[English] 日本語
Yorodumi
- PDB-3qhe: Crystal structure of the complex between the armadillo repeat dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qhe
TitleCrystal structure of the complex between the armadillo repeat domain of adenomatous polyposis coli and the tyrosine-rich domain of Sam68
Components
  • Adenomatous polyposis coli proteinFamilial adenomatous polyposis
  • KH domain-containing, RNA-binding, signal transduction-associated protein 1
Keywordssignaling protein/splicing / Armadillo repeat superhelix / Regulation of Wnt signaling / tumor suppressor protein / adaptor protein / RNA-binding protein / signaling protein-splicing protein complex / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / signaling protein-splicing complex
Function / homology
Function and homology information


regulation of RNA export from nucleus / Grb2-Sos complex / APC truncation mutants are not K63 polyubiquitinated / PTK6 Regulates Proteins Involved in RNA Processing / positive regulation of RNA export from nucleus / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly ...regulation of RNA export from nucleus / Grb2-Sos complex / APC truncation mutants are not K63 polyubiquitinated / PTK6 Regulates Proteins Involved in RNA Processing / positive regulation of RNA export from nucleus / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity / negative regulation of microtubule depolymerization / negative regulation of cyclin-dependent protein serine/threonine kinase activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / microtubule plus-end binding / beta-catenin destruction complex / poly(A) binding / regulation of microtubule-based process / heart valve development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / catenin complex / Wnt signalosome / poly(U) RNA binding / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / regulation of alternative mRNA splicing, via spliceosome / endocardial cushion morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / positive regulation of translational initiation / mitotic cytokinesis / bicellular tight junction / lateral plasma membrane / signaling adaptor activity / protein tyrosine kinase binding / SH2 domain binding / Deactivation of the beta-catenin transactivating complex / adherens junction / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / kinetochore / mRNA processing / ruffle membrane / beta-catenin binding / Wnt signaling pathway / SH3 domain binding / positive regulation of protein catabolic process / G2/M transition of mitotic cell cycle / cell migration / Ovarian tumor domain proteases / lamellipodium / insulin receptor signaling pathway / nervous system development / positive regulation of cold-induced thermogenesis / T cell receptor signaling pathway / microtubule binding / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / microtubule / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / protein domain specific binding / negative regulation of cell population proliferation / mRNA binding / centrosome / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr ...Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / K Homology domain, type 1 superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / K Homology domain / K homology RNA-binding domain / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Adenomatous polyposis coli protein / KH domain-containing, RNA-binding, signal transduction-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMorishita, E.C.J. / Murayama, K. / Kato-Murayama, M. / Ishizuku-Katsura, Y. / Tomabechi, Y. / Terada, T. / Handa, N. / Shirouzu, M. / Akiyama, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2011
Title: Crystal structures of the armadillo repeat domain of adenomatous polyposis coli and its complex with the tyrosine-rich domain of sam68
Authors: Morishita, E.C. / Murayama, K. / Kato-Murayama, M. / Ishizuka-Katsura, Y. / Tomabechi, Y. / Hayashi, T. / Terada, T. / Handa, N. / Shirouzu, M. / Akiyama, T. / Yokoyama, S.
History
DepositionJan 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenomatous polyposis coli protein
B: KH domain-containing, RNA-binding, signal transduction-associated protein 1
C: Adenomatous polyposis coli protein
D: KH domain-containing, RNA-binding, signal transduction-associated protein 1


Theoretical massNumber of molelcules
Total (without water)87,9914
Polymers87,9914
Non-polymers00
Water4,720262
1
A: Adenomatous polyposis coli protein
B: KH domain-containing, RNA-binding, signal transduction-associated protein 1


Theoretical massNumber of molelcules
Total (without water)43,9962
Polymers43,9962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-7 kcal/mol
Surface area15200 Å2
MethodPISA
2
C: Adenomatous polyposis coli protein
D: KH domain-containing, RNA-binding, signal transduction-associated protein 1


