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- PDB-3vr2: Crystal structure of nucleotide-free A3B3 complex from Enterococc... -

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Basic information

Entry
Database: PDB / ID: 3vr2
TitleCrystal structure of nucleotide-free A3B3 complex from Enterococcus hirae V-ATPase [eA3B3]
Components
  • V-type sodium ATPase catalytic subunit A
  • V-type sodium ATPase subunit B
KeywordsHYDROLASE / V-ATPase / Enterococcus hirae / Rotary motor / P-loop / Na(+)-ATPase / ATP Binding
Function / homology
Function and homology information


Na+-transporting two-sector ATPase / sodium-transporting ATP synthase activity, rotational mechanism / sodium-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism ...Na+-transporting two-sector ATPase / sodium-transporting ATP synthase activity, rotational mechanism / sodium-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / lysosomal membrane / ATP binding
Similarity search - Function
Rossmann fold - #12240 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily ...Rossmann fold - #12240 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
V-type sodium ATPase catalytic subunit A / V-type sodium ATPase subunit B
Similarity search - Component
Biological speciesEnterococcus hirae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArai, S. / Saijo, S. / Suzuki, K. / Mizutani, K. / Kakinuma, Y. / Ishizuka-Katsura, Y. / Ohsawa, N. / Terada, T. / Shirouzu, M. / Yokoyama, S. ...Arai, S. / Saijo, S. / Suzuki, K. / Mizutani, K. / Kakinuma, Y. / Ishizuka-Katsura, Y. / Ohsawa, N. / Terada, T. / Shirouzu, M. / Yokoyama, S. / Iwata, S. / Yamato, I. / Murata, T.
CitationJournal: Nature / Year: 2013
Title: Rotation mechanism of Enterococcus hirae V(1)-ATPase based on asymmetric crystal structures
Authors: Arai, S. / Saijo, S. / Suzuki, K. / Mizutani, K. / Kakinuma, Y. / Ishizuka-Katsura, Y. / Ohsawa, N. / Terada, T. / Shirouzu, M. / Yokoyama, S. / Iwata, S. / Yamato, I. / Murata, T.
History
DepositionApr 3, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-type sodium ATPase catalytic subunit A
B: V-type sodium ATPase catalytic subunit A
C: V-type sodium ATPase catalytic subunit A
D: V-type sodium ATPase subunit B
E: V-type sodium ATPase subunit B
F: V-type sodium ATPase subunit B


Theoretical massNumber of molelcules
Total (without water)359,6936
Polymers359,6936
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21290 Å2
ΔGint-61 kcal/mol
Surface area116700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.800, 121.500, 128.260
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein V-type sodium ATPase catalytic subunit A / Na(+)-translocating ATPase subunit A / V-type sodium pump catalytic subunit A


Mass: 67473.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae (bacteria) / Gene: ntpA / Production host: Cell free synthesis / References: UniProt: Q08636, EC: 3.6.3.15
#2: Protein V-type sodium ATPase subunit B / Na(+)-translocating ATPase subunit B / V-type sodium pump subunit B


