[English] 日本語
Yorodumi
- PDB-3b5n: Structure of the yeast plasma membrane SNARE complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b5n
TitleStructure of the yeast plasma membrane SNARE complex
Components
  • (Protein transport protein SEC9Protein targeting) x 2
  • Protein SSO1
  • Synaptobrevin homolog 1
KeywordsMEMBRANE PROTEIN / SNARE complex / syntaxin / synaptobrevin / snap-25 / Sso1p / Snc1p / Sec9p / Sec9 / Sso1 / Snc1 / Coiled coil / Lipoprotein / Membrane / Palmitate / Transmembrane / Ubl conjugation / Phosphorylation / Protein transport / Transport
Function / homology
Function and homology information


: / vesicle fusion to plasma membrane / Disinhibition of SNARE formation / Clathrin-mediated endocytosis / ascospore-type prospore assembly / Retrograde transport at the Trans-Golgi-Network / Cargo recognition for clathrin-mediated endocytosis / sporulation / Golgi vesicle fusion to target membrane / cellular bud ...: / vesicle fusion to plasma membrane / Disinhibition of SNARE formation / Clathrin-mediated endocytosis / ascospore-type prospore assembly / Retrograde transport at the Trans-Golgi-Network / Cargo recognition for clathrin-mediated endocytosis / sporulation / Golgi vesicle fusion to target membrane / cellular bud / trans-Golgi Network Vesicle Budding / prospore membrane / ascospore formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / COPII-mediated vesicle transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / Golgi to plasma membrane transport / cellular bud neck / phosphatidic acid binding / phosphatidylinositol-3,4-bisphosphate binding / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / SNARE complex assembly / syntaxin binding / transport vesicle membrane / extrinsic component of plasma membrane / exocytosis / endomembrane system / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / SNARE binding / cell periphery / intracellular protein transport / trans-Golgi network / endocytosis / protein transport / membrane => GO:0016020 / endosome / Golgi membrane / plasma membrane / cytosol
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Synaptobrevin-like / Syntaxin/epimorphin, conserved site ...Synaptobrevin/Vesicle-associated membrane protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Synaptobrevin / Syntaxin / epimorphin family signature. / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Synaptobrevin homolog 1 / Protein SSO1 / Protein transport protein SEC9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsStrop, P. / Brunger, A.T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Structure of the Yeast Plasma Membrane SNARE Complex Reveals Destabilizing Water-filled Cavities.
Authors: Strop, P. / Kaiser, S.E. / Vrljic, M. / Brunger, A.T.
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptobrevin homolog 1
B: Protein SSO1
C: Protein transport protein SEC9
D: Protein transport protein SEC9
E: Synaptobrevin homolog 1
F: Protein SSO1
G: Protein transport protein SEC9
H: Protein transport protein SEC9
I: Synaptobrevin homolog 1
J: Protein SSO1
K: Protein transport protein SEC9
L: Protein transport protein SEC9


Theoretical massNumber of molelcules
Total (without water)88,81312
Polymers88,81312
Non-polymers00
Water10,665592
1
A: Synaptobrevin homolog 1
B: Protein SSO1
C: Protein transport protein SEC9
D: Protein transport protein SEC9


Theoretical massNumber of molelcules
Total (without water)29,6044
Polymers29,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
MethodPISA
2
E: Synaptobrevin homolog 1
F: Protein SSO1
G: Protein transport protein SEC9
H: Protein transport protein SEC9


Theoretical massNumber of molelcules
Total (without water)29,6044
Polymers29,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11980 Å2
MethodPISA
3
I: Synaptobrevin homolog 1
J: Protein SSO1
K: Protein transport protein SEC9
L: Protein transport protein SEC9


Theoretical massNumber of molelcules
Total (without water)29,6044
Polymers29,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.956, 48.113, 110.265
Angle α, β, γ (deg.)90.00, 97.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Synaptobrevin homolog 1


Mass: 6771.594 Da / Num. of mol.: 3 / Fragment: Residues 27-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNC1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31109
#2: Protein Protein SSO1


