[English] 日本語
Yorodumi
- PDB-5zoj: Crystal structure of human SMAD2-MAN1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zoj
TitleCrystal structure of human SMAD2-MAN1 complex
Components
  • Inner nuclear membrane protein Man1
  • Mothers against decapentaplegic homolog 2
KeywordsDNA BINDING PROTEIN / Transcription / Complex / TGF-beta signaling
Function / homology
Function and homology information


regulation of binding / zygotic specification of dorsal/ventral axis / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / endoderm formation ...regulation of binding / zygotic specification of dorsal/ventral axis / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / endoderm formation / heteromeric SMAD protein complex / co-SMAD binding / Depolymerization of the Nuclear Lamina / odontoblast differentiation / determination of left/right asymmetry in lateral mesoderm / Nuclear Envelope Breakdown / pericardium development / FOXO-mediated transcription of cell cycle genes / secondary palate development / regulation of transforming growth factor beta receptor signaling pathway / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / Transcriptional regulation of pluripotent stem cells / embryonic foregut morphogenesis / transforming growth factor beta receptor binding / Germ layer formation at gastrulation / primary miRNA processing / pulmonary valve morphogenesis / type I transforming growth factor beta receptor binding / Formation of definitive endoderm / activin receptor signaling pathway / SMAD protein signal transduction / signal transduction involved in regulation of gene expression / embryonic cranial skeleton morphogenesis / negative regulation of activin receptor signaling pathway / Signaling by Activin / Initiation of Nuclear Envelope (NE) Reformation / positive regulation of BMP signaling pathway / Formation of axial mesoderm / U1 snRNP binding / response to cholesterol / Signaling by NODAL / RHOD GTPase cycle / I-SMAD binding / pancreas development / aortic valve morphogenesis / ureteric bud development / insulin secretion / RND1 GTPase cycle / nuclear inner membrane / RND2 GTPase cycle / RND3 GTPase cycle / anterior/posterior pattern specification / organ growth / endocardial cushion morphogenesis / adrenal gland development / SMAD binding / TGF-beta receptor signaling activates SMADs / R-SMAD binding / mesoderm formation / RHOG GTPase cycle / negative regulation of BMP signaling pathway / cell fate commitment / anatomical structure morphogenesis / RAC2 GTPase cycle / RAC3 GTPase cycle / phosphatase binding / cis-regulatory region sequence-specific DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of epithelial to mesenchymal transition / gastrulation / RAC1 GTPase cycle / post-embryonic development / transforming growth factor beta receptor signaling pathway / Downregulation of TGF-beta receptor signaling / cellular response to glucose stimulus / lung development / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / tau protein binding / disordered domain specific binding / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / DNA-binding transcription factor binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / cell population proliferation / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / Ub-specific processing proteases / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding
Similarity search - Function
MAN1, RNA recognition motif / : / Man1/Src1, C-terminal / MAN1, winged-helix domain / Man1-Src1p-C-terminal domain / Tumour Suppressor Smad4 - #10 / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins ...MAN1, RNA recognition motif / : / Man1/Src1, C-terminal / MAN1, winged-helix domain / Man1-Src1p-C-terminal domain / Tumour Suppressor Smad4 - #10 / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins / LEM/LEM-like domain superfamily / 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 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mothers against decapentaplegic homolog 2 / Inner nuclear membrane protein Man1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.794 Å
AuthorsMiyazono, K. / Ohno, Y. / Ito, T. / Tanokura, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K14708 Japan
Japan Society for the Promotion of Science17K19581 Japan
Japan Society for the Promotion of Science23228003 Japan
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis for receptor-regulated SMAD recognition by MAN1
Authors: Miyazono, K.I. / Ohno, Y. / Wada, H. / Ito, T. / Fukatsu, Y. / Kurisaki, A. / Asashima, M. / Tanokura, M.
History
DepositionApr 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name / _entity.formula_weight
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 2
B: Mothers against decapentaplegic homolog 2
C: Mothers against decapentaplegic homolog 2
D: Inner nuclear membrane protein Man1
E: Inner nuclear membrane protein Man1


