[English] 日本語
Yorodumi
- PDB-9hza: SMAD4 MH2, residues 272-552 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hza
TitleSMAD4 MH2, residues 272-552
ComponentsMothers against decapentaplegic homolog 4
KeywordsTRANSCRIPTION / Transcription factor / SMAD4 MH2 domain
Function / homology
Function and homology information


: / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / activin responsive factor complex / atrioventricular valve formation / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / epithelial cell migration / SMAD protein complex ...: / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / activin responsive factor complex / atrioventricular valve formation / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / epithelial cell migration / SMAD protein complex / neuron fate specification / cardiac muscle hypertrophy in response to stress / heteromeric SMAD protein complex / RUNX2 regulates bone development / filamin binding / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / response to transforming growth factor beta / FOXO-mediated transcription of cell cycle genes / secondary palate development / left ventricular cardiac muscle tissue morphogenesis / cardiac conduction system development / positive regulation of extracellular matrix assembly / atrioventricular canal development / Transcriptional regulation of pluripotent stem cells / sulfate binding / negative regulation of cardiac muscle hypertrophy / Germ layer formation at gastrulation / SMAD protein signal transduction / cellular response to BMP stimulus / Signaling by BMP / Formation of definitive endoderm / Signaling by Activin / activin receptor signaling pathway / outflow tract septum morphogenesis / Signaling by NODAL / adrenal gland development / I-SMAD binding / embryonic digit morphogenesis / TGFBR3 expression / Cardiogenesis / endothelial cell activation / RUNX3 regulates CDKN1A transcription / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / ovarian follicle development / R-SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / ERK1 and ERK2 cascade / BMP signaling pathway / epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / anatomical structure morphogenesis / positive regulation of cardiac muscle cell apoptotic process / positive regulation of epithelial to mesenchymal transition / extrinsic apoptotic signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / collagen binding / transcription corepressor binding / cellular response to glucose stimulus / negative regulation of protein catabolic process / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of cell growth / positive regulation of miRNA transcription / transcription coactivator binding / osteoblast differentiation / transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / intracellular signal transduction / transcription cis-regulatory region binding / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA-templated transcription
Similarity search - Function
MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain ...MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / SMAD-like domain superfamily / SMAD/FHA domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / SMAD family member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsTorner, C. / Condeminas, M. / Pluta, R. / Pous, J. / Macias, M.J.
Funding support Spain, 5items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)BFU2017-82675-P Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2021-122909NB-I00 Spain
Generalitat de Catalunya2021 SGR-866 Spain
Ministerio de Ciencia e Innovacion (MCIN)PDC_2021-121162-I00 Spain
Other privateBBVA
CitationJournal: To Be Published
Title: (RUNNING TITLE:) Insights into the structure-activity relationship of SMAD4 variants linked to Myhre syndrome and hereditary hemorrhagic telangiectasia
Authors: Torner, C. / Condeminas, M. / Pluta, R. / Aragon, E. / Khan, R.J. / Martin-Malpartida, P. / Rodriguez de Regil, M. / Pous, J. / Humm, A.-S. / Niebling, S. / Garcia-Alai, M. / Marquez, J.A. / ...Authors: Torner, C. / Condeminas, M. / Pluta, R. / Aragon, E. / Khan, R.J. / Martin-Malpartida, P. / Rodriguez de Regil, M. / Pous, J. / Humm, A.-S. / Niebling, S. / Garcia-Alai, M. / Marquez, J.A. / Martinez, A. / Macias, M.J.
History
DepositionJan 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 4
B: Mothers against decapentaplegic homolog 4
C: Mothers against decapentaplegic homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,71423
Polymers92,9773
Non-polymers1,73720
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-160 kcal/mol
Surface area28630 Å2
Unit cell
Length a, b, c (Å)140.863, 140.863, 191.951
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Components on special symmetry positions
IDModelComponents
11B-602-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 286 through 293 or resid 313...
d_2ens_1(chain "C" and (resid 286 through 458 or resid 491...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYPROPROAA286 - 29316 - 23
d_12PROPROALAALAAA313 - 45843 - 188
d_13GLYGLYILEILEAA491 - 518221 - 248
d_14GLUGLUPROPROAA520 - 522250 - 252
d_15TRPTRPPROPROAA524 - 544254 - 274
d_21GLYGLYALAALACC286 - 45816 - 188
d_22GLYGLYILEILECC491 - 518221 - 248
d_23GLUGLUPROPROCC520 - 522250 - 252
d_24TRPTRPPROPROCC524 - 544254 - 274

