[English] 日本語
Yorodumi
- PDB-6u08: Double-stranded DNA-specific cytidine deaminase type VI secretion... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u08
TitleDouble-stranded DNA-specific cytidine deaminase type VI secretion system effector and cognate immunity complex from Burkholderia cenocepacia
Components
  • DddI
  • Double-stranded DNA-specific cytidine deaminase
KeywordsTOXIN / type VI secretion system / immunity / deaminase
Function / homology
Function and homology information


membrane => GO:0016020 / membrane / metal ion binding
Similarity search - Function
Double-stranded DNA deaminase immunity protein DddI / Immunity protein Imm1 / Double-stranded DNA deaminase toxin A / Double-stranded DNA deaminase toxin A / Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / PAAR motif / PAAR motif ...Double-stranded DNA deaminase immunity protein DddI / Immunity protein Imm1 / Double-stranded DNA deaminase toxin A / Double-stranded DNA deaminase toxin A / Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / PAAR motif / PAAR motif / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / :
Similarity search - Domain/homology
DUF6531 domain-containing protein / YD repeat (Two copies) / Immunity protein Imm1
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.491 Å
AuthorsBosch, D.E. / de Moraes, M.M.H. / Mougous, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI080609 United States
CitationJournal: Nature / Year: 2020
Title: A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing.
Authors: Mok, B.Y. / de Moraes, M.H. / Zeng, J. / Bosch, D.E. / Kotrys, A.V. / Raguram, A. / Hsu, F. / Radey, M.C. / Peterson, S.B. / Mootha, V.K. / Mougous, J.D. / Liu, D.R.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 5, 2020Group: Database references / Derived calculations / Category: citation / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Double-stranded DNA-specific cytidine deaminase
B: DddI
C: Double-stranded DNA-specific cytidine deaminase
D: DddI
E: Double-stranded DNA-specific cytidine deaminase
F: DddI
G: Double-stranded DNA-specific cytidine deaminase
H: DddI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,09512
Polymers131,8338
Non-polymers2624
Water1,60389
1
A: Double-stranded DNA-specific cytidine deaminase
B: DddI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0243
Polymers32,9582
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-47 kcal/mol
Surface area11120 Å2
MethodPISA
2
C: Double-stranded DNA-specific cytidine deaminase
D: DddI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0243
Polymers32,9582
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-47 kcal/mol
Surface area11120 Å2
MethodPISA
3
E: Double-stranded DNA-specific cytidine deaminase
F: DddI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0243
Polymers32,9582
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-47 kcal/mol
Surface area11310 Å2
MethodPISA
4
G: Double-stranded DNA-specific cytidine deaminase
H: DddI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0243
Polymers32,9582
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-49 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.760, 144.953, 64.186
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Double-stranded DNA-specific cytidine deaminase


Mass: 18890.197 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: A8E72_33435 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V2VU04, UniProt: A0A1V6L4E7*PLUS
#2: Protein
DddI


Mass: 14068.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: A8E72_33440, UE95_03835 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V6L5G6
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.1 M Bis-Tris:Hcl pH 6.5, 200 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.491→38.603 Å / Num. obs: 78988 / % possible obs: 98.9 % / Redundancy: 13 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 32.7