Theoretical massNumber of molelcules
Total (without water)97,4965
Polymers97,4965
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-25 kcal/mol
Surface area35420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.813, 176.813, 73.854
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain D and (resid 762 through 866 or resid 878 through 888))
21chain E
12(chain A and resid 272 through 456)
22chain B
32(chain C and resid 272 through 456)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLEULEU(chain D and (resid 762 through 866 or resid 878 through 888))DD762 - 8664 - 108
121ALAALASERSER(chain D and (resid 762 through 866 or resid 878 through 888))DD878 - 888120 - 130
211SERSERSERSERchain EEE762 - 8884 - 130
112ALAALAMETMET(chain A and resid 272 through 456)AA272 - 45614 - 198
212ALAALAMETMETchain BBB272 - 45614 - 198
312ALAALAMETMET(chain C and resid 272 through 456)CC272 - 45614 - 198

NCS ensembles :
ID
1
2

-
Components

#1: Protein Mothers against decapentaplegic homolog 2 / Mothers against DPP homolog 2 / JV18-1 / Mad-related protein 2 / hMAD-2 / SMAD family member 2 / hSMAD2


Mass: 22518.482 Da / Num. of mol.: 3 / Fragment: UNP residues 262-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15796
#2: Protein Inner nuclear membrane protein Man1 / LEM domain-containing protein 3


Mass: 14970.151 Da / Num. of mol.: 2 / Fragment: UNP residues 762-890
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2U8

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 0.1M acetate, 7.5% PEG4000, 10% 2-propanol

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→45.55 Å / Num. obs: 31950 / % possible obs: 96.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 63.69 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.065 / Rrim(I) all: 0.162 / Net I/σ(I): 8.2 / Num. measured all: 171576
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.79-2.943.61.08844710.5310.6151.25792.8
8.83-45.555.40.07110400.9940.0320.07994.4