Mass: 7797.670 Da / Num. of mol.: 3 / Fragment: Residues 189-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SSO1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32867
#3: Protein Protein transport protein SEC9 / Protein targeting


Mass: 7685.770 Da / Num. of mol.: 3 / Fragment: Residues 433-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC9, HSS7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40357
#4: Protein Protein transport protein SEC9 / Protein targeting


Mass: 7349.194 Da / Num. of mol.: 3 / Fragment: Residues 589-650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC9, HSS7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40357
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 100 mM MES pH 6.25, 30 % MPD, 200 mM Sodium bromide, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 90852 / % possible obs: 83.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Χ2: 1.131 / Net I/σ(I): 16
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4177 / Χ2: 0.983 / % possible all: 38.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N7S

1n7s


Resolution: 1.6→34.571 Å / FOM work R set: 0.759 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.248 4521 5.02 %
Rwork0.206 --
obs-90025 84.97 %
Solvent computationBsol: 72.531 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 146.93 Å2 / Biso mean: 44.18 Å2 / Biso min: 19.08 Å2
Baniso -1Baniso -2Baniso -3
1-9.437 Å20 Å20.803 Å2
2--1.729 Å20 Å2
3----14.876 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 0 592 6656
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_deg0.4631
X-RAY DIFFRACTIONf_bond_d0.0031
X-RAY DIFFRACTIONf_chiral_restr0.0331
X-RAY DIFFRACTIONf_dihedral_angle_d9.3981
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.0431
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)
10.7901-0.0992-0.33421.7478-1.4752.27150.3520.0272-0.29590.85720.0989-0.4378-1.60741.32250.02720.5182-0.1474-0.00450.3456-0.00870.359714.13351.786569.7046
20.3445-0.2195-0.1507-0.206-0.28573.7066-0.03040.11440.1551-0.13110.01950.2037-1.12440.0198-0.16440.37450.01960.00070.29490.01860.3397.64483.691645.1131
31.080.34710.23492.3055-0.47950.6991-0.01310.367-0.1072-0.4726-0.25280.04910.2557-0.90730.0380.27850.0648-0.08710.3504-0.01790.28875.9277-5.609911.5318
41.1840.8654-0.57441.4651-1.05484.08240.2402-0.04090.2610.55990.01270.1621-1.4864-0.3641-0.24810.49560.08520.10360.21590.00780.36614.79860.972277.6895
5-0.5246-0.7012-0.48150.69730.25475.03240.09020.0595-0.0764-0.0061-0.10530.1657-0.2905-1.2665-0.25240.2175-0.00160.01630.34850.01680.353.5267-4.104453.2193
61.06360.49581.42621.8991-0.43963.5624-0.08110.3787-0.1793-0.1778-0.0304-0.05660.9823-0.2043-0.22570.21210.0719-0.07990.26440.0240.277210.4339-8.779418.8376
70.914-0.3473-0.6431.320.60643.4197-0.1096-0.0585-0.06050.41440.06140.26440.1851-0.8307-0.1040.25730.03790.07220.26520.03310.35091.8152-7.598579.2375
8-0.5021-0.2231.49270.29280.71051.26550.0057-0.056-0.0071-0.0529-0.03630.04330.79760.5202-0.15380.23420.0461-0.03580.29180.00430.280712.3081-9.07742.3436
