.61310.0931.33031.58581.323.078-0.0209-0.0332-0.43540.0902-0.15040.1353-0.176-0.1036-0.20430.22880.0745-0.14350.53040.25650.465572.6902-64.746257.3981
91.7732-0.6639-0.28531.3284-0.33170.83690.16470.3367-0.2769-0.226-0.3509-0.36020.21770.43260.14130.21540.3052-0.24390.5617-0.06820.593274.5495-59.859741.579
103.0076-0.70073.95130.859-1.12876.444-0.0694-0.9055-0.49410.46360.34460.19560.257-0.2037-0.20150.5610.15470.23830.71170.01730.441524.1503-30.48477.2729
110.39770.0729-0.14291.1759-0.3542.2339-0.0154-0.111-0.03320.1722-0.2632-0.0240.187-0.1483-0.13030.9842-0.2707-0.1281.49260.22740.263743.1466-41.858897.2901
123.69040.1427-2.97736.87620.65883.1906-0.0514-0.1992-0.7716-0.14280.0723-1.12550.16561.0142-0.02120.31760.00070.11670.6448-0.18820.795119.7416-44.024445.5645
130.32940.95980.3263.51351.89221.57110.3956-0.0313-0.65250.45990.16480.0440.5515-0.4363-0.37530.5863-0.29360.02010.64880.09121.097914.7987-61.795239.3844
141.8291-0.4001-0.3981.428-0.68881.9765-0.0716-0.14020.1183-0.3758-0.2112-0.57190.39980.45990.24550.42190.24210.1670.48950.22110.474934.5558-31.915852.2403
151.2388-0.20141.60042.07280.34153.0039-0.4495-1.18330.41670.73160.3062-0.1201-0.4211-0.36320.12581.05770.25580.31611.047-0.11190.528327.4219-24.730687.5527
160.63150.36860.08192.13-0.73111.21520.06060.94640.4983-0.3007-0.00140.22380.03970.29980.00920.430.2710.11160.87760.48380.631826.8335-9.45924.246
172.8145-0.0625-0.17492.00830.44352.8325-0.1395-0.75010.61820.1160.00870.07490.2306-0.31290.13350.3280.13930.0460.5738-0.02160.410820.0351-15.867362.1065
182.2303-0.392-0.11911.06510.21141.25190.01830.22930.1131-0.061-0.11220.2581-0.0083-0.21260.13220.24680.19820.20350.43980.13960.534513.7668-21.92548.323
192.9349-3.724-1.46245.17691.51175.1744-0.1186-1.08150.46570.877-0.2178-1.3345-0.10541.32290.35180.59650.04-0.16341.65630.51750.87759.7942-19.222949.1705
205.183-1.6043-0.60772.22150.45851.60460.16960.6660.2235-0.2621-0.3909-0.1704-0.01330.20680.00530.3930.28610.19510.93950.25130.467476.4094-33.574824.9797
211.5831-0.2888-0.1471.5595-0.20230.83790.13040.32960.30690.0951-0.07060.1581-0.1145-0.0689-0.09130.17090.20820.12920.68790.34680.460857.228-21.564725.6753
221.5952-0.82921.92684.37940.22573.4754-0.08-1.4575-0.16210.66580.02571.3629-0.0021-1.08320.02520.41290.07990.05831.5754-0.37570.851128.6383-60.175352.7087
232.2842-0.28640.39390.3477-0.27280.67820.10720.0679-0.2509-0.0739-0.0250.1860.0839-0.08790.0920.28690.1475-0.2440.7457-0.19971.06287.8948-49.014434.668
242.634-0.4395-0.30961.8029-0.11960.81470.44270.0966-0.3608-0.2324-0.20790.25270.13190.0982-0.07450.130.2427-0.32280.4231-0.23620.598726.5927-61.542130.9116
254.89861.06-0.49840.2219-0.11180.02650.31021.7318-0.1392-0.4331-0.22060.3120.115-0.1288-0.09960.57970.3789-0.06071.15650.00180.695342.1001-41.489429.4742
261.2055-1.026-0.01732.2110.05242.76860.04-0.20270.15070.5084-0.3802-0.066-0.1364-0.78270.22690.49610.0054-0.17040.998-0.00590.147421.191527.634323.0567
272.6886-2.36890.65343.0139-0.04081.8935-0.1077-0.7153-0.53980.42470.3042-0.13230.36140.4709-0.17740.53390.26490.00960.85390.16670.590261.9114-111.643522.3869
281.4015-0.7720.27692.44710.21392.36430.13820.260.1495-0.2982-0.2647-0.03730.32280.61390.09920.55680.13860.01250.75610.40880.490941.12765.65594.6774
292.609-0.3977-0.75863.23340.08872.815-0.5705-0.2121-0.12480.31120.2110.0262-0.5991-0.33280.33160.63360.1782-0.22990.60870.01690.603738.7171-89.26478.4458