Mass: 52424.312 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae (bacteria) / Gene: ntpB / Production host: Cell free synthesis / References: UniProt: Q08637, EC: 3.6.3.15
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 24% PEG 3350, 0.1M Tris, 0.2M Ammonium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: Rotated-inclined double-crystal monochromator, Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→44.18 Å / Num. all: 91463 / Num. obs: 91463 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 77.186 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.5 / Num. unique all: 13339 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GQB
Resolution: 2.8→44.18 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 30.555 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24293 4572 5 %RANDOM
Rwork0.19837 ---
all0.20061 86877 --
obs0.20061 86877 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.336 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.63 Å2
2--1.48 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23964 0 0 89 24053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02224373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.97132966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08553094
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06424.5221108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.755154285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.30315176
X-RAY DIFFRACTIONr_chiral_restr0.0870.23697
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118436
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4571.515341
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.922224718
X-RAY DIFFRACTIONr_scbond_it1.80439032
X-RAY DIFFRACTIONr_scangle_it3.0064.58248
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 311 -
Rwork0.287 6411 -
obs-6722 99.38 %
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)
10.8579-0.298-0.44610.35020.73243.23630.02490.2753-0.2904-0.2202-0.07930.08680.11810.18610.05440.47410.03910.00520.2078-0.08430.299315.284-35.37131.354
23.4947-1.2127-0.35132.699-0.12781.1656-0.1081-0.2747-0.7439-0.13520.01740.02280.70870.42510.09070.71890.22380.0440.3696-0.12070.34423.603-49.19911.659
31.1582-0.0015-0.17170.9094-0.3242.3020.12290.2304-0.0423-0.2407-0.14910.07580.02640.28040.02630.48840.09080.04070.459-0.09290.165425.926-25.3057.174
44.6576-1.9447-1.75264.93612.20774.25140.0819-0.02340.17580.01510.03730.06240.05430.2548-0.11920.33620.0220.0550.4101-0.01770.176628.684-20.823.401
51.03430.56110.18793.2165-1.62054.2573-0.0583-0.00810.23860.09470.0282-0.0249-0.64510.30820.03010.3936-0.01920.09550.5822-0.06580.107133.912-13.7267.28
64.9001-1.6864-0.601217.7451-0.48272.220.31050.51480.878-0.0158-0.7161-0.6103-0.38550.4270.40570.5433-0.27890.15650.78060.09550.34843.079-0.395-6.465
76.03975.4766-0.61166.78161.36795.9658-0.00730.53080.168-0.3814-0.0793-0.053-0.29430.79260.08660.71960.02870.13820.81630.10710.175134.992-8.629-12.596
86.58735.5843-4.83737.594-3.59724.10480.00150.86070.318-0.78320.3384-0.3922-0.5438-0.1033-0.340.9246-0.04520.16891.22480.17630.17139.54-2.819-23.429
95.43011.66323.10385.01464.22077.2309-0.0878-0.0869-0.0457-0.13790.11030.0950.0066-0.1655-0.02260.3510.05030.01420.12870.06990.28386.709-7.31368.197
101.7529-0.63290.08620.7502-0.00971.24160.0273-0.29830.00490.1317-0.0234-0.1537-0.1220.2139-0.00380.2978-0.04540.01890.16950.04090.253-6.26311.53569.421
111.10130.2422-0.15761.4595-0.25411.66630.0502-0.0812-0.08790.0082-0.02280.1277-0.0594-0.1143-0.02730.26590.03160.01830.15320.01180.2559-13.33514.4554.926
127.8324-2.15872.01867.18011.08738.28280.26950.1944-0.43210.09850.1839-0.90340.74310.6798-0.45340.3018-0.04170.02790.1677-0.01960.28287.8615.11947.685
133.71983.5367-0.39257.4191-0.60933.25860.04310.2658-0.2353-0.37440.0138-0.3618-0.12340.0984-0.0570.36290.0226-0.01140.1418-0.00080.1686-10.17811.8244.381
141.8234-1.78911.08843.8496-0.76212.28650.15040.24650.0064-0.4514-0.1409-0.6005-0.06780.338-0.00940.520.03070.11130.265-0.02950.22521.21822.5135.097
1515.25057.8835-5.9157.858-4.096.3190.10560.7072-0.4105-0.87610.0093-0.5154-0.27650.3388-0.1150.78390.06690.06730.3032-0.01570.1434-4.54732.74421.593
162.7409-0.2330.53152.7876-0.83164.7943-0.08180.52550.4881-0.5380.0263-0.0534-0.7570.05610.05540.65690.01460.04730.17220.10220.2316-10.2544.24727.229
173.1556-0.3823-1.99897.63292.80014.4502-0.0308-0.0731-0.24660.00110.12130.205-0.0272-0.0907-0.09050.26150.0044-0.06250.14970.04260.2433-1.655-20.64250.764
182.8732-3.15893.20033.5595-3.21854.95970.30260.1318-0.1914-0.3738-0.34840.33870.4405-0.6860.04570.25990.0139-0.06620.5143-0.17430.2969-11.707-16.94331.367
191.7833-0.3046-0.56983.3665-0.08763.75560.33060.4152-0.056-0.7522-0.3230.4173-0.2441-0.5809-0.00760.45070.159-0.07860.3006-0.13520.1566-4.857-7.83616.167
201.0021-1.0121-0.31974.6710.86314.61580.14310.267-0.0467-0.1793-0.31540.1434-0.2938-0.08680.17240.36340.05240.00250.1873-0.08170.2007-4.127-6.21928.384