91.0738-0.28051.07151.76610.01661.17570.0383-0.01880.0256-0.43110.13410.1821-0.5689-0.3293-0.01730.45960.0657-0.00880.48950.03920.302918.1023-0.47656.5714
102.7689-0.34570.84610.51470.10552.73370.1432-0.3721-0.15890.143-0.02440.0937-0.19640.9304-0.03770.2075-0.0009-0.00010.26260.00280.313712.3918-9.867375.0999
110.3-0.32770.03530.5665-0.42952.12280.16450.06350.0136-0.2023-0.01280.0999-0.38051.1139-0.15620.2457-0.07030.02080.4281-0.01630.297616.8421-1.313450.2544
120.5526-0.14850.18410.48830.36144.70940.02220.23450.064-0.258-0.07780.0212-1.1641-0.0048-0.10440.27690.0239-0.02670.36630.03910.295411.60823.081620.3631
130.6413-0.07460.80782.24440.16592.6407-0.1770.03630.1971-0.40230.2001-0.20640.64010.58780.09420.31350.0074-0.00180.2081-0.02360.265940.98083.2268.9386
140.20161.32791.20661.83340.51063.9647-0.02310.0535-0.1753-0.0425-0.27120.12711.09-0.60610.11610.29560.0112-0.00320.3501-0.04570.284227.15876.597636.2398
150.7841-0.41730.38782.79150.90263.3533-0.1073-0.1789-0.32150.8271-0.34190.60680.5022-1.19620.38150.4062-0.08480.15240.4592-0.09850.386524.630316.00862.329
161.19950.2656-0.19981.2599-0.49763.3019-0.37750.3435-0.1637-0.3102-0.02830.02440.763-0.58440.12450.3532-0.05850.00220.2030.00410.276637.44887.505-2.4742
17-0.2501-0.1722-0.89610.6406-0.79472.14670.0053-0.17460.1263-0.0596-0.0920.0331-0.5312-0.41010.14640.15230.0149-0.00710.3487-0.06010.302129.814215.479937.1893
180.94150.2277-0.38471.5408-0.07390.90680.0012-0.8648-0.531.73060.3866-0.0250.2707-0.43940.13120.49540.00940.00330.5404-0.02710.263933.086416.793665.0112
190.79580.2957-1.46680.82610.33684.14460.29090.7420.6391-1.32310.44690.65890.4098-0.7112-0.08690.7397-0.0871-0.01690.46580.03780.40838.650512.833-19.5764
200.31120.2268-1.32880.15821.08353.3996-0.0276-0.16240.0967-0.03220.0016-0.0363-0.00030.5117-0.06820.14180.0336-0.01250.3105-0.01710.279438.030214.106225.2567
210.5548-0.0748-0.94751.23930.22353.5718-0.2048-0.6476-0.16450.7856-0.065-0.54350.95391.32320.06720.82080.11970.04350.64160.00190.422834.23877.323767.4532
221.05420.41-1.5011.2481-0.16332.9050.11510.04760.1452-0.0388-0.1826-0.2685-0.12860.89710.04150.3029-0.01740.02220.36610.01670.381747.218816.2301-4.8457
230.3101-0.0928-0.89740.7755-0.45613.97010.1912-0.29580.0655-0.0606-0.3467-0.2788-0.63060.94560.09590.15990.0243-0.04130.2411-0.00710.228443.46017.340720.5258
240.31090.5515-2.47410.55790.29823.4081-0.2863-0.3524-0.30440.3493-0.33310.17880.82580.27860.07890.38420.00750.01290.4418-0.03590.349131.99323.944447.833
250.00180.1733-0.42243.933-1.49431.98350.6486-0.11420.2482.2142-0.0744-0.1637-1.75011.351-0.35430.7384-0.08540.04370.313-0.03050.3873-14.07023.242.3087
260.20220.1186-0.60312.5818-1.24710.0207-0.02950.4187-0.0456-0.81490.18720.71130.0486-1.085-0.39720.3921-0.0659-0.14470.49160.03290.424-17.41491.163511.7107
270.09150.2761-1.51913.9126-1.318-0.89680.33150.09060.3371-2.18020.6902-0.46830.8708-1.1549-0.11972.3429-0.4586-0.32840.5638-0.02090.3499-12.4179-8.3256-21.3601
280.77220.3618-0.48232.4794-1.4881.26090.2835-0.12050.56191.31790.06460.6202-0.8997-0.3638-0.30560.7785-0.00540.29070.26490.00740.5875-23.15680.526749.0395
