[English] 日本語
Yorodumi
- PDB-7q43: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q43
TitleCrystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10
Components
  • Dedicator of cytokinesis protein 10 peptide
  • E3 ubiquitin-protein ligase HERC2
KeywordsPROTEIN BINDING / 7-bladed beta-propeller E3 ubiquitin-protein ligase HERC2 RCC1-like Domain 2 RLD2 ubiquitin ligase dedicator of cytokinesis protein 10 Dock 10 DXDKDED motif
Function / homology
Function and homology information


marginal zone B cell differentiation / SUMO binding / HECT-type E3 ubiquitin transferase / dendritic spine morphogenesis / small GTPase-mediated signal transduction / B cell homeostasis / CDC42 GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / SUMOylation of DNA damage response and repair proteins ...marginal zone B cell differentiation / SUMO binding / HECT-type E3 ubiquitin transferase / dendritic spine morphogenesis / small GTPase-mediated signal transduction / B cell homeostasis / CDC42 GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / SUMOylation of DNA damage response and repair proteins / regulation of cell migration / RAC1 GTPase cycle / centriole / guanyl-nucleotide exchange factor activity / Nonhomologous End-Joining (NHEJ) / intracellular protein transport / G2/M DNA damage checkpoint / small GTPase binding / positive regulation of GTPase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / dendritic spine / protein ubiquitination / DNA repair / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / extracellular exosome / zinc ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dedicator of cytokinesis D, C2 domain / HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / Beta-propeller repeat TECPR / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. ...Dedicator of cytokinesis D, C2 domain / HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / Beta-propeller repeat TECPR / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe C / DHR-2, Lobe B / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / C2 DOCK-type domain profile. / DOCKER domain profile. / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Galactose-binding-like domain superfamily / PH-like domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
CITRIC ACID / E3 ubiquitin-protein ligase HERC2 / Dedicator of cytokinesis protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4000234708 Å
AuthorsDemenge, A. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / McEwen, A.G. / Trave, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10
Authors: Demenge, A. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / McEwen, A.G. / Trave, G.
History
DepositionOct 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: E3 ubiquitin-protein ligase HERC2
A: E3 ubiquitin-protein ligase HERC2
E: E3 ubiquitin-protein ligase HERC2
B: Dedicator of cytokinesis protein 10 peptide
D: Dedicator of cytokinesis protein 10 peptide
F: Dedicator of cytokinesis protein 10 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,0027
Polymers136,8106
Non-polymers1921
Water9,440524
1
C: E3 ubiquitin-protein ligase HERC2
D: Dedicator of cytokinesis protein 10 peptide


Theoretical massNumber of molelcules
Total (without water)45,6032
Polymers45,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: E3 ubiquitin-protein ligase HERC2
B: Dedicator of cytokinesis protein 10 peptide


Theoretical massNumber of molelcules
Total (without water)45,6032
Polymers45,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: E3 ubiquitin-protein ligase HERC2
F: Dedicator of cytokinesis protein 10 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7963
Polymers45,6032
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.820, 108.820, 243.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein E3 ubiquitin-protein ligase HERC2 / HECT domain and RCC1-like domain-containing protein 2 / HECT-type E3 ubiquitin transferase HERC2


Mass: 42770.566 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HERC2 / Production host: Escherichia coli (E. coli)
References: UniProt: O95714, HECT-type E3 ubiquitin transferase
#2: Protein/peptide Dedicator of cytokinesis protein 10 peptide / Zizimin-3 / Dedicator of cytokinesis protein 10


Mass: 2832.874 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: n-terminally biotinylated peptide via 1,13-diamino-4,7,10-trioxatridecan-succinamic acid
Source: (synth.) Homo sapiens (human) / References: UniProt: Q96BY6
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: hanging drop 20% PEG 3350 0.18M tris amonium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999997 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999997 Å / Relative weight: 1
ReflectionResolution: 2.4→49.665 Å / Num. obs: 57945 / % possible obs: 99.7 % / Redundancy: 37.6713780309 % / Biso Wilson estimate: 33.6856059616 Å2 / CC1/2: 0.983 / Net I/σ(I): 5.77
Reflection shellResolution: 2.4→2.46 Å / Num. unique obs: 4230 / CC1/2: 0.41

