[English] 日本語
Yorodumi
- PDB-5vxn: Structure of two RcsB dimers bound to two parallel DNAs. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vxn
TitleStructure of two RcsB dimers bound to two parallel DNAs.
Components
  • DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')
  • Transcriptional regulatory protein RcsB
Keywordsdna binding protein/dna / Rcs phosphorelay / response regulator / FixJ/NarL / Center for Structural Genomics of Infectious Diseases / CSGID / DNA-binding protein / dna binding protein-dna complex
Function / homology
Function and homology information


regulation of capsule organization / regulation of carbohydrate catabolic process / single-species biofilm formation on inanimate substrate / positive regulation of cell projection organization / cellular stress response to acidic pH / regulation of bacterial-type flagellum-dependent cell motility / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / phosphorelay signal transduction system / transcription regulator complex ...regulation of capsule organization / regulation of carbohydrate catabolic process / single-species biofilm formation on inanimate substrate / positive regulation of cell projection organization / cellular stress response to acidic pH / regulation of bacterial-type flagellum-dependent cell motility / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / phosphorelay signal transduction system / transcription regulator complex / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / identical protein binding / cytosol
Similarity search - Function
Transcriptional regulatory protein RcsB / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...Transcriptional regulatory protein RcsB / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulatory protein RcsB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.375 Å
AuthorsFilippova, E.V. / Minasov, G. / Pshenychnyi, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: MBio / Year: 2018
Title: Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB.
Authors: Filippova, E.V. / Zemaitaitis, B. / Aung, T. / Wolfe, A.J. / Anderson, W.F.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulatory protein RcsB
B: Transcriptional regulatory protein RcsB
E: DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')
F: DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')
C: Transcriptional regulatory protein RcsB
D: Transcriptional regulatory protein RcsB
G: DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')
H: DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)116,8538
Polymers116,8538
Non-polymers00
Water21612
1
A: Transcriptional regulatory protein RcsB
B: Transcriptional regulatory protein RcsB
E: DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')
F: DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)58,4264
Polymers58,4264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-59 kcal/mol
Surface area23490 Å2
MethodPISA
2
C: Transcriptional regulatory protein RcsB
D: Transcriptional regulatory protein RcsB
G: DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')
H: DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)58,4264
Polymers58,4264
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-61 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.116, 113.231, 76.868