290.37190.1658-0.00452.9008-0.5873.6497-0.23990.4626-0.1555-0.7170.17710.41281.2482-1.2982-0.15310.51-0.2556-0.18690.33860.03290.3378-15.9315-8.12337.9922
302.76960.2073-1.91253.0894-1.52360.47590.16550.5031-0.0514-2.12730.1919-0.37081.4613-1.19830.2872.6255-0.1312-0.07230.36860.0050.2923-1.5869-8.9642-22.8719
310.5620.2461-0.50792.79690.70780.6225-0.3146-0.4538-0.08341.25580.14770.76110.8373-0.92080.40230.87520.00080.33840.49530.06480.522-26.5207-7.257456.2842
32-1.0273-0.01060.33831.0687-0.96311.3718-0.44340.1353-0.2541-0.36260.06690.18991.4565-0.09260.1650.5205-0.0723-0.00660.2619-0.00630.3684-13.6644-9.752424.1695
33-0.3699-0.12130.69642.09570.1630.9761-0.10120.03520.3171-0.65310.011-0.2415-0.34851.34280.14081.4479-0.17510.03730.4082-0.01150.3056-1.8574-1.3151-13.7754
341.25571.1687-2.07012.7648-0.34814.08840.702-0.5307-0.32392.2861-0.6472-0.070.07981.16170.2451.0168-0.20790.08250.39970.01450.4003-17.0176-10.213156.8461
351.74850.548-1.08272.04241.40141.9525-0.0769-0.0496-0.0798-0.0327-0.06010.0136-0.25110.4703-0.00680.13840.0293-0.01910.2042-0.00150.3325-9.2086-1.137723.3236
361.40890.7702-0.67442.28141.16130.67040.3850.52090.4482-1.37930.4142-0.3021-1.4424-0.5251-0.02861.3468-0.0914-0.19870.62260.06390.5258-10.81192.7648-14.1809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 26:40
2X-RAY DIFFRACTION2chain A and resid 41:60
3X-RAY DIFFRACTION3chain A and resid 61:86
4X-RAY DIFFRACTION4chain B and resid 189:209
5X-RAY DIFFRACTION5chain B and resid 210:222
6X-RAY DIFFRACTION6chain B and resid 223:257
7X-RAY DIFFRACTION7chain C and resid 431:450
8X-RAY DIFFRACTION8chain C and resid 451:482
9X-RAY DIFFRACTION9chain C and resid 483:500
10X-RAY DIFFRACTION10chain D and resid 587:608
11X-RAY DIFFRACTION11chain D and resid 609:622
12X-RAY DIFFRACTION12chain D and resid 623:650
13X-RAY DIFFRACTION13chain E and resid 29:51
14X-RAY DIFFRACTION14chain E and resid 52:71
15X-RAY DIFFRACTION15chain E and resid 72:86
16X-RAY DIFFRACTION16chain F and resid 189:219
17X-RAY DIFFRACTION17chain F and resid 220:244
18X-RAY DIFFRACTION18chain F and resid 245:256
19X-RAY DIFFRACTION19chain G and resid 431:440
20X-RAY DIFFRACTION20chain G and resid 441:490
21X-RAY DIFFRACTION21chain G and resid 491:499
22X-RAY DIFFRACTION22chain H and resid 588:608
23X-RAY DIFFRACTION23chain H and resid 609:623
24X-RAY DIFFRACTION24chain H and resid 624:650
25X-RAY DIFFRACTION25chain I and resid 29:41
26X-RAY DIFFRACTION26chain I and resid 42:71
27X-RAY DIFFRACTION27chain I and resid 72:86
28X-RAY DIFFRACTION28chain J and resid 191:211
29X-RAY DIFFRACTION29chain J and resid 212:248
30X-RAY DIFFRACTION30chain J and resid 249:254
31X-RAY DIFFRACTION31chain K and resid 434:444
32X-RAY DIFFRACTION32chain K and resid 445:479
33X-RAY DIFFRACTION33chain K and resid 480:498
34X-RAY DIFFRACTION34chain L and resid 588:598
35X-RAY DIFFRACTION35chain L and resid 599:635
36X-RAY DIFFRACTION36chain L and resid 636:649

+
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