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KCI

3kci


Resolution: 2.4000234708→49.6652591346 Å / SU ML: 0.336717390306 / Cross valid method: FREE R-VALUE / σ(F): 1.34350427896 / Phase error: 25.8287899636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264969422568 2916 5.04123230123 %
Rwork0.202444119505 54927 -
obs0.205598267093 57843 99.753388749 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.167441888 Å2
Refinement stepCycle: LAST / Resolution: 2.4000234708→49.6652591346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8386 0 13 524 8923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007774019179198557
X-RAY DIFFRACTIONf_angle_d0.91059276313311554
X-RAY DIFFRACTIONf_chiral_restr0.05487021457981289
X-RAY DIFFRACTIONf_plane_restr0.005512420657951492
X-RAY DIFFRACTIONf_dihedral_angle_d18.77938190463055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4000234708-2.43940.328064837691400.2709398619582585X-RAY DIFFRACTION100
2.4394-2.48140.3265495463751550.2709425392762575X-RAY DIFFRACTION99.8902305159
2.4814-2.52660.3225197572741460.2584287962862546X-RAY DIFFRACTION100
2.5266-2.57510.3319428159661250.2599725132592563X-RAY DIFFRACTION99.8885172798
2.5751-2.62770.3390697345261220.2607576373952590X-RAY DIFFRACTION99.9631404349
2.6277-2.68480.2948363469041410.2550318355622596X-RAY DIFFRACTION100
2.6848-2.74730.326910553881220.2412071035012616X-RAY DIFFRACTION99.9634903249
2.7473-2.8160.2966299218761400.230767093062557X-RAY DIFFRACTION100
2.816-2.89210.3281541380291480.2199813221692589X-RAY DIFFRACTION100
2.8921-2.97720.2658417283561260.2185004843632588X-RAY DIFFRACTION100
2.9772-3.07330.3167342663711540.2130960473092598X-RAY DIFFRACTION99.9636759898
3.0733-3.18310.2987052172771310.2143608742382613X-RAY DIFFRACTION99.9635701275
3.1831-3.31050.2559354804421460.2080081704472596X-RAY DIFFRACTION100
3.3105-3.46120.2712558643151510.2095507232422586X-RAY DIFFRACTION100
3.4612-3.64360.2814681684071390.197251165642571X-RAY DIFFRACTION97.7986286539
3.6436-3.87180.2457626781391350.2152481119692572X-RAY DIFFRACTION97.7609245215
3.8718-4.17060.225306777021350.1656036091172645X-RAY DIFFRACTION99.892202659
4.1706-4.590.2194756073541330.1507349255722661X-RAY DIFFRACTION100
4.59-5.25360.1900552729981270.1491780638522684X-RAY DIFFRACTION100
5.2536-6.61650.2360784026711650.1738159148172693X-RAY DIFFRACTION100
6.6165-49.66525913460.2376567635071350.2022364823362903X-RAY DIFFRACTION99.7701149425
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)
13.948820682231.54075589423-1.716127611741.88839795020.05944658705042.312056517-0.0266450406990.227874597242-0.264142254639-0.207171529120.08870525386040.02589078430920.150699396497-0.119870612644-0.06892778374130.2615434691250.0126133616853-0.06944569934280.1871235053180.007986334523210.24214223587732.7478649994-25.136695482516.6400097522
21.17942687525-0.0752125604132-0.3948023712526.479287784680.6470041091442.632960372710.209562955297-0.144640318442-0.183441073635-0.0382722189032-0.1121221078880.6742224554280.0990574092963-0.336461060587-0.09252867558640.186324771871-0.0516101954342-0.01972840981450.3488974404380.06170169107680.28047283900722.6600484545-19.222709543233.4631498506
34.657558779070.816039978250.1720973297084.26452722378-0.5389616432363.193921748760.0429696766429-0.1660572143640.2313446173710.1837149395810.01603036143840.294893771223-0.265433501061-0.141446750507-0.0544442050150.188708599978-0.01468473149960.007059135513170.1579224609820.003436064139670.18346955362533.757706956-3.4120359283732.5405342269
47.30384870148-1.414183146030.5753553266853.93897467495-0.3724750913484.709180695980.05713131322240.140974839690.0981575149354-0.150004862702-0.08390148245310.0359592919431-0.321019653515-0.009531967419020.01916265814180.240384684033-0.0344367207215-0.006262264015130.1962340703430.0234122590780.13266786063240.6985681278-6.818310630715.2420412722
51.50583320266-0.396765175121-0.0789172641523.36277065066-0.8775285872962.44927783711-0.04513731273040.229733346716-0.268695589906-0.248050685-0.034384621809-0.009259897283320.2813845414080.1219916467880.07809736972320.2232316016950.02166045484480.03652410022110.256302644634-0.0572069470960.20058866351860.3757295791-25.714315730754.1803256796
62.782969939581.117266833831.839655057895.276181278421.472679848696.57615442220.102591680487-0.00676143234181-0.5086467922780.305901565497-0.0175788450793-0.1964457971870.8336753586410.179809983446-0.08716520374140.311478920020.08399348997650.08898094685890.2768290832420.03581532301080.33968251492258.2676941698-35.330267713869.8183777186