Angle α, β, γ (deg.)90.00, 115.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Transcriptional regulatory protein RcsB / Capsular synthesis regulator component B


Mass: 23699.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rcsB, b2217, JW2205 / Plasmid: pCA24n / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 magic / References: UniProt: P0DMC7
#2: DNA chain DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')


Mass: 5562.653 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')


Mass: 5464.577 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Sodium Chloride, 0.1 M HEPES, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2016 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.37→113.23 Å / Num. obs: 15089 / % possible obs: 93 % / Redundancy: 4.3 % / Biso Wilson estimate: 103 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 3.37→3.39 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / Num. unique all: 163 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata processing
XDSdata scaling
PHASERphasing
BLU-MAXdata collection
Cootmodel building
RefinementResolution: 3.375→56.615 Å / SU ML: 0.5 / σ(F): 1.36 / Phase error: 29.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 794 5.28 %
Rwork0.1985 --
obs0.202 15041 92.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.375→56.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 1464 0 12 7617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037854
X-RAY DIFFRACTIONf_angle_d0.55610912
X-RAY DIFFRACTIONf_dihedral_angle_d18.4864584
X-RAY DIFFRACTIONf_chiral_restr0.0411314
X-RAY DIFFRACTIONf_plane_restr0.0031118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3755-3.58690.3267940.28341874X-RAY DIFFRACTION74
3.5869-3.86380.32191320.26732559X-RAY DIFFRACTION99
3.8638-4.25250.31751090.22852270X-RAY DIFFRACTION88
4.2525-4.86760.27921160.19712548X-RAY DIFFRACTION99
4.8676-6.13140.27261970.20072486X-RAY DIFFRACTION99
6.1314-56.62340.22011460.15592510X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.4249-0.3804-0.71740.9705-0.12921.4549-1.6904-0.29330.0045-1.08880.0171-0.0285-0.17060.2304-0.05120.51070.0393-0.08341.177-0.28850.922721.6213-33.146586.4114
26.5274-3.3668-0.20784.0963-0.02550.00060.4770.55851.193-0.37280.55550.53011.9831-2.32620.32960.9853-0.0485-0.06141.390.21150.685523.1362-25.709780.67
31.144-0.7527-1.43322.5441.60373.0516-0.2976-0.0684-0.22780.0167-0.44310.5994-0.0993-0.5751-1.34390.4963-0.0610.04061.14480.06290.494723.2006-32.165392.2953
43.1308-0.308-2.25674.843-0.2273.04940.0123-1.7622-2.8021-0.2996-1.28541.06710.55231.2234-1.73450.5698-0.29810.58390.92531.1081-0.244528.6266-40.23395.1987
51.4609-0.4446-0.33890.40820.68620.61440.5432-0.0091-0.57310.154-0.65711.14071.11410.0806-0.00010.9224-0.04770.15961.0208-0.05450.903333.6249-39.554182.1954
60.24880.46060.03330.7137-0.04230.00470.2532-0.3236-0.9261.03391.4548-2.25792.6193-0.18350.13030.9556-0.2007-0.5211.5043-0.39812.706626.1303-47.449979.123
70.4547-0.07250.13460.9827-0.89260.75510.91682.4619-1.3505-3.30550.63881.97312.68920.67450.06591.41-0.20620.17351.0911-0.20721.449642.8889-44.036677.3289
81.44671.1830.06770.8022-0.00370.32930.9595-2.47820.1866-2.0533-0.09890.48731.4161-1.05260.0082-1.80032.5775-1.8455-0.41441.6969-0.507331.6882-14.717969.7349