NCS oper: (Code: givenMatrix: (-0.42198897154, 0.768338459935, -0.481228967212), (-0.243243846507, 0.415389454581, 0.876518129966), (0.873360028302, 0.486936969236, 0.0116038336871)Vector: 11. ...NCS oper: (Code: given
Matrix: (-0.42198897154, 0.768338459935, -0.481228967212), (-0.243243846507, 0.415389454581, 0.876518129966), (0.873360028302, 0.486936969236, 0.0116038336871)
Vector: 11.6750722383, 5.65887564549, -12.2270428099)

-
Components

#1: Protein Mothers against decapentaplegic homolog 4 / MAD homolog 4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / SMAD ...MAD homolog 4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / SMAD family member 4 / SMAD 4 / Smad4 / hSMAD4


Mass: 30992.170 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD4, DPC4, MADH4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13485
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG Smear Broad (mixture of PEG 400, 550 MME, 600, 1000, 2000, 3350, 4000, 5000 MME, 6000, 8000, and 10000), 0.2 M lithium sulfate, 0.1 M HEPES pH 7.2 200 nL sample + 100 nL precipitant solution

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.03→99.605 Å / Num. obs: 52111 / % possible obs: 89.8 % / Redundancy: 7.9 % / Biso Wilson estimate: 36.58 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.3
Reflection shellResolution: 2.034→2.151 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2606 / CC1/2: 0.484 / % possible all: 41.1

