[English] 日本語
Yorodumi
- PDB-5vok: Crystal structure of the C7orf59-HBXIP dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vok
TitleCrystal structure of the C7orf59-HBXIP dimer
Components
  • Ragulator complex protein LAMTOR4
  • Ragulator complex protein LAMTOR5
KeywordsSIGNALING PROTEIN / C7orf59 / Ragulator / Roadblock / mTOR
Function / homology
Function and homology information


positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to lysosome / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cell size / Macroautophagy ...positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to lysosome / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cell size / Macroautophagy / mTORC1-mediated signalling / positive regulation of TOR signaling / positive regulation of TORC1 signaling / viral genome replication / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein localization to nucleus / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / protein-containing complex / cytosol
Similarity search - Function
Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR5 / Ragulator complex protein LAMTOR5 / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ragulator complex protein LAMTOR5 / Ragulator complex protein LAMTOR4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsRasheed, N. / Nascimento, A.F.Z. / Bar-Peled, L. / Shen, K. / Sabatini, D.M. / Aparicio, R. / Smetana, J.H.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq-Brazil)190174/2012-9 Brazil
Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP-Brazil)2014/12445-0 Brazil
CitationJournal: Febs Open Bio / Year: 2019
Title: C7orf59/Lamtor4 phosphorylation and structural flexibility modulate Ragulator assembly.
Authors: Rasheed, N. / Lima, T.B. / Mercaldi, G.F. / Nascimento, A.F.Z. / Silva, A.L.S. / Righetto, G.L. / Bar-Peled, L. / Shen, K. / Sabatini Shen, D.M. / Gozzo, F.C. / Aparicio, R. / Smetana, J.H.C.
History
DepositionMay 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ragulator complex protein LAMTOR5
B: Ragulator complex protein LAMTOR4
C: Ragulator complex protein LAMTOR5
D: Ragulator complex protein LAMTOR4
E: Ragulator complex protein LAMTOR5
F: Ragulator complex protein LAMTOR4
G: Ragulator complex protein LAMTOR5
H: Ragulator complex protein LAMTOR4


Theoretical massNumber of molelcules
Total (without water)82,6988
Polymers82,6988
Non-polymers00
Water362
1
A: Ragulator complex protein LAMTOR5
B: Ragulator complex protein LAMTOR4


Theoretical massNumber of molelcules
Total (without water)20,6742
Polymers20,6742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-14 kcal/mol
Surface area10680 Å2
MethodPISA
2
C: Ragulator complex protein LAMTOR5
D: Ragulator complex protein LAMTOR4


Theoretical massNumber of molelcules
Total (without water)20,6742
Polymers20,6742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-13 kcal/mol
Surface area10280 Å2
MethodPISA
3
E: Ragulator complex protein LAMTOR5
F: Ragulator complex protein LAMTOR4


Theoretical massNumber of molelcules
Total (without water)20,6742
Polymers20,6742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-13 kcal/mol
Surface area10630 Å2
MethodPISA
4
G: Ragulator complex protein LAMTOR5
H: Ragulator complex protein LAMTOR4


Theoretical massNumber of molelcules
Total (without water)20,6742
Polymers20,6742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-15 kcal/mol
Surface area9890 Å2
MethodPISA
5
A: Ragulator complex protein LAMTOR5
B: Ragulator complex protein LAMTOR4

C: Ragulator complex protein LAMTOR5
D: Ragulator complex protein LAMTOR4


Theoretical massNumber of molelcules
Total (without water)41,3494
Polymers41,3494
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area6970 Å2
ΔGint-50 kcal/mol
Surface area17510 Å2
MethodPISA
6
E: Ragulator complex protein LAMTOR5
F: Ragulator complex protein LAMTOR4