92.53780.1515-1.72243.5779-1.15834.4586-0.18120.7774-2.7291-1.3048-0.12350.43480.7329-1.1689-1.29630.1171-0.1789-0.17061.11720.07021.210227.6102-21.756974.1546
101.21580.24070.70191.2798-0.30170.5488-0.50210.98880.91170.22560.32210.2619-0.0787-0.9081-00.79720.1771-0.00890.93910.13880.673833.4871-14.813766.1849
111.39620.06540.51620.0627-0.1560.9103-0.07120.73370.5175-0.3480.37610.7203-0.3028-0.0320.00060.84060.10850.06750.93130.160.765547.7165-14.585271.203
120.69450.52710.39720.32740.17690.09851.11380.3271-0.42180.1032-1.5251-0.6103-0.19990.9938-0.03770.79930.20480.3480.88650.14051.116539.0598-8.8372.0288
130.7280.26910.00061.8331-2.14072.9346-1.0523-1.1438-0.7191.72122.22690.5819-2.40111.1660.05251.5433-0.07750.65961.2617-0.40261.988744.0329-12.107186.2788
145.36094.7339-3.75667.3419-8.53662.01790.2061-0.30892.5472-1.84250.2270.29680.8338-0.94140.26811.16540.01770.35850.7152-0.11530.778738.2512-7.158479.9567
153.25772.61225.31612.46394.20568.92232.4485-0.58210.93830.1145-0.77410.57111.2585-0.47971.19340.85630.64270.33361.2171-0.0921.585128.0374-9.764580.6802
160.91120.28940.3050.24490.09980.0914-2.8365-0.693-0.4749-0.34630.31560.37290.0668-0.7083-0.09091.43330.45150.10521.629-0.62231.838933.139-4.92489.1043
170.1474-0.11380.23850.0479-0.17910.3911-1.46130.58311.4487-1.31281.1824-0.0683-0.56020.10970.00051.6467-0.0272-0.21781.05920.22441.468169.0165-50.083292.3429
180.247-0.0491-1.070.20830.86942.31770.4864-0.6715-0.32760.1337-0.4438-3.3557-0.6030.28370.00971.0726-0.0948-0.16011.0083-0.16611.643371.9477-28.150386.3891
190.0333-0.0350.06730.0304-0.0111-0.00910.3093-0.18863.95560.4073-1.3957-0.2743-0.6302-0.7794-0.00041.4185-0.0208-0.12531.0984-0.08872.125872.5467-5.385983.6818
200.0884-0.25620.21650.5334-0.5650.35310.74490.6283-0.13831.1338-1.2605-0.0667-0.1587-0.81530.00271.2305-0.2720.12430.8406-0.09491.507766.4654-11.223482.1079
21-0.115-0.26570.08491.7817-1.19522.11671.0162-0.2727-0.48060.7754-0.9228-2.6416-0.53510.694-0.02530.9530.0213-0.00361.0221-0.08211.405172.0924-32.688686.7328
220.031-0.05520.1360.0331-0.09760.07471.4761-1.1499-0.9056-0.7199-0.93460.1096-0.5690.7861-0.00331.46790.0010.07211.14040.02641.482873.2633-55.543887.3815
230.6182-0.4846-1.0140.94620.07331.78680.01490.4343-0.51020.2814-0.31940.10040.46150.4930.00060.9362-0.17770.1440.8002-0.04511.105911.5406-30.2952120.6757
241.5876-1.9499-0.88872.4291-0.05294.2313-0.04760.0431-0.42710.7588-0.16540.84830.4798-0.2702-0.00091.0063-0.17670.14230.6948-0.07740.713815.0095-36.4383129.7908
250.36240.4328-0.21090.78680.33830.3773-0.29010.63170.8194-0.88710.64072.5193-0.24040.49370.00250.8306-0.15690.10440.88320.05480.803930.5312-40.2737122.6961
26-0.140.13050.14130.10890.27540.3484-0.20420.7954-0.25130.5784-0.04570.03170.82480.3648-0.01680.6948-0.1409-0.11090.8441-0.08030.589118.3954-41.6269115.1885
275.49842.904-3.93657.0806-6.52676.41271.25351.68480.2085-2.1651.1941-1.35011.81071.59731.90881.23110.05840.05020.9236-0.38911.033233.3307-44.0935113.3265
280.28080.1674-0.49530.22290.34221.6261-0.01470.6835-0.1269-0.5342-0.15490.4750.1609-0.9994-0.51480.63170.0217-0.08791.00450.43310.807818.3192-18.9846110.4563
290.40920.4522-0.64851.79730.12312.53770.72331.63341.2184-0.5499-0.89711.1555-0.8171-1.0925-0.22150.94090.4582-0.3750.86080.5353-0.126720.4982-15.8093105.3135
302.37711.2191-0.79690.25780.12371.44950.2710.795-0.0704-0.56740.0224-0.121-0.54720.003-00.7981-0.0940.02790.77160.1210.719532.0136-13.328107.4417
