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- PDB-3eih: Crystal structure of S.cerevisiae Vps4 in the presence of ATPgammaS -

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Basic information

Entry
Database: PDB / ID: 3eih
TitleCrystal structure of S.cerevisiae Vps4 in the presence of ATPgammaS
ComponentsVacuolar protein sorting-associated protein 4Vacuole
KeywordsPROTEIN TRANSPORT / AAA ATPase / ATP-binding cassette / ATP-binding / Endosome / Membrane / Nucleotide-binding / Phosphoprotein / Transport
Function / homology
Function and homology information


ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / vacuole organization ...ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / vacuole organization / multivesicular body sorting pathway / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / nucleus organization / endosomal transport / ATPase complex / autophagosome maturation / nuclear pore / macroautophagy / autophagy / protein transport / midbody / endosome / endoplasmic reticulum / ATP hydrolysis activity / protein homodimerization activity / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 4, MIT domain / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Vps4 C terminal oligomerisation domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain ...Vacuolar protein sorting-associated protein 4, MIT domain / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Vps4 C terminal oligomerisation domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Vacuolar protein sorting-associated protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsGonciarz, M.D. / Whitby, F.G. / Eckert, D.M. / Kieffer, C. / Heroux, A. / Sundquist, W.I. / Hill, C.P.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Biochemical and structural studies of yeast vps4 oligomerization.
Authors: Gonciarz, M.D. / Whitby, F.G. / Eckert, D.M. / Kieffer, C. / Heroux, A. / Sundquist, W.I. / Hill, C.P.
History
DepositionSep 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2012Group: Non-polymer description
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 4
B: Vacuolar protein sorting-associated protein 4
C: Vacuolar protein sorting-associated protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2749
Polymers112,0923
Non-polymers1,1816
Water0
1
A: Vacuolar protein sorting-associated protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9123
Polymers37,3641
Non-polymers5482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vacuolar protein sorting-associated protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9123
Polymers37,3641
Non-polymers5482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Vacuolar protein sorting-associated protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4503
Polymers37,3641
Non-polymers862
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.956, 119.804, 156.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vacuolar protein sorting-associated protein 4 / Vacuole / Protein END13 / DOA4-independent degradation protein 6 / Vacuolar protein-targeting protein 10


Mass: 37364.098 Da / Num. of mol.: 3 / Fragment: UNP residues 104-437 / Mutation: E233Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10
Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P52917
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2