71.73356619942-0.428628845348-0.09937615878542.82073307755-0.8794272123631.60773825403-0.078328882939-0.252388421764-0.06674427773180.313334904940.04440757614290.0895447223764-0.00228381483715-0.05515628163470.03781530886450.229120065103-0.000287104478630.01479649314090.219233712986-0.02911115539050.16180314687747.7323483331-19.994112907576.8437735608
86.50195628585-0.1328020312662.130043258824.58529342559-0.7082349198155.231666780590.0214411256839-0.1615030831380.0965757881204-0.00511557461902-0.02713482748290.102324462025-0.138191453403-0.2968483800980.009592401079260.162669603812-0.01394414390040.01635825490660.220222518691-0.008508897815740.14711991235449.0488403554-10.764363117956.9194136023
92.623383013621.504469842780.5648570146244.082948486790.3111077995964.44136913424-0.02169022592520.1246830021720.425721405817-0.4258901312020.07667555853980.23245218256-0.810227413719-0.00302876330797-0.04483543862630.4345116802910.0337131619770.01519054931190.2137428611410.003570342948910.31671432081856.271006810228.649855254434.0845802478
107.787598484780.7541816015731.464725981894.15310738503-0.2787142430743.81104623875-0.1410057702590.2460240595931.070285833-0.162769089495-0.01202055962470.156222631157-0.9044885480860.4436847744150.1696820594030.808058511785-0.1558551414430.007250731427030.367780021473-0.03996027596670.43092469202464.803275438437.645618284245.0946047304
112.18579193111.34576033042-0.2544409713674.490185472450.8804390240422.621354860770.182514595603-0.3279575531880.2535985612070.445082241002-0.0687914852779-0.361769964844-0.334587700060.414065518472-0.1237081569230.358786716324-0.071450678063-0.06583168226030.301540080147-0.03426137037920.30018871793764.831207701818.077401663853.8566855564
122.128807049580.5004537256411.223008700773.880009698961.085586958413.57930095435-0.113612028401-0.0453291010982-0.309785396878-0.01719366209470.0560286929945-0.1503283071780.3568093324790.1169746324810.02556641415630.273021704944-0.01300259592950.0416228495150.2169869110640.01123490584620.20165195622857.19962810156.4763668046437.8501439909
137.064933872-4.70316584925-2.559642731698.782794213178.782297960572.106521965920.0605393259857-0.07081136084020.276610394844-0.1111830288920.172485381174-0.1848404573350.0954398983570.234285016931-0.2227549462870.290226158385-0.02260811937660.04067702107420.3408372897360.06105021883850.22361827562559.911444131913.173454300529.8688852555
145.011056007242.32092307678-3.531244931057.1928447318-5.177947033257.967795183071.19248758128-1.561906966280.5283206656340.311137942349-0.4583008802880.213411502397-0.09589820552351.7364455882-0.675613702820.46121180608-0.112963239534-0.02807371264081.07988481541-0.1732939919790.69525069038167.6378032965-11.107622088164.3493963953
156.759962177145.480279935293.157525177542.00109048186-3.96205287617.37362935257-0.386999004547-2.1605846576-0.2746859142612.367452311140.77703251773-0.5006782968871.082102523210.750547450351-0.4034209820090.8851603145190.2763988961220.03903061009641.24490916391-0.3330829488630.82428531229448.235092242-18.775879213828.5814306954
161.997693108732.51449719461-8.171920694482.00125028987-0.3406702020051.998559634240.507869982288-0.6477593137380.5014336350010.2670201263621.040111264792.14893583813-0.898064188143-3.00355850128-1.501219504360.82307996220.1270662336690.1631544959421.174387232160.284198638151.0059342184344.12566723617.503792241345.1794966505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 2958 through 3082 )
2X-RAY DIFFRACTION2chain 'C' and (resid 3083 through 3169 )
3X-RAY DIFFRACTION3chain 'C' and (resid 3170 through 3250 )
4X-RAY DIFFRACTION4chain 'C' and (resid 3251 through 3326 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2959 through 3052 )
6X-RAY DIFFRACTION6chain 'A' and (resid 3053 through 3106 )
7X-RAY DIFFRACTION7chain 'A' and (resid 3107 through 3250 )
8X-RAY DIFFRACTION8chain 'A' and (resid 3251 through 3326 )
9X-RAY DIFFRACTION9chain 'E' and (resid 2959 through 3082 )
10X-RAY DIFFRACTION10chain 'E' and (resid 3083 through 3106 )
11X-RAY DIFFRACTION11chain 'E' and (resid 3107 through 3250 )
12X-RAY DIFFRACTION12chain 'E' and (resid 3251 through 3302 )
13X-RAY DIFFRACTION13chain 'E' and (resid 3303 through 3326 )
14X-RAY DIFFRACTION14chain 'B' and (resid 158 through 166 )
15X-RAY DIFFRACTION15chain 'D' and (resid 158 through 163 )
16X-RAY DIFFRACTION16chain 'F' and (resid 158 through 164 )

+
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