G: Ragulator complex protein LAMTOR5
H: Ragulator complex protein LAMTOR4


Theoretical massNumber of molelcules
Total (without water)41,3494
Polymers41,3494
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area7010 Å2
ΔGint-51 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.884, 64.763, 79.231
Angle α, β, γ (deg.)90.00, 115.18, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Ragulator complex protein LAMTOR5 / Hepatitis B virus X-interacting protein / HBX-interacting protein / Late endosomal/lysosomal ...Hepatitis B virus X-interacting protein / HBX-interacting protein / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 5


Mass: 9622.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR5, HBXIP, XIP / Plasmid: pACYC-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43504
#2: Protein
Ragulator complex protein LAMTOR4 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 4


Mass: 11051.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR4, C7orf59 / Plasmid: pACYC-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0VGL1
#3: 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: 2.54 Å3/Da / Density % sol: 51.56 %
Description: Crystals were 2D, small, plate-like and very fragile. Most of them forming clusters.
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 4M sodium formate, 5%(v/v) glycerol and 0.01M barium chloride (as additive).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.89→81.846 Å / Num. obs: 18719 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 86.24 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.171 / Net I/σ(I): 6.5
Reflection shellResolution: 2.89→3.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 3.5 / Num. unique obs: 3004 / CC1/2: 0.337 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DIALS1.2data reduction
Aimless0.5.31data scaling
MrBUMP00.9.00phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MSH, 3MS6
Resolution: 2.89→81.846 Å / Cross valid method: FREE R-VALUE / σ(F): 131.26 / Phase error: 45.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.3124 968 5.19 %Random selection
Rwork0.2802 ---
obs0.2854 18656 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→81.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 0 2 5252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085300
X-RAY DIFFRACTIONf_angle_d1.3957168
X-RAY DIFFRACTIONf_dihedral_angle_d11.1543236
X-RAY DIFFRACTIONf_chiral_restr0.065882
X-RAY DIFFRACTIONf_plane_restr0.007932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8909-3.04320.36041360.36042461X-RAY DIFFRACTION92
3.0432-3.23380.38491500.34832485X-RAY DIFFRACTION93
3.2338-3.48340.35961240.33482508X-RAY DIFFRACTION95
3.4834-3.83380.33381240.33022529X-RAY DIFFRACTION95
3.8338-4.38820.3431490.30042524X-RAY DIFFRACTION94
4.3882-5.5270.28681400.2632534X-RAY DIFFRACTION94
5.527-44.65490.27681270.24282640X-RAY DIFFRACTION95
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)
19.714.1099-1.58684.66343.78847.0934-0.20910.6968-1.8635-1.48620.92330.66930.5535-1.6437-0.52761.0238-0.2132-0.52061.1261-0.03161.69135.5682-17.448434.927