311.5761-0.5396-0.8599-0.1722-0.00120.65350.0606-0.06731.0820.30190.70330.6739-0.93570.320.04821.01820.17160.11550.4610.02730.997431.1647-11.2775118.7071
320.35120.1307-0.22910.2373-0.72831.93020.17110.11560.8646-0.123-0.09240.573-0.0069-1.0707-0.00620.83910.10650.08590.59250.04970.88920.7267-10.5454120.2198
332.14371.18540.99690.64880.50840.4278-0.24261.2671-0.16960.43291.5032.0625-0.45930.78160.0141.37750.24340.00460.92820.01851.317224.2909-2.2724123.5423
343.83693.6975-4.09323.7965-3.39875.737-0.0583-1.1473-0.31151.2931-0.5651.413-1.55190.79520.05621.16950.2215-0.3660.9460.1021.25259.6766-49.7694125.869
350.86950.0252-0.33870.0684-0.33010.1024-0.83570.72611.2583-0.4327-0.3534-2.46190.22570.0979-0.00490.99320.11550.1240.88520.05811.559962.8748-36.3538115.3363
360.1373-0.20690.49840.6786-0.87070.80520.3024-0.9285-0.0744-1.3019-0.6931-1.606-1.0438-0.22690.00451.1305-0.0924-0.23490.8977-0.11781.380860.7922-19.6329122.9426
370.3882-0.2666-0.98830.23220.50923.34891.4321-0.32070.2763.3173-3.2945-1.6318-1.15780.2617-0.10921.8331-0.0744-0.38471.0895-0.17852.383762.1203-5.4131116.2296
380.0420.2704-0.14990.6-0.274-0.00031.099-1.1372-0.52870.48840.3444-1.60110.55510.68770.0141.3581-0.1688-0.08840.9044-0.05241.710255.6673-11.3115.6728
390.3765-0.1301-0.40910.06720.20640.14780.14220.670.59170.5302-0.489-2.5686-0.5830.78810.01631.157-0.1229-0.19831.17240.0092.01765.9827-24.6965120.842
400.5766-1.03561.24481.3671-1.73631.9621-0.383-0.0377-1.23370.12820.627-1.20460.19440.44790.16510.8377-0.0715-0.14370.7246-0.20461.292857.8155-41.0208117.6117
41-0.02590.0380.03840.56720.37160.2217-0.17450.6518-2.4092-0.97590.0856-0.4823-0.9321-0.105-0.00451.08140.23150.02141.23410.12011.374363.132-55.464120.428
423.5637-3.2425-0.09822.3872-0.160.6343-0.1694-0.10360.60840.46410.4522-1.0339-0.09880.08640.01250.5465-0.1857-0.05870.4878-0.0960.845646.4936-18.2352120.1058
432.31471.6151.52298.4356-4.83125.80060.0012-1.10440.13261.50561.05430.72251.41861.07263.04531.0454-0.00620.02690.7119-0.15230.631543.1854-23.4488132.2163
444.1319-0.3844-3.48082.67462.62635.5634-1.6167-0.584-1.28421.844-0.137-0.53581.9497-1.9632-1.08580.84850.3568-0.3260.94940.14840.547355.1094-44.822397.0499
450.30551.12810.05923.64860.0181-0.01790.4058-1.77430.5027-0.31590.0348-1.8522-0.8572-0.0399-0.06971.33610.09-0.24960.8622-0.04640.867865.6855-38.7822100.8414
460.9333-0.40451.7951.3163-0.00192.6962-0.1763-1.0207-1.2922-0.02120.30470.30890.058-0.6867-0.00030.82030.15360.04250.94420.04250.954955.2933-39.80790.1885
477.49793.4791-5.21362.4427-1.51874.71110.5514-0.36531.82520.59312.02230.5656-2.12451.07165.08010.29880.403-0.62160.4733-0.07230.482252.5053-15.508585.3228
480.3776-0.27450.04320.72670.55430.5396-0.2097-0.04271.8807-0.61561.07630.1724-0.21820.06310.00710.50120.0483-0.05630.772-0.00040.881758.0185-22.939678.0614
496.8434-1.40380.24871.8414-1.11510.8097-1.105-3.39330.76790.3096-0.2928-0.4826-1.75920.2105-5.70561.0163-0.1363-0.23050.579-0.57221.053556.3659-19.960692.2374
508.7034.71043.93935.29162.23621.7175-0.283-3.13490.62680.8677-0.02520.8672-0.0920.7786-0.59210.74750.21970.08281.24440.5420.199646.398-44.5271132.4015
510.14440.1938-0.15490.3032-0.05970.1476-0.3443-2.8497-0.01821.25420.7145-0.62720.35361.3773-0.00141.1050.2572-0.221.1295-0.11650.986357.3807-38.3349134.4699