-
Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIX1.12rc2_2821: ???refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementResolution: 2.794→42.469 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 30.27
RfactorNum. reflection% reflection
Rfree0.2692 2818 4.82 %
Rwork0.2419 --
obs0.2433 31934 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.66 Å2 / Biso mean: 78.4638 Å2 / Biso min: 28.76 Å2
Refinement stepCycle: final / Resolution: 2.794→42.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6383 0 0 0 6383
Num. residues----801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026549
X-RAY DIFFRACTIONf_angle_d0.5748889
X-RAY DIFFRACTIONf_chiral_restr0.044954
X-RAY DIFFRACTIONf_plane_restr0.0051150
X-RAY DIFFRACTIONf_dihedral_angle_d11.0293871
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D1056X-RAY DIFFRACTION13.439TORSIONAL
12E1056X-RAY DIFFRACTION13.439TORSIONAL
21A2601X-RAY DIFFRACTION13.439TORSIONAL
22B2601X-RAY DIFFRACTION13.439TORSIONAL
23C2601X-RAY DIFFRACTION13.439TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.794-2.84220.38271070.36972233234071
2.8422-2.89380.35941240.34932640276488
2.8938-2.94950.36881290.35082719284888
2.9495-3.00970.34021220.35272745286791
3.0097-3.07510.34331240.35452822294691
3.0751-3.14660.35071760.30922803297994
3.1466-3.22530.33391310.2942815294692
3.2253-3.31240.32391650.27152808297393
3.3124-3.40990.28271770.26782826300393
3.4099-3.51990.29281310.25522775290692
3.5199-3.64560.30141540.23672841299594
3.6456-3.79150.26491520.22772813296593
3.7915-3.96390.22921460.22722844299093
3.9639-4.17280.19871350.21022863299893
4.1728-4.43390.23711310.19832865299694
4.4339-4.77590.23471630.19292827299094
4.7759-5.25570.24221110.19312838294993
5.2557-6.01440.29291330.24122888302194
6.0144-7.57050.26231810.24872809299094
7.5705-42.4740.24491260.22942874300093
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)
12.37040.6817-2.96212.35060.02664.1525-0.15520.6937-0.082-0.43350.01770.2245-0.1633-1.06330.1590.29590.03020.03160.6307-0.05690.450260.014-43.8084-6.6652
24.2250.5209-1.79815.33791.65932.2053-0.06070.4870.3738-0.32790.2319-0.1553-0.6423-0.0312-0.14060.4121-0.0594-0.00840.37630.06570.363471.5679-44.2675-5.5355
37.78990.07175.96824.82091.08518.66910.1450.1165-0.91360.40220.2198-0.17710.27760.3958-0.34090.4211-0.02220.12810.36430.10940.171372.3131-53.0749-2.7713
43.40160.51520.52872.88120.3063.72390.11960.0267-0.26480.4623-0.21980.53940.2346-0.71420.06780.4348-0.12160.08240.4853-0.03720.492359.6272-58.87971.6295
53.0124-1.73130.55644.5113-0.16221.59860.3855-0.56850.82880.4373-0.14861.4322-0.2133-0.3853-0.26780.5184-0.08570.21010.64410.00970.941648.5559-49.62612.1093
67.7052-0.13072.06254.7296-0.35061.28390.1823-0.38360.38630.5332-0.10970.813-0.1325-0.2297-0.11140.4449-0.06270.18360.5064-0.02350.454858.301-47.23054.3021
74.98812.1822-2.56196.41510.23272.23910.00630.37960.7158-0.6696-0.14450.9322-0.1391-0.3560.02490.3953-0.0062-0.07480.47120.08630.550375.1842-24.5514-6.9533
85.4831-1.6104-2.7947.0792.32782.75320.13030.39950.4456-0.0097-0.10790.4219-0.4856-0.7351-0.13020.4662-0.0578-0.09540.48690.05140.640882.7129-18.6619-5.684
93.2741.58920.99553.7318-0.69960.6863-0.28470.4552-0.0622-0.4620.2383-0.25690.12360.08220.01090.5469-0.10410.07090.4415-0.04270.388194.1544-27.5347-8.7299
102.63410.94150.92596.98971.61330.2907-0.27570.1912-0.4436-0.06990.2086-0.21040.0740.18580.07090.5174-0.03850.05470.5412-0.09970.350490.6277-41.1192-10.2462
113.3091-0.5351-1.03325.55331.47510.9980.0078-0.10850.18590.4901-0.04650.33830.01970.17890.0710.4177-0.09690.05580.42220.05250.176186.144-35.05-3.8658
125.3601-1.0524-1.29017.2579-3.69648.4806-0.0439-0.18571.08670.13330.04241.3411-0.4025-0.2449-0.320.50040.0020.02610.4302-0.03331.124361.0347-26.3505-0.6477
138.63-0.1742-0.49516.9726-1.25562.70370.05850.66550.05770.2286-0.00771.9460.132-0.25160.03250.614-0.0251-0.1940.5894-0.04691.519551.2062-29.1274-6.6325
142.2327-3.4785-1.59176.99911.39015.75880.2412-0.66510.021.1172-0.10661.89950.32040.4395-0.06570.7403-0.06850.35530.6418-0.06531.204454.2777-34.718910.408
156.49898.8551-5.60132.0387-7.04958.0964-0.36690.51382.5657-1.32120.71993.99960.4243-1.6751-0.98160.85630.13270.16450.6108-0.02272.777947.4904-20.8738-3.979
163.21942.5097-0.53761.9557-0.32913.40470.48040.6080.24140.5065-0.22912.5306-0.6554-0.1143-0.19350.7484-0.10080.20630.4274-0.05022.319550.4526-13.54622.1194