214.6124-1.1270.61817.34022.35296.42520.0997-0.0138-0.1344-0.41380.1771-0.6924-0.41840.5562-0.27670.41650.07690.06430.1974-0.04490.13925.14-10.11621.467
225.3124-0.1230.45194.98770.89324.30730.6458-0.0560.0355-1.13320.1383-0.968-1.41880.64-0.78410.9578-0.04250.40360.2501-0.12360.27726.4522.2511.631
236.1788-2.15852.69480.7916-1.00911.3366-0.67260.26731.9775-0.0403-0.2227-0.77340.02890.36430.89532.49020.00360.62060.48960.07130.909811.2719.1841.635
241.7610.5019-2.78455.8208-1.8299.18110.79280.90020.6449-1.02740.0471-0.1985-2.3891-1.0806-0.83991.97180.70540.27980.6330.30970.2861-1.20710.91-1.486
2511.8402-4.411-1.33374.7460.54781.01420.0711-0.43340.57-0.00920.2026-0.59370.04090.2424-0.27370.34640.00780.03050.2454-0.0870.320530.049-7.2276.079
266.3709-0.3345-0.04223.5027-0.85923.60660.0439-1.0038-0.68110.70080.1521-0.611-0.08990.4853-0.1960.2918-0.0112-0.11870.298-0.09510.525228.02116.83779.443
272.17691.582-0.6743.9463-2.12542.88430.15760.04310.32010.13910.0365-0.0888-0.43720.3595-0.1940.2616-0.04360.02240.1314-0.16390.379523.93830.68761.199
283.3926-0.30271.1830.1597-0.51061.65820.3878-0.65840.06710.1982-0.3090.0117-0.56981.0224-0.07880.548-0.6978-0.07171.4245-0.27480.793738.60423.00668.349
292.4967-1.046-0.02293.22850.53471.66810.14860.2435-0.4719-0.38920.02030.00120.11330.3479-0.16890.25250.0511-0.09660.1635-0.16660.512223.37514.48561.618
303.311.57232.16258.3428-1.8435.9759-0.06080.90170.3812-1.00520.49620.2256-0.21610.3734-0.43540.3329-0.01580.12920.28320.08150.30123.71234.55348.311
317.712-1.357-1.59115.5685-3.39863.18120.58832.29140.6843-0.7181-1.405-0.819-0.16240.84540.81671.188-0.5781-0.10371.69370.60940.58531.30640.01233.58
329.4317-4.89655.66277.6588-6.327112.41370.33531.47131.8311-0.6236-0.3962-0.4606-1.17860.84460.06090.6617-0.12980.23990.32570.2330.6426.01446.97348.071
335.88582.18282.471.05650.9062.1290.04380.2578-0.2794-0.01570.0143-0.20760.40750.1152-0.05820.33670.15350.05830.2832-0.05460.388638.472-35.64144.47
346.5040.05352.14860.23780.01823.76340.04810.8372-0.3665-0.23060.0687-0.2830.53671.056-0.11680.33930.16680.25540.6076-0.13820.393462.072-23.98733.192
3511.5944.7062.65275.27782.45467.3721-0.68492.66551.3884-0.74610.9209-0.40590.24950.9174-0.2360.2099-0.02390.11250.99970.56270.595262.448-9.25121.763
365.3671-0.61110.88680.63990.14433.15510.2271.32190.0221-0.4299-0.1681-0.2760.2860.6268-0.05890.35880.14820.19430.6309-0.05780.298454.02-21.24726.501
375.8436.32590.10138.04461.90493.59050.31510.13261.17030.0234-0.10571.0399-0.4139-0.5944-0.20940.25630.10780.15410.29490.12510.32342.681-11.21439.592
380.13720.1596-0.68381.28250.61436.61590.03220.14350.0914-0.43390.2937-0.2871-0.81990.11-0.32590.22930.00250.19190.52290.30890.52655.063-6.7131.397
3910.2532-1.10583.82695.47364.35045.6715-0.42271.06882.0637-0.99410.144-0.5575-0.98590.68030.27870.4906-0.5185-0.04761.29640.75330.860462.1690.83420.712
400.04210.40850.1265.5160.91360.6788-0.09260.08520.06-0.4904-0.047-0.0563-0.7690.23770.13960.9887-0.4602-0.15351.20930.59720.500364.86510.02712.442
417.4603-1.2711-2.5264.72243.33056.38980.1352-0.18230.20560.05780.0257-0.22240.03680.5606-0.16080.240.0972-0.01410.26480.00440.390345.915-20.88663.956
422.15240.0464-0.41922.77691.11982.2819-0.0231-0.3138-0.06080.37380.0146-0.27550.20340.69710.00840.1444-0.0045-0.01690.62880.01210.520665.839-1.43671.787
431.50040.5882-1.8650.4446-0.06597.2144-0.33190.24840.0648-0.30280.1991-0.02910.59481.41170.13280.4430.19140.00780.79440.2560.446158.715.21346.903
442.02162.94312.98296.10464.52824.6784-0.38440.4895-0.0992-0.75780.4811-0.49-0.4330.9047-0.09680.19610.02170.0780.4798-0.02630.474363.2391.86553.75
454.44731.08861.1032.26721.12773.24660.050.5843-0.1378-0.2753-0.17040.1771-0.07090.37450.12050.23710.1688-0.07470.3009-0.11890.479447.4274.45856.025
464.30382.88740.40693.8186-2.458310.2476-0.55460.33520.4025-1.3506-0.25040.13840.10360.31950.8050.8330.2667-0.07880.39760.19710.44653.04221.55545.822
474.96-1.2642.2272.186-1.48914.3967-0.1611.20430.3805-0.5303-0.477-0.2377-0.37681.19060.6380.3425-0.00640.04420.84870.56590.43956.73129.89135.425
482.71760.9817-0.16522.744-0.72881.8134-0.13040.210.2496-0.4715-0.0319-0.3305-0.69461.39450.16240.6676-0.42860.28481.62020.50470.49466.64338.40131.91
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 95
2X-RAY DIFFRACTION2B96 - 190
3X-RAY DIFFRACTION3B191 - 326
4X-RAY DIFFRACTION4B327 - 376
5X-RAY DIFFRACTION5B377 - 444
6X-RAY DIFFRACTION6B445 - 486
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8X-RAY DIFFRACTION8B531 - 586
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11X-RAY DIFFRACTION11A121 - 326
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19X-RAY DIFFRACTION19E95 - 178
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24X-RAY DIFFRACTION24E409 - 451
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28X-RAY DIFFRACTION28D184 - 215
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32X-RAY DIFFRACTION32D415 - 452
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36X-RAY DIFFRACTION36F177 - 262
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