-
Processing

Software
NameVersionClassification
autoPROC1.0.5 (20180515)data reduction
XDSJan 10, 2022 (BUILT 20220110)data reduction
Aimless0.7.4data scaling
STARANISO2.3.24 (20200129)data scaling
PHASER1.18.2-3874-000phasing
PHENIX1.21rc1_5107refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→99.6 Å / SU ML: 0.203 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 2613 5.02 %
Rwork0.1902 49485 -
obs0.1914 52098 84.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.31 Å2
Refinement stepCycle: LAST / Resolution: 2.03→99.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5307 0 98 225 5630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00855535
X-RAY DIFFRACTIONf_angle_d0.83497510
X-RAY DIFFRACTIONf_chiral_restr0.0536794
X-RAY DIFFRACTIONf_plane_restr0.0126973
X-RAY DIFFRACTIONf_dihedral_angle_d15.16372008
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.640003315 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.070.2497260.2715445X-RAY DIFFRACTION15
2.07-2.110.2578470.2644755X-RAY DIFFRACTION25.09
2.11-2.150.2821730.26881359X-RAY DIFFRACTION44.82
2.15-2.20.29631140.25862046X-RAY DIFFRACTION66.71
2.2-2.250.29891430.24082520X-RAY DIFFRACTION83.06
2.25-2.310.29361460.23652766X-RAY DIFFRACTION89.35
2.31-2.370.26821460.2232803X-RAY DIFFRACTION92.19
2.37-2.440.24341270.22372873X-RAY DIFFRACTION92.79
2.44-2.520.25821510.23442893X-RAY DIFFRACTION93.86
2.52-2.610.2611580.22882977X-RAY DIFFRACTION96.43
2.61-2.710.20561640.19673019X-RAY DIFFRACTION97.97
2.71-2.840.20811710.19163011X-RAY DIFFRACTION98.64
2.84-2.990.21931660.19633065X-RAY DIFFRACTION99.17
2.99-3.170.23691370.19513120X-RAY DIFFRACTION99.85
3.17-3.420.20371550.17313109X-RAY DIFFRACTION99.88
3.42-3.760.20881560.16173130X-RAY DIFFRACTION99.91
3.76-4.310.17391980.15113103X-RAY DIFFRACTION99.97
4.31-5.430.16831790.14873163X-RAY DIFFRACTION99.94
5.43-99.60.2381560.23653328X-RAY DIFFRACTION99.57
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)
13.8658774250.2913790973181.890089713562.26680329950.5394257671422.06313978088-0.110363330633-0.02492882453570.6178406476-0.0147924733252-0.0447042474090.244912807502-0.362089801083-0.4634164968130.04647346484360.2371687104720.01512013332650.0905343330350.3852053334040.07425415895290.376828707809-18.3093900697-30.0087433482-25.4691247114
21.58950167152-0.211798538020.3195231755063.365253622960.05931003725431.946910252590.08531481198230.0519688619721-0.0110604456902-0.0506139904775-0.02065334247680.1740115252260.1493298917560.136461617134-0.05732717089870.1942627132540.01278023054930.003287198140220.4017889755490.09423537829410.24445770125911.7152838515-42.1300221157-31.7217031924
34.43709424566-0.301376796893-2.151609484676.687857887780.1255467013723.47337438130.1545048630680.341515137230.433048731555-0.74823092244-0.0798609824943-1.38025018867-0.2385079046430.5691171354-0.02989603244920.193832878463-0.0155815424946-0.06983345951180.6416078798710.1864154191990.38788723799719.7071514377-36.1849604169-34.0921532198
42.643080876550.853709193909-0.6326604794072.3388673078-0.7393999232733.55470360425-0.068989974071-0.05975920548660.009877923162980.156638987496-0.0675735041299-0.2764708624270.1363617754350.7105829199740.2026492063850.2519127177790.0967742169845-0.04291330351320.4465369200020.09479024899950.34818385390823.2064916154-47.1921791783-23.5743571954
54.262938898491.11607039372-1.465598233623.98323435443-0.6978861974338.259180455970.095060515477-0.583740735907-0.1951834591660.420182234537-0.2534496358420.097735088055-0.407695949486-0.433869463957-0.09049356605370.3686501594820.0386769652421-0.07112623514730.4909578564070.1351006511510.3857853836958.91557359737-55.5294570583-6.66458772145
63.06126354522.775376589960.730780049865.61729046431-3.237195328495.130643427770.116076333740.6557910314840.800278568111-0.03240334359720.3504714776750.2156224640331.42657991558-0.0362275365126-0.5227393307170.734341912918-0.0490473735130.08570187427330.8152705610120.1539423612160.517392501554-4.76605307458-48.54747795562.33424217578
74.118120285420.7817608582850.3384115903978.71786665705-2.464905658122.788433321940.0608898402361-0.8251353172760.1337280122070.983141980267-0.383228244374-0.763594744147-0.4058541998240.4227096301150.2525439175770.330287576555-0.00164562675137-0.105950833370.4633185112990.03749074006140.33433589060517.3166316606-37.1639771781-19.7953237014
81.724138388720.7627555841710.5402198209163.43013584222-0.04698630952712.59353815613-0.00520347390045-0.564655823843-0.2744117841450.516587367621-0.02991782511090.2440180976880.259560047375-0.2278378741250.0596007387350.2905785237660.05124244360520.01768175221050.4464485785470.1346362133830.3950802114332.96174973039-52.4276419146-15.8142432142
92.54483004555-2.35625373438-1.130523910815.942264742050.5375336092992.992571246180.128128471380.482393941589-0.0243423181261-0.8803708469440.0851455195520.156271194888-0.224208950462-0.157990283738-0.1739655652380.332512311493-0.06015007786380.005205061166760.5579381709140.09954298168410.3431808909220.168785815991-24.2518904268-55.0682806002
102.05006932807-1.00274233753-1.83284572184.245691515843.251172622035.118960957360.08129662844190.12286074425-0.2523682130580.0637306850891-0.08608735458110.113078610380.010953901248-0.3502013711020.003471780250880.233695731309-0.00583105938881-0.01045648321030.3540536307240.1595516172080.29555753555-7.26073027062-31.6923517241-40.8598574961
