[English] 日本語
Yorodumi
- PDB-3wb8: Crystal Structure of MyoVa-GTD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wb8
TitleCrystal Structure of MyoVa-GTD
ComponentsUnconventional myosin-Va
KeywordsMOTOR PROTEIN / Helix bundle
Function / homology
Function and homology information


actomyosin, myosin complex part / establishment of endoplasmic reticulum localization to postsynapse / regulation of postsynaptic cytosolic calcium ion concentration / axo-dendritic protein transport / positive regulation of cellular response to insulin stimulus / melanosome localization / endoplasmic reticulum localization / locomotion involved in locomotory behavior / melanin metabolic process / vesicle transport along actin filament ...actomyosin, myosin complex part / establishment of endoplasmic reticulum localization to postsynapse / regulation of postsynaptic cytosolic calcium ion concentration / axo-dendritic protein transport / positive regulation of cellular response to insulin stimulus / melanosome localization / endoplasmic reticulum localization / locomotion involved in locomotory behavior / melanin metabolic process / vesicle transport along actin filament / negative regulation of dopamine secretion / unconventional myosin complex / insulin-responsive compartment / post-Golgi vesicle-mediated transport / secretory granule localization / developmental pigmentation / reactive gliosis / Regulation of MITF-M-dependent genes involved in pigmentation / Regulation of actin dynamics for phagocytic cup formation / melanin biosynthetic process / filopodium tip / hair follicle maturation / regulation of exocytosis / melanocyte differentiation / actin filament-based movement / actomyosin / melanosome transport / postsynaptic actin cytoskeleton / ATP-dependent protein binding / positive regulation of vascular associated smooth muscle cell migration / myosin complex / intermediate filament / negative regulation of synaptic transmission, glutamatergic / odontogenesis / long-chain fatty acid biosynthetic process / syntaxin-1 binding / insulin secretion / microfilament motor activity / pigmentation / exocytosis / smooth endoplasmic reticulum / dopamine metabolic process / cytoskeletal motor activity / photoreceptor outer segment / vesicle-mediated transport / ruffle / myelination / visual perception / secretory granule / actin filament organization / SNARE binding / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / macroautophagy / synapse organization / recycling endosome / Schaffer collateral - CA1 synapse / small GTPase binding / cellular response to insulin stimulus / endocytosis / disordered domain specific binding / calcium-dependent protein binding / synaptic vesicle / actin filament binding / melanosome / actin cytoskeleton / actin binding / protein-containing complex assembly / chemical synaptic transmission / calmodulin binding / postsynapse / ribonucleoprotein complex / axon / neuronal cell body / calcium ion binding / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Myosin 5a, cargo-binding domain / : / Unconventional myosin-Va domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like ...Myosin 5a, cargo-binding domain / : / Unconventional myosin-Va domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-Va
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.499 Å
AuthorsWei, Z. / Liu, X. / Yu, C. / Zhang, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis of cargo recognitions for class V myosins
Authors: Wei, Z. / Liu, X. / Yu, C. / Zhang, M.
History
DepositionMay 13, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Unconventional myosin-Va
B: Unconventional myosin-Va
C: Unconventional myosin-Va
D: Unconventional myosin-Va
E: Unconventional myosin-Va