172.86751.4696-0.99132.4021.03511.40490.00910.19891.75750.09740.12631.8793-0.5392-0.173-0.22450.7532-0.03870.10740.62760.03782.052859.4613-8.27010.8461
183.72881.3789-1.27696.506-2.06773.72520.2934-0.19851.23390.4997-0.28831.2566-0.4586-0.1981-0.09970.5442-0.03810.06680.5125-0.11621.371861.9077-16.18183.4707
199.65853.464-0.0243.2886-1.84371.66740.0388-0.8922-0.99290.6499-0.8727-0.90060.11720.4590.68030.61840.01920.03730.70480.1380.718564.4169-70.8163.8675
202.88390.73291.85882.97413.42656.13142.3649-0.86681.57532.0287-1.50411.1809-0.6483-0.0993-0.87561.132-0.18080.17930.88580.10580.756553.8534-67.129516.8775
215.12361.5262-2.72147.5239-5.15557.5754-0.00350.33920.0576-0.3738-0.05050.37050.0529-0.71940.17550.4266-0.0235-0.07620.4893-0.03480.457652.9878-77.9734-2.8736
227.64962.39690.48076.59771.35918.7570.3865-0.1827-1.1426-0.16540.4722-0.26090.70561.1207-0.60940.5083-0.10460.11560.66450.11460.995260.0931-83.7368-0.9716
238.91842.3104-0.79353.1113-4.19876.8744-0.3385-0.2545-0.6860.0192-0.05240.0183-0.37230.08970.16390.5727-0.04560.02240.60810.05230.792553.4756-81.66662.1447
243.89611.481-0.42428.4281.7631.66920.0791-0.4476-0.361-0.0385-0.2533-0.65360.21950.35080.12560.4523-0.02590.00620.57380.1940.53155.3725-76.31198.1731
253.26213.42222.57284.05123.68954.45160.3257-0.14730.01950.2173-0.43380.8742-0.523-0.38780.41380.4247-0.0041-0.00470.63180.14790.942841.1468-82.8086.5345
262.9011.63052.3314.3081-0.1452.60040.443-0.6941-0.9987-0.4003-0.4929-1.08620.74680.28030.08230.73230.01830.00940.62110.251.173652.0697-91.60336.239
275.35113.9669-3.43523.3679-2.0942.9046-0.291-0.3706-0.5821-0.0786-0.0778-0.90790.0140.83480.39160.6347-0.09990.04770.5891-0.09760.6994106.3512-25.4408-4.5189
286.53630.70563.44387.1958-0.64994.4882-0.44651.01860.0179-1.41570.0152-0.91580.23961.00170.38380.8131-0.11890.36990.82880.01670.7358113.3062-19.8856-18.1015
295.01480.4133-1.55415.6139-2.27551.75130.16720.11260.1528-0.7735-0.2239-0.62180.30060.5110.14120.655-0.08620.19880.6859-0.03930.5689111.742-25.3-13.461
301.3248-2.3062-0.24864.04830.49190.5413-0.6613-0.62680.6480.80990.2794-2.2810.90191.09570.23470.74820.10130.35321.17350.3551.0426125.3686-20.4678-16.1771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 270 through 280 )A270 - 280
2X-RAY DIFFRACTION2chain 'A' and (resid 281 through 322 )A281 - 322
3X-RAY DIFFRACTION3chain 'A' and (resid 323 through 341 )A323 - 341
4X-RAY DIFFRACTION4chain 'A' and (resid 342 through 380 )A342 - 380
5X-RAY DIFFRACTION5chain 'A' and (resid 381 through 418 )A381 - 418
6X-RAY DIFFRACTION6chain 'A' and (resid 419 through 456 )A419 - 456
7X-RAY DIFFRACTION7chain 'B' and (resid 272 through 322 )B272 - 322
8X-RAY DIFFRACTION8chain 'B' and (resid 323 through 341 )B323 - 341
9X-RAY DIFFRACTION9chain 'B' and (resid 342 through 380 )B342 - 380
10X-RAY DIFFRACTION10chain 'B' and (resid 381 through 418 )B381 - 418
11X-RAY DIFFRACTION11chain 'B' and (resid 419 through 456 )B419 - 456
12X-RAY DIFFRACTION12chain 'C' and (resid 271 through 289 )C271 - 289
13X-RAY DIFFRACTION13chain 'C' and (resid 290 through 312 )C290 - 312
14X-RAY DIFFRACTION14chain 'C' and (resid 313 through 331 )C313 - 331
15X-RAY DIFFRACTION15chain 'C' and (resid 332 through 341 )C332 - 341
16X-RAY DIFFRACTION16chain 'C' and (resid 342 through 365 )C342 - 365
17X-RAY DIFFRACTION17chain 'C' and (resid 366 through 418 )C366 - 418
18X-RAY DIFFRACTION18chain 'C' and (resid 419 through 456 )C419 - 456
19X-RAY DIFFRACTION19chain 'D' and (resid 762 through 771 )D762 - 771
20X-RAY DIFFRACTION20chain 'D' and (resid 772 through 781 )D772 - 781
21X-RAY DIFFRACTION21chain 'D' and (resid 782 through 801 )D782 - 801
22X-RAY DIFFRACTION22chain 'D' and (resid 802 through 813 )D802 - 813
23X-RAY DIFFRACTION23chain 'D' and (resid 814 through 833 )D814 - 833
24X-RAY DIFFRACTION24chain 'D' and (resid 834 through 865 )D834 - 865
25X-RAY DIFFRACTION25chain 'D' and (resid 866 through 874 )D866 - 874
26X-RAY DIFFRACTION26chain 'D' and (resid 875 through 888 )D875 - 888
27X-RAY DIFFRACTION27chain 'E' and (resid 762 through 781 )E762 - 781
28X-RAY DIFFRACTION28chain 'E' and (resid 782 through 825 )E782 - 825
29X-RAY DIFFRACTION29chain 'E' and (resid 826 through 865 )E826 - 865
30X-RAY DIFFRACTION30chain 'E' and (resid 866 through 888 )E866 - 888

+
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