28.39371.8582-1.72510.4605-0.11288.0980.08850.3930.7406-0.64110.14971.1483-0.2043-1.3749-0.61220.58170.0887-0.35771.001-0.12731.255410.861-10.011742.8482
31.5773-0.2299-3.04126.8772-1.81388.66740.07190.1462-0.7456-0.247-0.7813-1.1886-1.0115-0.33070.44390.660.0576-0.3830.8359-0.0691.339822.8952-6.354841.2992
47.5578-6.17954.77545.1203-4.08273.29340.83360.2454-0.7522-0.4375-0.15520.0615-0.02430.9192-0.04750.57090.1212-0.19810.8337-0.1910.904717.0607-13.290740.6636
57.5865-3.67674.54379.40865.19279.8656-0.4193-5.0031-2.4254.1180.22162.6612.4451-3.2474-0.20461.0852-0.35780.12141.5492-0.03061.085849.725-37.186542.3032
64.0437-3.292-1.51082.87551.10830.62340.23150.97320.63990.18770.7231-0.72740.25610.464-0.61370.65110.2118-0.11061.25050.15820.817542.8884-12.358643.1298
75.51140.35434.06168.5173-0.36055.3361-0.4376-0.04470.28840.01910.5685-0.7347-0.7611-0.1227-0.38750.5677-0.3090.05760.850.04491.346943.2862.038550.8803
86.9471-0.914-8.14393.38150.6549.60830.10961.29860.239-2.04120.63871.5504-1.185-0.7815-0.82731.0125-0.2293-0.58171.35810.24910.838141.26372.524241.1406
96.42585.3307-6.24154.4227-5.11288.99180.41340.23552.45610.6360.00310.9343-3.3399-0.8838-0.42861.28820.0439-0.39790.45280.09471.447428.66050.649448.2235
105.8216-1.1394-6.83245.77744.60989.9189-0.2929-5.58710.82683.26080.11450.6123-0.6463-0.4748-0.12174.9472.09411.88684.0976-2.34943.694921.439-8.348855.4532
118.25211.38888.24023.5006-0.71689.5781-0.13482.73830.3638-0.6169-0.8358-0.3783-0.06921.20380.98080.45210.2427-0.07640.88950.01180.968332.4562-9.788937.7402
121.67680.041-0.96420.42430.09580.5941-0.0604-0.1135-0.26710.2798-0.0151-0.21480.10450.197-0.06320.2023-0.1885-0.20491.05180.39041.78434.9526-8.564848.199
131.5684-1.4925-2.7041.41872.3615.9171-0.4226-1.13151.24460.43670.0495-0.2211-0.3185-0.59010.68690.2527-0.0788-0.71141.31450.16691.28937.968-4.143852.8911
142.0453.82262.81977.1835.02885.0756-0.29560.9869-0.67970.62950.0041-1.008-0.27-0.09560.29850.52370.05310.02941.1123-0.12380.962538.9003-15.036637.5673
153.5348-2.42293.76165.6481-1.12584.5495-0.0101-0.5074-0.92270.02140.11361.72650.2241-1.2020.38170.55240.0013-0.03060.98740.29231.2683-3.5807-8.004133.9456
166.00476.1597-4.637.247-5.41574.0423-1.18910.84171.0834-1.36530.73941.44990.4022-1.14590.68311.08720.023-0.86580.9623-0.74352.3213-11.683-2.396221.6594
171.17050.39731.95854.12520.11143.7057-0.3883-1.39870.3919-0.05670.21840.34010.2268-0.2689-0.06770.47040.1026-0.49091.22210.08511.0652-2.44514.711422.5376
189.55.94946.56014.27183.79524.7227-0.0504-0.67280.91340.70971.2066-0.50340.21230.1866-0.80020.71570.297-0.17481.01020.23641.3414-0.32892.002929.1643
195.8922-4.22646.55422.7514-4.45437.068-0.40011.6802-0.87780.24840.04260.366-0.11860.79560.47720.5018-0.0033-0.08711.0373-0.13510.957522.517416.603725.928
202.9442-0.44281.67562.8218-0.85226.00680.5357-0.1348-1.0447-0.25540.08630.51910.4603-0.2333-0.31351.6473-0.0313-1.15010.97570.35021.126.342226.964713.9466
212.00284.0726-1.48092.61250.27360.5861-1.11693.65282.5768-3.92450.22363.8345-1.0751-1.29330.38521.42110.0253-1.02131.11010.26121.31739.366518.63599.3047
226.7988-2.73890.57082.37672.93728.4469-0.6165-0.15480.11730.05850.00620.18120.0772-1.28440.32230.6591-0.1098-0.57690.98190.28251.2443-1.994915.868118.151