F: Unconventional myosin-Va
G: Unconventional myosin-Va
H: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,34430
Polymers368,9798
Non-polymers1,36522
Water6,413356
1
A: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3715
Polymers46,1221
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2463
Polymers46,1221
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3094
Polymers46,1221
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3094
Polymers46,1221
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2463
Polymers46,1221
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3094
Polymers46,1221
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3094
Polymers46,1221
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Unconventional myosin-Va
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2463
Polymers46,1221
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.984, 165.355, 173.020
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Unconventional myosin-Va / Dilute myosin heavy chain / non-muscle


Mass: 46122.316 Da / Num. of mol.: 8
Fragment: Globular Tail Domain (GTD), UNP residues 1469-1853
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo5a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99104
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20-30%(w/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorDate: Apr 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. all: 131888 / Num. obs: 131888 / % possible obs: 98.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 50.82 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.64

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.499→41.793 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8356 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 23.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 6651 5.05 %
Rwork0.1731 --
obs0.1756 131807 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 249.63 Å2 / Biso mean: 63.0533 Å2 / Biso min: 20.37 Å2
Refinement stepCycle: LAST / Resolution: 2.499→41.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22825 0 88 356 23269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823273
X-RAY DIFFRACTIONf_angle_d1.06431402
X-RAY DIFFRACTIONf_chiral_restr0.0733659
X-RAY DIFFRACTIONf_plane_restr0.0053990
X-RAY DIFFRACTIONf_dihedral_angle_d15.2358803
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4989-2.52730.32061510.25553303345478
2.5273-2.5570.31912100.23253967417792
2.557-2.58820.30812190.22883964418395
2.5882-2.6210.28652230.22554139436298
2.621-2.65550.2742360.213142514487100
2.6555-2.69180.27792510.208641034354100
2.6918-2.73030.26462340.203342704504100
2.7303-2.7710.29062410.203442064447100
2.771-2.81430.24992230.203441894412100
2.8143-2.86050.29412280.200742314459100
2.8605-2.90980.29912100.201342694479100
2.9098-2.96270.26772000.198142264426100
2.9627-3.01960.28762290.203542204449100
3.0196-3.08120.27282540.209142024456100
3.0812-3.14820.26782180.208342644482100
3.1482-3.22140.26182130.205641904403100
3.2214-3.3020.27312120.199942864498100
3.302-3.39120.26612200.198142254445100
3.3912-3.49090.22392410.191641854426100
3.4909-3.60360.23012250.175142694494100
3.6036-3.73230.2212390.1742094448100
3.7323-3.88160.23182430.166642374480100
3.8816-4.05810.20422350.156142454480100
4.0581-4.27190.18732010.145642304431100
4.2719-4.53920.1962270.13742274454100
4.5392-4.88920.17762210.13864213443499
4.8892-5.38030.19682040.15534140434497
5.3803-6.15670.21832030.17894175437897
6.1567-7.74880.18332410.170942624503100
7.7488-41.79920.17041990.14014259445898
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)
18.4351-2.121-1.11387.9439-2.91088.22010.37921.2709-0.0454-0.9137-0.19140.24720.1334-0.2114-0.15240.4353-0.0225-0.06810.5045-0.02990.25953.84-8.8417-32.826