Reflection shellResolution: 2.491→2.53 Å / Redundancy: 12.6 % / Num. unique obs: 1339 / CC1/2: 0.865 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.491→38.603 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2275 3778 4.78 %
Rwork0.1718 75210 -
obs0.1745 78988 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.95 Å2 / Biso mean: 59.1849 Å2 / Biso min: 25.68 Å2
Refinement stepCycle: final / Resolution: 2.491→38.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7796 0 4 89 7889
Biso mean--172.24 50.7 -
Num. residues----1017
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4914-2.52290.33871350.2661265496
2.5229-2.55610.35871370.2684276197
2.5561-2.59110.34171450.2558279899
2.5911-2.62810.30921410.24322793100
2.6281-2.66740.28811390.2411274197
2.6674-2.7090.26431360.2358275999
2.709-2.75340.32971430.23432845100
2.7534-2.80090.33371350.2316271397
2.8009-2.85180.34441430.22442798100
2.8518-2.90670.31131450.2123278898
2.9067-2.9660.32951340.2241279199
2.966-3.03040.26161410.20642808100
3.0304-3.10090.25321390.2096274698
3.1009-3.17840.22671400.19992821100
3.1784-3.26430.25861410.1849277498
3.2643-3.36030.24971480.1892280899
3.3603-3.46870.23861390.1847276499
3.4687-3.59260.22551400.1617279599
3.5926-3.73630.21631410.16092820100
3.7363-3.90620.19191410.1523277499
3.9062-4.11190.21721390.1424280999
4.1119-4.36920.15861380.1264279999
4.3692-4.7060.14981400.11542804100
4.706-5.17860.18051350.12172806100
5.1786-5.92570.19851430.14962817100
5.9257-7.45690.20921380.17312819100
7.4569-38.6030.22271420.1729280599
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)
13.76340.2309-2.00588.16861.81613.2828-0.30720.4860.0632-0.51990.29211.02990.2151-0.31020.05540.4409-0.0501-0.0880.38490.09640.348121.628761.70480.1405
21.41051.79770.50129.01423.47093.9385-0.17370.4578-0.02890.68590.3395-0.34810.23310.4763-0.08830.321-0.03020.04350.32190.04030.294929.397455.942584.5255
35.59641.0236-2.93846.6862-1.09222.1148-0.01750.0434-0.1385-0.4742-0.0225-0.04070.23660.39840.03530.5212-0.0114-0.08210.49060.13760.480638.93566.33481.6028
42.8835-0.47120.05580.34940.27555.67540.21210.3255-0.1234-0.2389-0.10880.29030.2672-0.336-0.22240.3723-0.0584-0.00380.3110.09030.415127.800164.78276.978
56.39692.40522.89245.0387-2.07954.34730.39530.0285-0.1908-0.0277-0.1081-0.61850.51460.5492-0.20550.64770.09950.05880.53750.00790.481636.511863.719472.3449
65.2196-2.3499-1.53173.2539-2.38867.0884-0.35950.27670.3716-1.27940.82650.81090.2645-1.3731-0.25910.36090.004-0.13970.50590.10820.538722.549574.643470.9596
73.4784-0.4683-2.94996.63020.40433.19980.13560.69360.0969-0.76-0.1957-0.42230.75620.28080.05460.60540.03110.07940.43150.03460.292637.477965.386771.0319
85.95751.66020.8983.02970.98483.62250.37680.91340.0782-1.2134-0.3835-0.214-0.4904-0.3948-0.21950.97650.14810.01490.48080.13330.70929.969389.191666.1014
96.54662.47450.0245.4305-3.83933.28710.4406-0.37611.20840.8220.49930.4743-1.5788-0.5562-0.91780.82930.04820.20370.35060.09810.57235.991496.299168.4276
109.59175.0697-7.17949.3659-6.55766.47990.4180.1264-0.43290.39630.1101-0.2194-0.8951-0.55-0.49340.9850.02920.2890.4162-0.0650.502732.127391.868980.9255
113.14270.90140.86494.18435.01465.96160.1803-0.11970.23480.774-0.07250.5597-0.5569-0.3138-0.4830.63820.02490.05660.24880.07860.418734.448785.833171.9336
126.60193.8722-3.28571.9979-4.07712.2271-0.36940.6572-0.5457-0.97630.6581.251-0.3192-0.6462-0.48650.8955-0.0187-0.03990.430.08880.421633.864479.038860.1863
138.13280.7205-0.0626.2116-1.82478.36990.2860.0260.07890.1674-0.4091-0.1123-0.59890.1480.15930.5499-0.03880.06250.38110.04980.331440.825783.176673.7317