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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: 3.22 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 48 % Ethylene glycol, 0.1M Bis-Tris, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 23550 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8
Reflection shellResolution: 3.25→3.37 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.4.0054refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→33 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.88 / SU B: 26.645 / SU ML: 0.44 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30457 1208 5.1 %RANDOM
Rwork0.2255 ---
obs0.22958 22286 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.713 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---1.7 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 3.25→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7327 0 69 0 7396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227521
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9910181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5955941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.48724.922321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.443151361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5971547
X-RAY DIFFRACTIONr_chiral_restr0.1070.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215561
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_it0.6241.54703
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1727608
X-RAY DIFFRACTIONr_scbond_it1.26732818
X-RAY DIFFRACTIONr_scangle_it2.3194.52573
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 77 -
Rwork0.278 1587 -
obs--97.14 %
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)
16.030.6207-2.17752.577-0.76430.9024-0.40350.9286-0.2894-0.87960.27120.207-0.31630.10150.13240.46450.0945-0.00370.43860.05480.22619.209-40.8712-29.8547
24.8017-2.8961-1.79491.92741.67872.6381-0.0136-0.23710.21340.24390.0414-0.3424-0.17580.3671-0.02780.32050.0158-0.01380.35240.00810.359517.8444-35.8793-16.1509
35.4113-6.98485.95679.0159-7.68886.55710.08860.2597-0.6158-0.0955-0.3651-0.65180.22940.03690.27660.3945-0.0091-0.04350.3754-0.10850.384828.8261-49.6996-14.5364
44.6131.4236-1.51040.95650.39261.9205-0.15820.1537-0.04270.07050.2172-0.03320.1010.1931-0.05890.3441-0.0210.00550.3495-0.02530.33437.7613-39.777-16.5603
52.22220.73011.1211.44990.92643.1376-0.3940.29830.057-0.59270.24280.05950.1650.1080.15120.38890.02730.02360.3317-0.06640.3498.705-44.0215-26.0655
63.34211.0018-0.32876.75994.20672.9017-0.0954-0.00370.0736-0.0396-0.08030.48560.2159-0.28980.17560.47090.00450.0060.473-0.0350.448-4.7656-55.4549-27.1917
75.14761.1341-3.18975.66690.57592.8781-0.3115-0.0534-0.3449-0.16180.1692-0.1197-0.05840.18630.14230.38270.05060.00340.3994-0.0890.3118.5652-51.4173-25.824
84.25182.7253-3.410210.29540.57053.62381.51672.2303-2.0822.17680.48611.31090.7044-1.0808-2.00270.5658-0.0171-0.03020.47060.22910.7507-7.9534-56.6067-12.5869
95.273-1.02123.29260.5299-0.85812.20240.5047-0.3738-0.54840.2311-0.15640.32430.0988-0.8092-0.34830.6717-0.00870.01490.5215-0.07050.5695-4.7178-61.6505-17.7111
100.06210.0295-0.27590.79340.42221.61861.9284-0.1554-0.06280.8225-0.2238-1.321-0.11331.8562-1.70460.40230.0158-0.09680.56130.05780.599913.6632-58.7071-19.8205
110.4929-0.2119-2.01354.56360.66658.23460.3509-0.1489-0.84420.278-0.29850.26220.10040.3749-0.05250.3870.0344-0.02930.40290.0060.34064.034-49.5084-11.8229
121.4203-0.69220.27395.9254-2.0161.82930.06040.06320.07420.1688-0.0482-0.00050.05470.1976-0.01220.266-0.01870.00510.3815-0.02020.2815.6126-26.5932-15.9019
131.7924-1.1195-1.33456.02230.81075.3082-0.0025-0.11350.12220.27340.0667-0.0336-0.09130.1409-0.06420.33010.0426-0.00210.37570.01550.2725-1.0909-20.4978-13.5313
141.0392-1.66152.09652.6564-3.35194.22960.1233-0.0750.2043-0.51670.12150.3080.6247-0.698-0.24480.42520.0090.03080.36740.02780.2988-10.0712-17.5886-28.3168
155.78192.1175-0.1764.36791.56093.42450.0856-0.18940.7257-0.08070.1364-0.3794-0.2070.4333-0.2220.47110.00760.01060.39150.07950.4171-5.074-1.5946-40.1319
166.7750.90460.83634.28382.23243.03510.175-0.21280.2406-0.25460.05740.1374-0.2683-0.393-0.23240.437-0.02650.00420.42520.15640.3318-13.4595-4.4571-39.6648
170.2774-0.13121.4670.0621-0.69387.7572-0.08550.27420.1721-0.26730.03390.0924-0.27370.14910.05160.38810.00920.02660.34420.02790.3497-6.6616-11.6427-26.2123
180.8385-2.53871.84957.9503-5.42384.1972-0.2007-0.5940.3330.32780.46540.29710.509-0.7894-0.26460.4148-0.0460.0780.42280.04940.2918-6.6729-32.2379-6.6612
192.8816-0.17482.42195.378-0.34042.04260.0497-0.2508-0.07840.12270.035-0.26150.41720.6328-0.08470.52570.0316-0.0040.48730.05120.38487.1899-46.1795-0.8944