233.3921-0.4377-0.27772.8566-0.13281.53210.02080.97890.6276-0.35790.51310.1665-0.3654-0.7446-0.20160.4574-0.0593-0.03960.78890.08920.94762.857212.082926.1397
243.9721-0.2768-2.25482.37640.68592.95550.3273-0.66091.79470.70680.2-0.2984-0.1351-0.4990.7009-0.12540.1019-0.8581.566-0.62621.84365.326421.083323.8647
255.90914.58441.06034.21522.10652.7874-0.4182-0.1461-0.5084-0.55680.560.1453-0.48291.5954-0.27750.5331-0.1411-0.09690.88060.12961.150312.765215.608121.5647
268.1822-1.655-2.12730.8293-0.34271.78280.5905-0.6464-0.13570.345-0.2878-0.6932-0.05840.299-0.46030.6414-0.1424-0.18230.86220.02550.75156.12345.505116.3989
274.4274.85680.45835.35410.50540.31250.4879-0.3212-0.74830.7731-0.4269-0.1579-0.0849-0.16070.17740.51150.1777-0.49682.0138-0.43811.321448.12941.8322.4598
287.63920.14062.85669.4413-2.39346.40280.5930.5903-1.3181-0.4581-0.33850.35650.02830.8468-0.29210.4872-0.0185-0.11880.55080.03120.811445.42690.44177.5822
295.4995-1.64820.01535.6571.71876.14760.56550.63340.06370.18260.4826-0.96810.5503-0.7047-0.36380.5439-0.1046-0.10211.0981-0.0920.743828.572923.5135-10.6503
305.42584.9321-3.716.2921-0.27287.68370.29580.2693-1.2332-0.7502-1.09481.34140.0905-0.31520.77730.57580.0933-0.15270.8905-0.21050.997126.1042-5.6741-2.5301
312.04280.3732-1.81690.4413-1.04572.97990.3750.6816-1.3265-0.2421-0.2555-1.28471.1883-0.4750.06970.81820.0852-0.28820.88990.25521.267831.8533-8.9477-7.6648
321.67660.07671.43660.058-0.60529.3963-0.426-0.0814-1.62990.1685-0.46040.83971.67230.78631.00450.63910.1471-0.09080.73430.14611.102434.8221-8.28237.871
333.3744-1.63573.62464.7049-1.97436.36540.1151-0.1486-0.9307-0.0932-0.05580.71670.62260.7062-0.26720.79740.0362-0.55080.6347-0.0361.461736.60392.296710.8923
343.72713.5367-5.09996.2913-3.04038.1037-0.7348-1.3133-0.17740.47170.38640.42120.3778-0.79530.22950.76560.0684-0.34121.35780.15950.814728.9405-1.23075.4287
353.3653-3.4859-1.77465.4692-1.99669.23460.6628-0.1340.9457-0.55440.1870.77220.23260.2922-0.94060.66750.0114-0.25240.9006-0.21011.059632.6472.4986-3.1849
362.7305-2.2765.16163.3058-6.0961.99711.3843-2.16513.31543.9615-0.15066.8003-1.0461-5.8917-0.75721.43890.00050.78451.8234-0.5722.54469.2733.323722.5315
375.24120.1898-4.86550.3023-0.23434.5324-0.3944-0.8379-3.92431.44280.2995-0.3683-0.13780.70820.02820.90790.2804-0.33651.16550.03041.446173.5371-6.4323.4527
386.918-2.4182-1.22282.5707-1.08393.9394-0.0092-0.0193-0.02450.71320.7339-0.32480.09110.20230.06050.02970.5794-0.80530.76770.15071.60979.0339-14.456616.1977
391.99511.2743-0.07263.14411.86831.1533-0.89110.73562.5694-0.50680.1419-0.8178-1.8729-0.34521.06920.53150.4546-4.53870.8098-0.88723.90476.2492-9.95031.9144
407.1332-4.86231.42662.00594.73824.8261-0.87611.1419-0.2331-0.17731.70411.30720.5452-2.1884-0.27840.62460.1382-0.37770.89310.0921.042667.4134-13.797816.0135
417.2975-0.0433-1.69579.4560.50568.37110.6906-0.5332-0.7865-0.41711.1361-0.18530.3113-0.2277-0.77540.38840.4734-0.38381.21850.11021.488669.6047-7.972717.8103
428.7527-4.06837.78794.0576-4.29357.505-1.78060.95190.02511.5010.4579-0.9584-1.43160.61941.19561.01280.0245-0.26660.6503-0.02991.137961.6904-26.9914-0.8066