148.14324.2242.05212.35870.61916.94210.13570.5936-0.4105-0.2707-0.3738-0.8063-0.18241.2890.32010.5219-0.02360.07610.50770.08340.628544.960574.674267.4623
152.4857-2.6558-2.39535.1863-0.24655.11360.2833-1.2464-0.46950.9272-0.0354-0.1707-0.13830.531-0.17290.6328-0.1119-0.06290.42640.04680.411638.846382.325183.0602
162.2754-0.37061.27382.278-0.99964.5515-0.0987-0.8111-0.31180.5914-0.514-0.7179-0.41881.33140.53110.569-0.2372-0.01560.5980.11720.475344.480681.284482.2442
173.831-0.53031.56673.9532-0.5245.90870.3928-0.58220.36960.1291-0.6495-0.68690.68030.31560.0810.8226-0.07860.18060.51130.16540.711444.122291.015267.2767
185.4479-1.08072.12824.0751-5.68438.0651-0.08150.3358-0.2612-1.2624-0.3637-1.3891-0.53170.61880.24950.67140.02020.19490.44120.03020.677548.878381.344266.2722
195.97660.02750.87783.4386-0.77663.89870.3642-0.45570.8250.5233-0.228-0.0722-0.50360.0832-0.08140.4755-0.08750.10980.3722-0.00250.376612.094352.181148.3689
203.98764.3291-1.83663.6927-0.7932.68140.171-0.3466-0.38920.2197-0.3419-0.03760.2040.09350.12870.4015-0.00020.0750.3862-0.02940.399312.06138.900245.8831
213.7912-1.58740.04047.74750.84634.57840.1288-0.40610.35460.0872-0.01720.0196-0.36330.1019-0.16050.3996-0.04950.07130.28-0.01160.24359.921345.189851.1232
224.6006-1.3439-3.30956.69732.40013.1531-0.2006-0.0524-0.6374-0.22430.03620.0688-0.03470.33530.14230.4077-0.0063-0.030.4880.06370.400710.485837.309656.3171
236.1546-4.1294-2.19566.5774-2.95467.74940.6754-0.46670.6934-0.11480.07040.1549-0.44560.1519-0.74910.6740.07130.31230.34220.0190.5255-0.812150.877857.4154
244.33060.1386-0.03395.3967-0.86523.0118-0.422-0.4803-0.45320.78980.23410.13190.27280.59730.19810.5145-0.01820.09170.63050.06980.37118.706336.326357.6012
250.91520.20050.24923.40090.77042.51830.3142-0.12910.23630.45040.03430.9247-0.1729-1.0816-0.22430.39130.0550.11321.04850.03830.7877-17.763940.683458.5566
267.26430.41560.26824.4522-2.16666.89890.2538-0.04240.25060.03640.06280.5286-0.0995-0.8373-0.22530.2533-0.0830.09020.5384-0.00740.4429-9.572936.949758.4614
273.2718-1.90920.41791.09810.82866.90820.0846-0.17040.0113-0.0133-0.1183-0.18050.4794-0.14130.09940.4121-0.16250.05560.56030.08690.3998-4.341127.664556.2874
283.2129-1.94052.83812.0792-0.46215.9136-0.29540.68870.02160.04150.6690.41280.018-0.7575-0.14910.4053-0.07420.03980.71490.06380.541-8.296939.054544.5138
292.65252.3643-2.79916.86420.61315.5547-0.68440.8753-0.771-0.76540.1308-0.35771.3562-1.50570.58830.6074-0.19440.01750.5687-0.10460.4475-6.659828.619846.2472
302.62470.18642.00552.29331.83152.78740.02260.3959-0.1877-0.30560.12990.26640.1262-0.8334-0.39580.5391-0.2150.16480.83760.05980.7363-16.566328.836461.0149
317.3808-4.7433-5.28343.7613.9234.0933-0.6503-0.7152-1.40360.25830.32250.91150.92080.01710.43020.7007-0.09510.11790.55610.12850.5918-6.875224.331962.3426
323.19670.88960.68166.9323-0.36612.69840.4622-0.10950.46680.420.06860.9654-1.131-0.584-0.39840.6090.07340.21250.41910.09890.537219.900870.171135.0208
336.658-5.57690.54458.40073.22844.36490.0102-0.08850.96370.14080.2795-0.5409-1.20760.1234-0.32430.62460.01770.13290.33110.05940.467925.120478.337530.9392
348.8063-2.6571.56426.8149-1.5085.8080.0619-0.4390.45410.5652-0.109-0.2866-0.83430.7514-0.02320.5448-0.22370.03620.54610.03920.494437.905571.224934.3358
353.94840.96360.76013.9004-1.76985.0086-0.0062-0.21860.65730.6783-0.0481-0.2474-1.16130.33010.07080.6585-0.10120.08360.4236-0.04830.469331.281271.934541.1484
361.27081.3409-1.32678.3759-3.71442.82460.5173-0.2103-0.34140.37950.08960.8106-0.184-0.5807-0.420.3429-0.02640.09330.52350.06860.362524.906958.213644.7262
372.9494-2.62761.60473.1192-0.89121.2293-0.0837-0.25710.12310.98590.26480.7629-1.59950.202-0.03070.9139-0.04750.17430.5378-0.10480.459927.770868.67147.1248
383.8481-0.5110.35080.7597-0.06621.79230.01170.09111.60180.59370.6105-1.5273-0.71551.1514-0.31780.87-0.279-0.27210.78840.00030.929445.338876.027141.7999