302.24530.96073.88230.91381.7676.7316-0.15040.09630.8775-0.03080.62240.0053-0.0358-0.0549-0.44051.96290.14280.1841.6066-0.0271.393679.1371-79.825266.0498
312.40721.2409-3.94070.6392-2.02486.4598-0.2205-0.0292-0.95110.03970.4705-0.0675-0.0076-0.1274-0.2961.80020.1587-0.14251.49820.07061.476381.6578-80.895866.0264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain "A" and resseq 1343:1382A1343 - 1382
2X-RAY DIFFRACTION2chain "A" and resseq 1383:1429A1383 - 1429
3X-RAY DIFFRACTION3chain "A" and resseq 1018:1030A1018 - 1030
4X-RAY DIFFRACTION4chain "A" and resseq 1003:1017A1003 - 1017
5X-RAY DIFFRACTION5chain "A" and resseq 1031:1154A1031 - 1154
6X-RAY DIFFRACTION6chain "A" and resseq 1430:1455A1430 - 1455
7X-RAY DIFFRACTION7chain "A" and resseq 1239:1322A1239 - 1322
8X-RAY DIFFRACTION8chain "A" and resseq 1456:1482A1456 - 1482
9X-RAY DIFFRACTION9chain "A" and ( resseq 1155:1238 or resseq 1323:1342 or resseq 1483:1484 or resid 1700 or resid 1901 )A1155 - 1238
10X-RAY DIFFRACTION9chain "A" and ( resseq 1155:1238 or resseq 1323:1342 or resseq 1483:1484 or resid 1700 or resid 1901 )A1323 - 1342
11X-RAY DIFFRACTION9chain "A" and ( resseq 1155:1238 or resseq 1323:1342 or resseq 1483:1484 or resid 1700 or resid 1901 )A1483 - 1484
12X-RAY DIFFRACTION10chain "B" and resseq 1343:1382B1343 - 1382
13X-RAY DIFFRACTION11chain "B" and resseq 1383:1429B1383 - 1429
14X-RAY DIFFRACTION12chain "B" and resseq 1018:1030B1018 - 1030
15X-RAY DIFFRACTION13chain "B" and resseq 1002:1017B1002 - 1017
16X-RAY DIFFRACTION14chain "B" and resseq 1031:1154B1031 - 1154
17X-RAY DIFFRACTION15chain "B" and resseq 1430:1455B1430 - 1455
18X-RAY DIFFRACTION16chain "B" and resseq 1239:1322B1239 - 1322
19X-RAY DIFFRACTION17chain "B" and resseq 1456:1482B1456 - 1482
20X-RAY DIFFRACTION18chain "B" and ( resseq 1155:1238 or resseq 1323:1342 or resseq 1483:1484 or resid 1700 )B1155 - 1238
21X-RAY DIFFRACTION18chain "B" and ( resseq 1155:1238 or resseq 1323:1342 or resseq 1483:1484 or resid 1700 )B1323 - 1342
22X-RAY DIFFRACTION18chain "B" and ( resseq 1155:1238 or resseq 1323:1342 or resseq 1483:1484 or resid 1700 )B1483 - 1484
23X-RAY DIFFRACTION19chain "A" and resseq 539:581A539 - 581
24X-RAY DIFFRACTION20chain "A" and resseq 610:634A610 - 634
25X-RAY DIFFRACTION21chain "A" and ( resseq 414:538 or resseq 582:609 or resseq 635:642 )A414 - 538
26X-RAY DIFFRACTION21chain "A" and ( resseq 414:538 or resseq 582:609 or resseq 635:642 )A582 - 609
27X-RAY DIFFRACTION21chain "A" and ( resseq 414:538 or resseq 582:609 or resseq 635:642 )A635 - 642
28X-RAY DIFFRACTION22chain "B" and resseq 539:581B539 - 581
29X-RAY DIFFRACTION23chain "B" and resseq 610:634B610 - 634
30X-RAY DIFFRACTION24chain "B" and ( resseq 414:538 or resseq 582:609 or resseq 635:640 )B414 - 538
31X-RAY DIFFRACTION24chain "B" and ( resseq 414:538 or resseq 582:609 or resseq 635:640 )B582 - 609
32X-RAY DIFFRACTION24chain "B" and ( resseq 414:538 or resseq 582:609 or resseq 635:640 )B635 - 640
33X-RAY DIFFRACTION25chain "G" or chain "H"G8 - 27
34X-RAY DIFFRACTION26chain A and resid 24:220A24 - 220
35X-RAY DIFFRACTION27chain B and resid 20:220B20 - 220
36X-RAY DIFFRACTION28chain A and resid 221:396A221 - 396
37X-RAY DIFFRACTION29chain B and resid 221:396B221 - 396
38X-RAY DIFFRACTION30chain EE2 - 15
39X-RAY DIFFRACTION31chain FF2 - 15

+
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