23.83411.255-0.97485.5922-1.37932.84290.0010.2555-0.2532-0.28230.0697-0.22060.32540.0239-0.08190.25090.0297-0.04310.2765-0.04560.2147.7442-11.4152-21.0947
35.15984.3728-4.92185.2083-5.92197.31540.1250.53080.13730.53670.49320.3578-0.3194-0.8304-0.61790.31420.0445-0.06240.3523-0.00930.3522-2.8354-16.6499-4.8451
41.12910.0098-2.32032.3274-0.81917.1102-0.133-0.0268-0.34950.1592-0.05690.13620.69150.01820.16320.3646-0.02-0.07140.26910.02740.4352-0.4968-31.90999.3606
54.9833-0.9985-0.67355.6730.71175.8211-0.0832-0.3385-0.97380.957-0.03290.77360.9397-0.62360.09680.6087-0.03460.1160.33040.04810.559-7.5942-31.969826.7785
65.48872.3169-1.43922.183-1.30036.18080.2514-0.96480.07861.1034-0.43520.1945-0.3519-0.1723-0.06310.679-0.00240.03220.3839-0.00670.4281-2.6245-20.826631.2943
71.3420.1221-1.54331.4806-1.78941.74940.05910.2466-0.2231-0.0936-0.0123-0.17560.3701-0.17730.02820.3148-0.0229-0.08650.4264-0.14480.51317.0113-16.8271-16.8364
82.142-0.148-3.03683.65751.30915.24770.17371.64530.7116-0.8193-0.2736-0.208-0.3146-0.60820.00460.48190.14230.05290.84310.14490.47854.7238-5.7797-119.272
95.89651.3083-2.3083.9001-1.3564.53280.10350.34150.0798-0.22180.0983-0.16530.1043-0.158-0.2040.26410.0375-0.00450.381-0.04440.25158.0797-7.6265-107.247
106.56884.6624-5.79846.8264-5.52657.18790.2530.62710.19560.80330.39150.3904-0.5282-1.1156-0.68810.33820.0311-0.05210.5433-0.0460.3498-2.4833-12.2041-90.8283
114.1465-0.306-0.68474.044-0.83688.6156-0.18710.0884-0.64260.13130.14130.54371.3422-0.85260.17570.5018-0.0987-0.01390.4544-0.09450.5722-2.8319-29.0112-88.19
122.9453-0.0782-1.11146.4979-1.28347.17460.2848-0.5514-0.54341.6496-0.36970.41160.3521-0.22040.0550.7507-0.1793-0.00280.46330.02680.4606-1.4472-26.8696-76.7459
130.3414-0.00240.39762.2531-3.14165.4610.1513-0.6105-0.33442.4389-0.2461-0.52310.32290.52970.21741.5672-0.2751-0.04890.67850.06580.38943.5803-25.1651-68.2516
144.11060.3164-4.98820.0072-0.29995.9432-0.0057-1.5865-0.371.88240.21080.1205-0.2978-0.26140.27233.0529-0.53180.67021.27140.08270.177-7.2332-22.2084-55.5688
152.10120.93790.65082.8985-1.39881.18580.1261-0.0822-0.19190.5432-0.1262-0.2167-0.09840.13420.05640.35480.0115-0.01360.4018-0.03680.44785.8103-12.7969-95.1287
164.1413-1.80160.99614.0968-1.20324.6682-0.1191-0.4059-0.16640.60420.22270.7348-0.1703-0.5334-0.11580.42710.01410.19210.369-0.05990.4836-14.5150.370821.6594
171.4261-0.86810.51784.1294-4.67168.33340.09010.03980.15230.2455-0.05270.1373-0.4334-0.0714-0.03910.26330.01280.08120.2715-0.08150.4033-4.86319.8648.4603
181.5171-0.2648-1.91592.74790.42487.56990.16520.06380.5029-0.165-0.0421-0.1883-0.69880.0752-0.13640.29550.05630.04880.28770.02690.48565.57521.5306-13.8691
191.70470.4355-1.68551.99211.54935.16390.27550.54750.4349-0.7357-0.0955-0.5597-1.1008-0.2073-0.10140.62430.09660.23490.51060.12050.628312.534519.806-32.1212
200.06290.3322-0.09570.5753-0.49321.68420.05590.03370.10380.1785-0.0732-0.0004-0.3494-0.3296-0.06560.44020.10650.0370.4509-0.02470.4758-3.45167.6159.8143
219.3042.55352.31195.43220.15494.50680.1822-1.2407-0.60421.1687-0.1053-0.2972-0.0035-0.0556-0.16670.4411-0.0059-0.03080.50180.04330.2928-29.9617-3.5202-14.2613
223.6918-0.49120.88193.2023-0.85143.02370.0021-0.22090.0810.12580.0502-0.0124-0.1039-0.1033-0.05450.2324-0.02210.00560.229-0.02540.1989-26.6745-0.5443-25.9615
235.5125-5.15614.287.6205-5.76265.19410.2206-0.2943-0.4882-0.33220.38921.02620.1923-0.6112-0.55290.2527-0.01970.01710.3865-0.02760.3036-37.03986.2866-42.4382
246.4331-2.55584.33076.1912-4.12043.1517-0.01440.19530.51030.0219-0.22970.2524-0.7046-0.24370.39810.47750.1250.03720.384-0.06390.4462-36.870323.4613-43.0256
251.8602-0.37630.85453.995-1.32817.4629-0.15140.2750.4462-0.6459-0.01920.1248-0.75990.08150.19660.4146-0.0168-0.04510.31420.02530.4167-33.754921.0014-60.6607