392.16620.62471.04065.5611-1.46596.4376-0.0946-0.4492-0.120.75-0.3767-0.8649-0.1530.75980.18330.55130.035-0.06990.63950.10620.61437.140946.79949.3472
401.9417-4.28812.42829.4134-5.37163.08750.20610.251-1.3026-0.6338-0.721-0.70990.97370.85780.42340.54390.1657-0.05180.571-0.05340.564344.771542.254946.863
416.23440.2953.61228.53042.45148.74290.61020.4441-0.6628-1.237-0.1503-0.59890.25070.8045-0.49570.43950.1416-0.10310.542-0.00990.371240.144948.184338.0746
426.52361.11553.23815.0719-0.90242.11530.036-0.6921.07811.25340.07651.19180.33681.46920.17010.54250.0049-0.0380.5526-0.02440.283137.907757.528354.3834
439.60094.38551.33356.9399-0.14682.03970.43060.80410.0533-0.0417-0.1345-0.72340.73761.3708-0.23670.36650.139-0.03310.53660.05730.338846.239854.233638.6282
446.1812-1.6456-4.77882.944-0.76455.93970.1001-0.44940.25230.0566-0.5839-0.1233-1.14790.37020.31530.7696-0.2692-0.26270.74040.00880.773345.150764.627348.9502
455.2126-1.55855.59250.756-1.43837.40190.2779-0.020.0921-0.6009-0.3695-1.4603-0.15373.47450.35680.6334-0.02160.0451.50740.19331.008856.991462.234833.5758
465.04286.4326-3.0429.2449-2.81782.98130.4540.82330.3003-0.6326-0.1192-0.18020.63891.4064-0.26360.36050.0914-0.01850.64940.0940.463238.862454.879231.6067
473.6718-1.76650.40976.04972.38611.4788-0.23861.16330.8702-0.968-0.3538-1.1153-0.25581.26130.34790.3529-0.0140.1341.09460.18170.61448.109959.579133.4239
481.02240.86310.58952.36330.10644.12590.36470.6781-0.4281-0.0184-0.3096-0.85490.23540.6860.00690.46440.1138-0.17731.09090.06670.825251.014949.866848.1102
491.29970.0811-0.554.1626-2.45776.76110.3909-0.5880.5481-0.3144-0.4715-1.63360.02392.3157-0.01170.272-0.3818-0.36570.95430.06910.808452.346660.578249.4653
501.6013-1.57690.98173.25320.23612.1637-0.3487-0.2665-0.82550.29350.53230.66890.9658-0.8964-0.01270.5477-0.1630.00460.60990.15040.575167.149618.994734.8219
513.98671.5635-0.39697.58050.10743.9592-0.1442-0.1130.36420.07850.16330.6732-0.1777-1.138-0.02280.39820.0539-0.03830.58120.04020.368763.238331.783332.7709
525.1277-2.05351.95765.6041-0.67825.4508-0.192-0.61980.46810.55060.20420.5537-0.2329-1.36320.01690.49090.07240.02960.68020.04740.444766.137430.28741.2536
533.9199-4.48973.03897.8829-2.45582.89420.0272-0.2354-0.88010.1430.5356-0.11140.97820.4211-0.45220.55750.0350.02340.41830.00660.379779.429823.570344.3576
547.9959-1.4995-0.2644.96572.46733.9938-0.3394-0.91070.30830.7926-0.07020.5544-0.5693-1.32480.45430.60810.12610.01660.806-0.06330.34365.931135.088344.5529
554.33690.07270.85844.0692.1548.0528-0.0796-0.08420.09660.66140.2371-0.8764-0.29161.3705-0.2560.4818-0.0501-0.18240.4743-0.05180.553591.54738.467144.7949
566.84433.62184.72214.38513.45054.7170.2906-2.4642-0.51371.4082-0.1046-0.4957-0.9694-0.1975-0.15290.6949-0.03120.02170.6382-0.04850.365580.179536.13955.1406
576.6259-0.78121.70134.3174-0.60242.3017-0.16810.14391.15360.1847-0.04310.183-1.6225-0.24090.04490.8630.0386-0.1510.3233-0.04820.534778.511646.46141.3819
588.3898-5.8662.17966.4708-2.82353.0006-0.49760.72130.5698-0.55930.01070.9341-0.46620.02850.41560.4978-0.0463-0.09170.340.04730.441982.996237.368331.3062
599.3862-5.4723-4.63073.34942.77872.465-0.34561.35961.0423-0.9905-1.55751.8173-2.1937-0.38330.27781.2047-0.118-0.38430.25640.17720.591778.487946.757733.0854
603.7669-0.07662.98641.47611.01324.6712-0.4737-0.00621.0707-0.0181-0.0476-0.0551-1.7732-0.00590.42391.15740.0287-0.24030.438-0.1130.793883.305650.273148.3373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1290 through 1311 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1312 through 1330 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1331 through 1357 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1358 through 1373 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1374 through 1393 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1394 through 1403 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1404 through 1422 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 14 )B1 - 14