Theoretical massNumber of molelcules
Total (without water)43,9962
Polymers43,9962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-7 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.223, 148.223, 63.379
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Adenomatous polyposis coli protein / Familial adenomatous polyposis / APC / Protein APC / Deleted in polyposis 2.5


Mass: 37502.219 Da / Num. of mol.: 2 / Fragment: Armadillo repeat domain, residues 396-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: E. coli cell-free system / Plasmid: pCR2.1 / Production host: cell free synthsis (unknown) / References: UniProt: P25054
#2: Protein KH domain-containing, RNA-binding, signal transduction-associated protein 1 / Src-associated in mitosis 68 kDa protein / Sam68 / GAP-associated tyrosine phosphoprotein p62 / p21 ...Src-associated in mitosis 68 kDa protein / Sam68 / GAP-associated tyrosine phosphoprotein p62 / p21 Ras GTPase-activating protein-associated p62 / p68


Mass: 6493.303 Da / Num. of mol.: 2 / Fragment: Tyrosine-rich domain, residues 365-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: E. coli cell-free system / Plasmid: pCR2.1 / Production host: cell free synthsis (unknown) / References: UniProt: Q07666
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 46.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM BIS-TRIS (pH 5.5), 150mM NaCl, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→64.18 Å / Num. all: 31344 / Num. obs: 31344 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Rmerge(I) obs: 0.095 / Rsym value: 0.091 / Net I/σ(I): 7.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2 / Num. unique all: 4539 / Rsym value: 0.37 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AU3
Resolution: 2.4→64.18 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 14.657 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; ASN709-LEU710 and LEU710-ILE711 C-N bonds in chain C, 0.91A and 1.05A, respectively, lie outside of the accepted range for the peptide bond ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; ASN709-LEU710 and LEU710-ILE711 C-N bonds in chain C, 0.91A and 1.05A, respectively, lie outside of the accepted range for the peptide bond (1.30-1.45). depositors said that it was hard to build them suitably because these residues are in a region of poor density.
RfactorNum. reflection% reflectionSelection details
Rfree0.23046 1578 5 %RANDOM
Rwork0.18695 ---
all0.18915 31322 --
obs0.18915 29744 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.4→64.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 0 0 262 5362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215185
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.9577007
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3255654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66524.591220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13815942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9081530
X-RAY DIFFRACTIONr_chiral_restr0.0720.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023786
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4051.53282
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.825235
X-RAY DIFFRACTIONr_scbond_it1.50831903
X-RAY DIFFRACTIONr_scangle_it2.5244.51772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 118 -
Rwork0.196 2180 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
112.92195.0391-0.44836.05910.42923.4143-0.19310.56110.1772-0.5990.2430.0215-0.28730.1637-0.04990.31530.046-0.08080.20090.08880.129934.2271123.2103-17.8859
216.3804-9.468121.200127.565111.039852.0089-0.44910.0111-0.2392-0.51550.76660.2194-1.32620.8229-0.31750.5640.2592-0.08930.5180.32160.620330.5282132.8954-15.2446