264.2717-0.8834-0.67655.6288-0.16854.75380.10130.95690.5466-1.51040.02190.2157-0.1154-0.57260.07480.64-0.0352-0.14730.55070.03540.4502-38.050215.0923-71.7126
273.6595-0.50991.58392.684-1.66231.26690.0012-0.33930.21270.3845-0.0986-0.1492-0.5926-0.07220.08690.2530.0051-0.02920.399-0.1070.3627-23.48644.5496-21.5912
282.10322.40981.38978.5651-2.26322.19790.2823-1.7118-0.51131.34290.0083-0.457-0.4240.1697-0.26770.5635-0.0118-0.04710.9509-0.01910.4995-30.78411.443671.1937
293.2391-1.8091.88296.3111-3.37725.1408-0.1407-0.35120.39660.52370.2141-0.277-0.6248-0.2363-0.10670.3059-0.00620.05690.4334-0.10120.3538-31.21574.100459.4153
301.5016-1.65621.91865.619-4.00564.6113-0.0032-0.10330.3487-0.1674-0.0909-0.5058-0.11880.15650.06220.28-0.02830.16640.35-0.08080.4186-31.958910.365145.1061
313.32180.4672.22383.24740.39486.0507-0.09990.43820.5325-0.86520.01220.0953-0.28370.24630.10960.55060.01050.10270.28380.04580.4655-36.854417.074921.3289
322.70.24121.13182.8043-0.75474.9764-0.27960.69420.1987-1.11130.02360.04820.0612-0.17990.18671.0681-0.063-0.07370.48760.05450.4792-41.94038.68112.3064
331.9331-0.50771.42292.2902-1.6061.5886-0.3249-0.58070.5560.355-0.0774-0.4935-1.0496-0.38940.40670.47820.0482-0.13170.6258-0.18950.6953-23.68378.62762.2846
345.90890.9714-1.92783.846-1.46675.3728-0.01130.653-0.0292-0.77560.06050.4172-0.0984-0.2198-0.05860.5896-0.0188-0.17380.3473-0.06990.3659-50.8519-17.117316.9308
353.09020.7125-0.87513.4173-1.09933.9972-0.07250.15210.1048-0.30530.0972-0.031-0.26480.2539-0.01690.4736-0.0219-0.12850.3282-0.07630.3731-42.0793-14.605621.8742
362.30761.3448-0.7686.6882-6.08943.3920.0437-0.25060.00150.582-0.0274-0.1006-0.7707-0.0483-0.14310.56470.018-0.10990.3663-0.09860.5467-41.8428-17.883240.4825
373.63060.759-0.08962.81071.08123.51360.2174-0.4339-0.519-0.16960.04190.42661.1989-0.6567-0.10180.4489-0.0446-0.14150.4347-0.00250.6896-42.8102-34.638345.858
381.895-0.53281.79182.65510.11028.32290.2479-0.1366-0.54510.2174-0.0959-0.1370.78980.1221-0.17820.3653-0.0584-0.1330.34850.06110.576-32.4087-31.750952.1948
392.30540.64790.97682.90730.77253.83850.2146-0.6354-0.41060.6832-0.0692-0.47930.32050.2625-0.10360.5034-0.0752-0.21690.5760.11720.6273-24.2341-25.071964.9892
402.47210.5476-1.32210.5972-1.06721.89910.06470.6962-0.7782-0.50250.1479-0.11460.0117-0.3083-0.20140.66470.0466-0.05160.492-0.18570.4598-47.3316-23.307114.3315
413.80830.97160.53474.4388-1.11444.41850.01580.4461-0.045-0.73240.01720.280.5174-0.2837-0.02320.5688-0.0121-0.1320.426-0.08830.3458-42.2373-10.3325-69.7126
420.84610.6519-0.3315.6798-5.45666.04770.0572-0.1329-0.14530.8317-0.1175-0.218-0.6715-0.5918-0.00130.5377-0.0844-0.06250.5253-0.11850.4356-40.2507-16.7115-49.214
433.1838-0.24370.95213.9389-1.3443.75940.2671-0.1767-0.33-1.17090.37911.0641.3983-1.1222-0.33330.9021-0.2329-0.30020.5521-0.06350.7196-42.0331-33.0427-48.4318
440.1216-0.91611.09722.8083-2.35655.62740.03450.0653-0.3139-0.69740.0070.2360.9891-0.3427-0.0740.5392-0.1363-0.10380.3746-0.05180.6096-33.5783-33.0198-39.1335
451.80560.26420.12634.8393-1.24373.79280.00980.0277-0.2998-0.06160.0669-0.68250.62450.3567-0.09960.3486-0.0253-0.03230.2529-0.03490.605-23.826-32.8298-30.853
465.96174.90580.34299.32450.41192.77940.5324-0.4271-0.7441.4675-0.3364-0.71880.52250.2123-0.11010.6268-0.0421-0.23540.35560.05810.6335-24.3486-35.0267-17.1424
47-0.1549-0.6412-0.29740.7939-1.13491.55640.25350.1795-0.3398-0.45260.0992-0.00170.7074-0.3687-0.35490.6184-0.1417-0.09930.5495-0.04780.4636-36.7068-17.2398-58.2537
482.4578-0.3501-0.75922.44430.88883.26940.2589-0.45260.21591.2287-0.26350.8419-0.0222-0.52060.07891.4812-0.25180.62980.8191-0.26881.1113-12.54757.3603-68.2423