431.1755-1.0089-0.75250.89050.54230.99330.6952-0.697-3.2097-1.8571-1.65271.05872.78012.03410.61825.33711.1042-4.45.3788-0.23566.174878.0435-26.4632-3.9911
445.1471-1.783-4.6951.57211.85644.3387-0.2409-0.4944-0.1247-0.25570.6284-0.42720.36211.1663-0.49610.5012-0.1336-0.62761.00730.18821.965778.8831-24.175810.3185
453.105-0.49180.44432.3086-0.57272.1019-0.3876-0.68770.22260.63610.2875-1.0145-0.1661-0.44880.09770.49320.0884-0.43690.7938-0.11611.664569.0137-20.009510.2066
467.5129-3.14352.50414.5984-4.29434.07260.0781-0.06570.9780.50570.537-1.24590.2752-0.5128-0.12040.54890.0106-0.2330.9996-0.07991.004167.0042-25.94344.7335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 90 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 9 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 22 )
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 50 )
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 65 )
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 73 )
12X-RAY DIFFRACTION12chain 'B' and (resid 74 through 80 )
13X-RAY DIFFRACTION13chain 'B' and (resid 81 through 87 )
14X-RAY DIFFRACTION14chain 'B' and (resid 88 through 92 )
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 22 )
16X-RAY DIFFRACTION16chain 'C' and (resid 23 through 32 )
17X-RAY DIFFRACTION17chain 'C' and (resid 33 through 69 )
18X-RAY DIFFRACTION18chain 'C' and (resid 70 through 90 )
19X-RAY DIFFRACTION19chain 'D' and (resid 4 through 22 )
20X-RAY DIFFRACTION20chain 'D' and (resid 23 through 30 )
21X-RAY DIFFRACTION21chain 'D' and (resid 31 through 40 )
22X-RAY DIFFRACTION22chain 'D' and (resid 41 through 50 )
23X-RAY DIFFRACTION23chain 'D' and (resid 51 through 73 )
24X-RAY DIFFRACTION24chain 'D' and (resid 74 through 83 )
25X-RAY DIFFRACTION25chain 'D' and (resid 84 through 91 )
26X-RAY DIFFRACTION26chain 'E' and (resid 1 through 32 )
27X-RAY DIFFRACTION27chain 'E' and (resid 33 through 40 )
28X-RAY DIFFRACTION28chain 'E' and (resid 41 through 90 )
29X-RAY DIFFRACTION29chain 'F' and (resid 0 through 14 )
30X-RAY DIFFRACTION30chain 'F' and (resid 15 through 29 )
31X-RAY DIFFRACTION31chain 'F' and (resid 30 through 40 )
32X-RAY DIFFRACTION32chain 'F' and (resid 41 through 52 )
33X-RAY DIFFRACTION33chain 'F' and (resid 53 through 74 )
34X-RAY DIFFRACTION34chain 'F' and (resid 75 through 82 )
35X-RAY DIFFRACTION35chain 'F' and (resid 83 through 92 )
36X-RAY DIFFRACTION36chain 'G' and (resid 3 through 14 )
37X-RAY DIFFRACTION37chain 'G' and (resid 15 through 38 )
38X-RAY DIFFRACTION38chain 'G' and (resid 39 through 55 )
39X-RAY DIFFRACTION39chain 'G' and (resid 56 through 64 )
40X-RAY DIFFRACTION40chain 'G' and (resid 65 through 79 )
41X-RAY DIFFRACTION41chain 'G' and (resid 80 through 90 )
42X-RAY DIFFRACTION42chain 'H' and (resid 4 through 30 )
43X-RAY DIFFRACTION43chain 'H' and (resid 31 through 38 )
44X-RAY DIFFRACTION44chain 'H' and (resid 39 through 50 )
45X-RAY DIFFRACTION45chain 'H' and (resid 51 through 79 )
46X-RAY DIFFRACTION46chain 'H' and (resid 80 through 92 )

+
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://pdbjlvh1.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