201.03980.664-0.97014.71340.9174.2913-0.29921.3815-0.433-0.4310.44450.1283-0.17480.4818-0.14530.6326-0.1763-0.01690.40710.03020.353216.5897-72.4115-3.0781
211.46030.9656-0.43115.1727-0.54742.3901-0.1020.1989-0.207-0.05710.1286-0.17430.14710.1919-0.02660.43810.02080.00960.44790.00590.447920.5257-80.65639.2314
221.6894-0.1423-0.60043.03360.92940.5594-0.101-0.0169-0.2920.00890.06160.38720.27090.03720.03940.4204-0.0533-0.03060.30590.01960.435713.6935-79.54339.0787
233.7514-1.9819-1.69583.77751.97681.74110.06070.20930.0134-0.2824-0.11580.2369-0.2385-0.24940.05510.5057-0.0511-0.04320.45270.03170.44967.2154-72.0376-0.3285
245.72743.894-0.81432.79450.15793.5596-0.05820.1319-0.0947-0.64040.18280.809-0.0015-0.2908-0.12460.5223-0.0683-0.31640.24190.13280.4671-0.465-74.238-1.4838
258.3503-7.2031-2.32116.21362.00220.64520.2957-0.1696-0.17620.3167-0.11880.779-0.4798-0.6155-0.1770.5707-0.0155-0.05430.6380.05060.7021-3.423-62.179211.2382
263.5913.5264-0.88724.6711-3.81777.4052-0.2951-1.18140.8235-0.50450.37940.7033-0.0372-0.4511-0.08430.2983-0.2236-0.0690.61920.02160.7967-6.2796-75.25898.0231
276.1622-0.22621.75450.6308-1.63744.47430.2028-0.19540.31970.7364-0.10210.75320.7125-0.3411-0.10080.4423-0.11420.03770.39770.21290.43995.4777-71.764611.7755
283.26252.233-1.21895.0187-1.84953.5225-0.0027-0.10040.0420.41980.21620.37820.4626-0.4057-0.21350.4221-0.04680.04280.35120.02540.333211.6548-71.939615.6078
292.7341-0.5795-0.28721.2105-1.48453.39530.13570.3511-0.0341-0.18540.0285-0.00710.34310.4758-0.16430.44-0.005-0.03850.3364-0.11320.358634.3414-57.75811.7693
301.06690.9041-0.52953.7411-2.76774.14340.01830.0358-0.06070.12150.20960.022-0.1782-0.1899-0.22790.34450.0152-0.00120.3745-0.09030.281728.964-46.57970.0491
316.42390.487-0.96372.88021.68523.1305-0.09520.13050.32490.1765-0.1424-0.2204-0.15580.28330.23750.412-0.0191-0.03770.38930.06920.322939.9667-33.9869-15.2277
320.56330.55480.43343.2854-3.26795.3174-0.01130.1631-0.21830.0425-0.2836-0.1457-0.24870.05970.29490.33080.0339-0.05780.3673-0.08590.337932.8243-44.2453-3.5403
331.4128-0.28410.11330.57760.66750.92450.0261-0.75320.03570.6648-0.02240.09640.3352-0.2647-0.00380.483-0.10.1220.4475-0.00840.333313.2465-63.092921.6897
344.1558-2.5221.44862.71990.43591.9588-1.1177-0.76760.7489-0.14920.6220.00170.7083-0.13770.49570.94280.3886-0.03530.6059-0.1961-0.057821.8496-87.1012-25.6441
354.7929-3.20431.28673.8174-0.11710.6751-0.1270.08080.84640.0278-0.1114-0.81160.05840.62780.23840.54380.004-0.04990.5107-0.01010.521823.9676-80.748-37.5985
367.7179-0.88360.23110.3975-0.27823.1849-0.4103-0.1186-0.28390.60820.29410.4935-0.0228-0.32160.11620.47540.07530.08990.3919-0.09270.157211.2579-83.8741-39.958
370.01590.0051-0.31220.0017-0.1016.12760.30140.43421.38561.8286-1.0243-1.10040.6256-1.23370.7230.74790.2825-0.20410.407-0.05190.486524.1865-89.1944-30.6476
382.87180.71352.75535.6111-1.33373.39320.36940.0293-0.49171.269-0.46230.02720.3447-0.660.09290.6074-0.04580.50550.47120.32250.352114.0838-104.7706-30.0633
394.1944-0.33740.06164.47893.18542.28720.0051-0.4788-0.2137-0.27890.06920.2982-0.34950.0786-0.07430.71390.04890.06950.57490.14930.454616.3618-98.8637-33.6145
402.936-1.14882.48781.6776-2.393.7421-0.3147-0.22750.01010.45990.4971-0.16740.0013-0.1395-0.18250.665-0.0330.03450.6820.0130.682511.714-107.3571-41.8685
410.54290.3496-1.24626.10974.07296.9-0.97940.7093-0.01510.8524-0.05771.430.4792-0.73911.03710.65190.09310.37440.39330.0970.160915.5238-95.0113-37.8794
423.9251-0.78660.94560.2218-0.59372.772-0.55260.095-0.05210.26450.11010.27220.15640.06370.44250.25580.0532-0.03360.4560.0080.260327.834-90.7457-41.7593
431.3639-1.4763-1.85046.73950.58613.073-0.21240.20110.68-0.0011-0.3320.3511-0.40770.72430.54440.47570.0479-0.14530.57290.08880.386846.6554-80.205-30.3932
441.3022-0.0262.03650.3226-0.07613.1891.28731.30050.15630.5784-0.7525-0.00560.55130.7716-0.53480.3161-0.1346-0.12790.57650.02570.429755.4366-89.8483-22.1109
450.75230.8048-0.17856.4699-6.60647.38010.32490.11741.40060.1666-0.68460.3796-0.23-0.25020.35970.5134-0.1548-0.26330.24050.0480.667566.8081-75.4326-10.4094
464.748-0.34232.27170.1867-0.23331.11670.05891.04210.23180.1268-0.1286-0.1611-0.00790.80480.06970.4799-0.0052-0.24120.41110.13260.400660.1897-86.6771-21.9755
474.68021.0583-2.26756.2340.96725.05420.0692-0.21020.00050.01010.05040.0477-0.16130.0593-0.11960.4451-0.0159-0.00080.50230.00380.32828.4177-93.5724-50.7658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A119 - 132
2X-RAY DIFFRACTION2A133 - 154
3X-RAY DIFFRACTION3A155 - 165
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