491.4472-1.2982-3.0231.21013.46042.0296-0.3061-1.48040.3421.6494-0.1120.24931.4050.28040.09152.1432-0.32260.16950.9194-0.14481.05922.86745.3393-58.5428
501.40590.578-0.59475.1345-1.58823.12830.6430.10590.26340.5339-0.39151.4620.3381-0.0529-0.21450.8581-0.05380.41890.6396-0.29861.2996-5.805511.0949-86.3645
512.88810.2123-0.97015.6746-0.2634.72250.44110.26070.7264-0.0117-0.35010.1191-1.117-0.2505-0.130.61930.09430.23670.46350.0190.93054.634125.5781-100.9919
520.9821-0.1683-0.38120.8606-0.0914.22750.0654-0.46270.43040.6417-0.10830.17940.1175-0.26810.06680.9405-0.14610.31370.7234-0.23350.9395-3.318612.5822-77.5476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1471 : 1489 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 1490 : 1593 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 1594 : 1627 )
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 1628 : 1768 )
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 1769 : 1795 )
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 1796 : 1815 )
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 1816 : 1853 )
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 1470 : 1489 )
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 1490 : 1593 )
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 1594 : 1627 )
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 1628 : 1679 )
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 1680 : 1730 )
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 1731 : 1773 )
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 1774 : 1805 )
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 1806 : 1853 )
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 1471 : 1545 )
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 1546 : 1679 )
18X-RAY DIFFRACTION18CHAIN C AND (RESSEQ 1680 : 1783 )
19X-RAY DIFFRACTION19CHAIN C AND (RESSEQ 1784 : 1808 )
20X-RAY DIFFRACTION20CHAIN C AND (RESSEQ 1809 : 1853 )
21X-RAY DIFFRACTION21CHAIN D AND (RESSEQ 1470 : 1489 )
22X-RAY DIFFRACTION22CHAIN D AND (RESSEQ 1490 : 1593 )
23X-RAY DIFFRACTION23CHAIN D AND (RESSEQ 1594 : 1628 )
24X-RAY DIFFRACTION24CHAIN D AND (RESSEQ 1629 : 1679 )
25X-RAY DIFFRACTION25CHAIN D AND (RESSEQ 1680 : 1783 )
26X-RAY DIFFRACTION26CHAIN D AND (RESSEQ 1784 : 1824 )
27X-RAY DIFFRACTION27CHAIN D AND (RESSEQ 1825 : 1853 )
28X-RAY DIFFRACTION28CHAIN E AND (RESSEQ 1471 : 1489 )
29X-RAY DIFFRACTION29CHAIN E AND (RESSEQ 1490 : 1568 )
30X-RAY DIFFRACTION30CHAIN E AND (RESSEQ 1569 : 1679 )
31X-RAY DIFFRACTION31CHAIN E AND (RESSEQ 1680 : 1783 )
32X-RAY DIFFRACTION32CHAIN E AND (RESSEQ 1784 : 1824 )
33X-RAY DIFFRACTION33CHAIN E AND (RESSEQ 1825 : 1853 )
34X-RAY DIFFRACTION34CHAIN F AND (RESSEQ 1471 : 1523 )
35X-RAY DIFFRACTION35CHAIN F AND (RESSEQ 1524 : 1593 )
36X-RAY DIFFRACTION36CHAIN F AND (RESSEQ 1594 : 1627 )
37X-RAY DIFFRACTION37CHAIN F AND (RESSEQ 1628 : 1679 )
38X-RAY DIFFRACTION38CHAIN F AND (RESSEQ 1680 : 1751 )
39X-RAY DIFFRACTION39CHAIN F AND (RESSEQ 1752 : 1828 )
40X-RAY DIFFRACTION40CHAIN F AND (RESSEQ 1829 : 1853 )
41X-RAY DIFFRACTION41CHAIN G AND (RESSEQ 1470 : 1593 )
42X-RAY DIFFRACTION42CHAIN G AND (RESSEQ 1594 : 1627 )
43X-RAY DIFFRACTION43CHAIN G AND (RESSEQ 1628 : 1679 )
44X-RAY DIFFRACTION44CHAIN G AND (RESSEQ 1680 : 1730 )
45X-RAY DIFFRACTION45CHAIN G AND (RESSEQ 1731 : 1783 )
46X-RAY DIFFRACTION46CHAIN G AND (RESSEQ 1784 : 1808 )
47X-RAY DIFFRACTION47CHAIN G AND (RESSEQ 1809 : 1853 )
48X-RAY DIFFRACTION48CHAIN H AND (RESSEQ 1471 : 1568 )
49X-RAY DIFFRACTION49CHAIN H AND (RESSEQ 1569 : 1593 )
50X-RAY DIFFRACTION50CHAIN H AND (RESSEQ 1594 : 1627 )
51X-RAY DIFFRACTION51CHAIN H AND (RESSEQ 1628 : 1808 )
52X-RAY DIFFRACTION52CHAIN H AND (RESSEQ 1809 : 1853 )

+
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