9X-RAY DIFFRACTION9chain 'B' and (resid 15 through 23 )B15 - 23
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 29 )B24 - 29
11X-RAY DIFFRACTION11chain 'B' and (resid 30 through 36 )B30 - 36
12X-RAY DIFFRACTION12chain 'B' and (resid 37 through 43 )B37 - 43
13X-RAY DIFFRACTION13chain 'B' and (resid 44 through 60 )B44 - 60
14X-RAY DIFFRACTION14chain 'B' and (resid 61 through 67 )B61 - 67
15X-RAY DIFFRACTION15chain 'B' and (resid 68 through 86 )B68 - 86
16X-RAY DIFFRACTION16chain 'B' and (resid 87 through 97 )B87 - 97
17X-RAY DIFFRACTION17chain 'B' and (resid 98 through 111 )B98 - 111
18X-RAY DIFFRACTION18chain 'B' and (resid 112 through 123 )B112 - 123
19X-RAY DIFFRACTION19chain 'C' and (resid 1290 through 1311 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 1312 through 1356 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 1357 through 1373 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 1374 through 1393 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 1394 through 1403 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 1404 through 1422 )C0
25X-RAY DIFFRACTION25chain 'D' and (resid 1 through 29 )D1 - 29
26X-RAY DIFFRACTION26chain 'D' and (resid 30 through 52 )D30 - 52
27X-RAY DIFFRACTION27chain 'D' and (resid 53 through 75 )D53 - 75
28X-RAY DIFFRACTION28chain 'D' and (resid 76 through 86 )D76 - 86
29X-RAY DIFFRACTION29chain 'D' and (resid 87 through 97 )D87 - 97
30X-RAY DIFFRACTION30chain 'D' and (resid 98 through 111 )D98 - 111
31X-RAY DIFFRACTION31chain 'D' and (resid 112 through 123 )D112 - 123
32X-RAY DIFFRACTION32chain 'E' and (resid 1291 through 1311 )E0
33X-RAY DIFFRACTION33chain 'E' and (resid 1312 through 1330 )E0
34X-RAY DIFFRACTION34chain 'E' and (resid 1331 through 1356 )E0
35X-RAY DIFFRACTION35chain 'E' and (resid 1357 through 1393 )E0
36X-RAY DIFFRACTION36chain 'E' and (resid 1394 through 1403 )E0
37X-RAY DIFFRACTION37chain 'E' and (resid 1404 through 1413 )E0
38X-RAY DIFFRACTION38chain 'E' and (resid 1414 through 1422 )E0
39X-RAY DIFFRACTION39chain 'F' and (resid 1 through 14 )F1 - 14
40X-RAY DIFFRACTION40chain 'F' and (resid 15 through 23 )F15 - 23
41X-RAY DIFFRACTION41chain 'F' and (resid 24 through 35 )F24 - 35
42X-RAY DIFFRACTION42chain 'F' and (resid 36 through 44 )F36 - 44
43X-RAY DIFFRACTION43chain 'F' and (resid 45 through 57 )F45 - 57
44X-RAY DIFFRACTION44chain 'F' and (resid 58 through 67 )F58 - 67
45X-RAY DIFFRACTION45chain 'F' and (resid 68 through 75 )F68 - 75
46X-RAY DIFFRACTION46chain 'F' and (resid 76 through 86 )F76 - 86
47X-RAY DIFFRACTION47chain 'F' and (resid 87 through 97 )F87 - 97
48X-RAY DIFFRACTION48chain 'F' and (resid 98 through 111 )F98 - 111
49X-RAY DIFFRACTION49chain 'F' and (resid 112 through 123 )F112 - 123
50X-RAY DIFFRACTION50chain 'G' and (resid 1291 through 1311 )G0
51X-RAY DIFFRACTION51chain 'G' and (resid 1312 through 1357 )G0
52X-RAY DIFFRACTION52chain 'G' and (resid 1358 through 1393 )G0
53X-RAY DIFFRACTION53chain 'G' and (resid 1394 through 1403 )G0
54X-RAY DIFFRACTION54chain 'G' and (resid 1404 through 1422 )G0
55X-RAY DIFFRACTION55chain 'H' and (resid 1 through 36 )H1 - 36
56X-RAY DIFFRACTION56chain 'H' and (resid 37 through 43 )H37 - 43
57X-RAY DIFFRACTION57chain 'H' and (resid 44 through 75 )H44 - 75
58X-RAY DIFFRACTION58chain 'H' and (resid 76 through 86 )H76 - 86
59X-RAY DIFFRACTION59chain 'H' and (resid 87 through 97 )H87 - 97
60X-RAY DIFFRACTION60chain 'H' and (resid 98 through 123 )H98 - 123

+
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