527.74281.93080.45131.56320.2853-0.00210.30931.2153-1.4643-0.7703-0.5743-0.7901-0.0161-0.392-0.04780.83280.2268-0.08540.81710.14530.368251.0834-43.4876124.4822
530.2819-0.10640.52080.8228-1.4473.10360.7327-0.57080.35310.17120.74831.3758-1.557-2.10.08080.91330.00920.06790.736-0.01370.63839.8531-36.7675126.3919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 87 )
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 123 )
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 131 )
7X-RAY DIFFRACTION7chain 'A' and (resid 132 through 141 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 12 )
9X-RAY DIFFRACTION9chain 'B' and (resid 13 through 23 )
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 55 )
11X-RAY DIFFRACTION11chain 'B' and (resid 56 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 87 )
13X-RAY DIFFRACTION13chain 'B' and (resid 88 through 101 )
14X-RAY DIFFRACTION14chain 'B' and (resid 102 through 108 )
15X-RAY DIFFRACTION15chain 'B' and (resid 109 through 124 )
16X-RAY DIFFRACTION16chain 'B' and (resid 125 through 139 )
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 5 )
18X-RAY DIFFRACTION18chain 'E' and (resid 6 through 15 )
19X-RAY DIFFRACTION19chain 'E' and (resid 16 through 18 )
20X-RAY DIFFRACTION20chain 'F' and (resid 20 through 24 )
21X-RAY DIFFRACTION21chain 'F' and (resid 25 through 34 )
22X-RAY DIFFRACTION22chain 'F' and (resid 35 through 37 )
23X-RAY DIFFRACTION23chain 'C' and (resid 2 through 24 )
24X-RAY DIFFRACTION24chain 'C' and (resid 25 through 87 )
25X-RAY DIFFRACTION25chain 'C' and (resid 88 through 101 )
26X-RAY DIFFRACTION26chain 'C' and (resid 102 through 131 )
27X-RAY DIFFRACTION27chain 'C' and (resid 132 through 143 )
28X-RAY DIFFRACTION28chain 'D' and (resid 3 through 23 )
29X-RAY DIFFRACTION29chain 'D' and (resid 24 through 45 )
30X-RAY DIFFRACTION30chain 'D' and (resid 46 through 77 )
31X-RAY DIFFRACTION31chain 'D' and (resid 78 through 101 )
32X-RAY DIFFRACTION32chain 'D' and (resid 102 through 123 )
33X-RAY DIFFRACTION33chain 'D' and (resid 124 through 140 )
34X-RAY DIFFRACTION34chain 'G' and (resid 1 through 5 )
35X-RAY DIFFRACTION35chain 'G' and (resid 6 through 10 )
36X-RAY DIFFRACTION36chain 'G' and (resid 11 through 15 )
37X-RAY DIFFRACTION37chain 'G' and (resid 16 through 18 )
38X-RAY DIFFRACTION38chain 'H' and (resid 20 through 24 )
39X-RAY DIFFRACTION39chain 'H' and (resid 25 through 29 )
40X-RAY DIFFRACTION40chain 'H' and (resid 30 through 34 )
41X-RAY DIFFRACTION41chain 'H' and (resid 35 through 37 )
42X-RAY DIFFRACTION42chain 'K' and (resid 148 through 193 )
43X-RAY DIFFRACTION43chain 'K' and (resid 194 through 208 )
44X-RAY DIFFRACTION44chain 'L' and (resid 149 through 164 )
45X-RAY DIFFRACTION45chain 'L' and (resid 165 through 178 )
46X-RAY DIFFRACTION46chain 'L' and (resid 179 through 209 )
47X-RAY DIFFRACTION47chain 'M' and (resid 150 through 163 )
48X-RAY DIFFRACTION48chain 'M' and (resid 164 through 178 )
49X-RAY DIFFRACTION49chain 'M' and (resid 179 through 207 )
50X-RAY DIFFRACTION50chain 'N' and (resid 149 through 164 )
51X-RAY DIFFRACTION51chain 'N' and (resid 165 through 178 )
52X-RAY DIFFRACTION52chain 'N' and (resid 179 through 193 )
53X-RAY DIFFRACTION53chain 'N' and (resid 194 through 209 )

+
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