113.232257586340.03063868716470.234185366621.457559660431.534468159697.80653544780.268466451564-0.07774613015260.2077737311460.02458954419570.0425086116490.277735156466-0.159716748673-1.25850933028-0.2858894221010.2617549998760.03881894650650.02072498373040.3598774175860.1860073263260.393257803185-11.6328388461-23.0491898099-36.5852295698
122.83809762918-0.495558288261-0.6579730005522.586601373170.2649391357632.166338281370.1011379342140.4818579254180.375730962218-0.2555420886560.03489092789070.108327311775-0.322964439798-0.16265909839-0.1173456845420.313042932680.03033558949680.01980667805930.4169721287980.1720075927030.297060916396-1.98418197617-18.5932263922-51.993415829
138.190248099181.588692500121.752613746847.98929483261-2.192773117072.189387992580.361180537911-0.753224456186-0.3334040081980.222274919782-0.404767327696-0.5039299063370.2038979258620.2369865181550.05682299822060.358605010472-0.02370809514230.05130753936320.5252984960190.1260943660050.26914012247117.3173838361-25.9322012777-54.3478339444
149.25955022853-6.27482073736-3.805326110924.875968658951.226346846454.27805852294-0.204492760367-0.7031165265070.7705967589990.3934133657830.111343085448-0.654152132556-0.1547977540130.950924132328-0.02666666870350.322427071636-0.0559363265968-0.02177344419210.4733388658340.1221341138940.3747150889569.6366243743-23.6136669563-43.7751242552
152.13178915429.03689007022-3.718998708417.70955364372-4.51409403082.224843372280.2826816437480.1914682817531.250136025210.4190035179560.01304093227290.191046943815-1.40187189993-0.12413680949-0.283072735910.5603022786830.04926810299780.1091662236120.3876001318770.1060983526230.542755349476-2.63455539384-11.859502454-37.6381467235
165.70959350952-6.3377609044-3.179536272219.5073768312.855078334585.20708946017-0.0397202345965-0.4327160205090.00486784723419-0.353530199335-0.0024963214607-0.3966551039030.2612847488060.8729057187030.0007118985316150.277235884059-0.006018401148830.0202888446550.3861616811990.1403607783640.27576768133811.0193724332-32.0628883176-47.2826726758
173.856266446550.1056818650410.4349854424152.437206719290.2410225286312.366146856230.00732324845835-0.0270997956051-0.1893082686250.017968075337-0.007305475199550.1242238649190.145688625062-0.1652123408730.04391962995250.189249599144-0.01807864106110.03259786769220.2714844333640.09896695099810.246126718258-10.6983733871-42.4082694322-22.4032970851
184.477839278250.5305414086880.1945182877092.58667814304-0.3648926183582.681879458460.0230218016357-0.498745865561-0.04699652645050.288291135755-0.04187513637720.3636653079460.129887036084-0.3800774454580.05858187211910.257367579546-0.03296509478170.07599071733630.3919968615550.05911808095650.32006027241-18.6018283741-40.8253849353-14.6366573356
193.87252507215-3.542480244761.384473793342.1262695315-5.824067318755.970995106990.1487558558520.3027553325521.08386134140.6398831392420.0924438599366-0.224009247831-0.781404593478-0.454111294681-0.4036722267790.3616973976690.08126238783380.1273654414760.6209879560520.1519299759570.739473933166-31.4112889075-24.6368863951-32.10251855
202.15759018025-0.8178976929810.2863216714194.93382076548-1.758773077032.548886433940.5041813737580.346369513216-0.229510852612-0.572240456055-0.3331310555860.622662048337-0.08708640981960.111745207742-0.1690154246040.8994178261380.0853025400855-0.1258494539710.9828417320690.2270264064290.978822548458-25.2091015555-11.163048539-41.5298247532
214.62485644669-0.6974971398623.639095374451.67174076076-0.6144818016043.901764213060.03664973111680.0506721751070.459908517020.1853779867860.06740681492830.154922170103-0.352608745931-0.2154119685590.01865425862340.2861935218770.01381282132850.09977772811560.3806548649490.06495468468970.382796864525-18.1525641769-31.525518126-23.9116183849
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 506 through 550 )BB506 - 550191 - 235
22chain 'C' and (resid 286 through 373 )CC286 - 3731 - 69
33chain 'C' and (resid 374 through 392 )CC374 - 39270 - 88
44chain 'C' and (resid 393 through 439 )CC393 - 43989 - 135
55chain 'C' and (resid 440 through 464 )CC440 - 464136 - 160
66chain 'C' and (resid 465 through 491 )CC465 - 491161 - 172
77chain 'C' and (resid 492 through 523 )CC492 - 523173 - 204
88chain 'C' and (resid 524 through 549 )CC524 - 549205 - 230
99chain 'A' and (resid 286 through 321 )AA286 - 3211 - 20
1010chain 'A' and (resid 322 through 363 )AA322 - 36321 - 62
1111chain 'A' and (resid 364 through 392 )AA364 - 39263 - 91
1212chain 'A' and (resid 393 through 439 )AA393 - 43992 - 138
1313chain 'A' and (resid 440 through 457 )AA440 - 457139 - 156
1414chain 'A' and (resid 458 through 505 )AA458 - 505157 - 175
1515chain 'A' and (resid 506 through 523 )AA506 - 523176 - 193
1616chain 'A' and (resid 524 through 545 )AA524 - 545194 - 215
1717chain 'B' and (resid 286 through 373 )BB286 - 3731 - 71
1818chain 'B' and (resid 374 through 439 )BB374 - 43972 - 137
1919chain 'B' and (resid 440 through 465 )BB440 - 465138 - 163
2020chain 'B' and (resid 466 through 491 )BB466 - 491164 - 176
2121chain 'B' and (resid 492 through 505 )BB492 - 505177 - 190

+
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