33.4802-0.6402-0.74364.4473-0.29683.4360.12030.0643-0.2075-0.2176-0.0440.34580.2932-0.1936-0.07630.1686-0.0133-0.1250.21390.05340.230325.3739115.1394-8.7447
41.48280.56840.35783.18470.24511.61890.05250.080.0129-0.17110.02330.18020.0111-0.0619-0.07580.15490.0081-0.02180.16180.04010.16737.2305120.9559-4.1588
51.3087-0.3219-0.29288.94690.21762.60580.0917-0.072-0.04420.0778-0.05650.0633-0.041-0.1071-0.03520.13840.0076-0.01760.1820.03670.182436.6392120.08235.5129
62.9416-0.4619-0.55037.293.94336.35240.07370.0527-0.0423-0.21780.1273-0.038-0.03370.213-0.2010.1330.0218-0.03570.15310.08360.177346.0904114.28986.6286
70.4509-0.51710.06772.3280.03971.77710.0607-0.04070.07330.0727-0.01510.1812-0.127-0.1396-0.04560.1463-0.0132-0.00260.1620.02610.21442.6437116.645516.6754
833.4326-18.0476-4.54459.74912.04434.9194-1.3343-1.5974-1.52280.74420.92450.8252-0.93070.29690.40980.5899-0.08180.2320.54670.00390.660926.9979122.499125.0302
94.0014-0.5928-0.39932.71990.18883.95880.0097-0.20960.18290.1693-0.0056-0.0638-0.04540.0632-0.00410.2151-0.0258-0.00840.15840.03840.217545.944112.843726.4079
1021.74455.86485.6277.0891-3.80697.4779-0.0398-1.59951.64040.8182-0.09930.6912-0.5857-1.25140.13910.2909-0.02480.04360.4897-0.14780.382433.4733108.499932.9297
115.2778-1.07540.37642.9731-1.32122.7209-0.0492-0.0967-0.13240.00580.0175-0.08350.06950.05280.03170.1809-0.03060.01680.1620.01880.193544.4838104.61428.9115
1211.93753.0921-9.49055.4837-2.31219.78970.1061-1.06480.02340.83230.0854-0.2674-0.29410.7265-0.19150.2484-0.0329-0.06630.24710.03090.138446.4535104.565240.6974
1313.43091.69514.18433.68820.6575.12340.07890.1236-0.2638-0.04570.0077-0.2262-0.04220.0706-0.08660.197-0.03260.03040.13610.05720.215239.318696.596731.6382
1412.9335-5.82591.0979.10893.899313.39950.5994-0.05590.1737-0.8319-0.1382-0.180.1969-0.5571-0.46120.3788-0.0309-0.02220.2430.06940.428732.5679109.63819.2276
152.22962.8946-5.371611.8863-5.849513.26660.3355-0.07340.3054-0.03130.08890.5553-0.88870.2977-0.42440.31630.0724-0.07230.3190.08560.53837.2743108.49821.7159
166.78172.72-4.25245.8743-3.50017.4581-0.06690.120.4620.06930.09480.1201-0.2586-0.4732-0.0280.1880.0501-0.02110.2585-0.01930.106-4.261194.524128.0151
1724.713310.24592.43734.24851.020.4998-0.8612.1471-0.2461-0.33750.8314-0.09380.2687-0.3490.02961.337-0.35110.2711.6767-0.15610.2562-11.376985.915528.1442
1810.95585.33510.34725.23111.37531.6999-0.23490.37320.5224-0.29160.0670.1878-0.1441-0.12750.16790.2533-0.0115-0.01360.19520.0530.10357.604795.906718.8843
198.415-5.56831.097417.6408-7.078517.5995-0.0294-0.21241.478-0.3976-0.0986-1.4383-0.5861.2530.1280.2941-0.0564-0.06130.22890.01170.392618.6731107.558625.7926
2031.0818-1.43471.17754.1212-9.653522.7775-0.5229-1.14361.58820.84080.2106-0.1954-1.9299-0.37780.31230.42520.0815-0.15590.14-0.09960.401710.9877107.162930.2959
211.81580.39280.3850.8617-0.04582.1106-0.0566-0.06650.10130.00930.0111-0.0516-0.015-0.14030.04550.16620.0095-0.01660.18470.01340.13059.659491.373329.4775
223.8204-0.0478-0.21382.34140.59685.2905-0.0005-0.0172-0.09230.0847-0.0062-0.01320.0944-0.1450.00670.1530.0213-0.00780.15940.0370.139216.78986.275533.8381
235.9668-2.4678-3.54747.45254.82558.6085-0.11660.037-0.46060.1971-0.04310.1930.4493-0.30890.15970.1459-0.0211-0.04890.20340.06330.189917.951179.311337.8503
243.4331-1.06260.46932.22050.4922.28450.0434-0.0238-0.25790.03810.058-0.08880.11780.0307-0.10140.1648-0.0258-0.02520.17390.01130.18526.660878.182138.288
254.798-0.80720.66675.6338-1.48864.50710.06550.2877-0.141-0.11510.0336-0.11480.20560.1983-0.09910.1509-0.0115-0.0650.2542-0.03370.294534.178573.950439.957
265.58770.23721.26676.3566-2.20994.52070.1971-0.0833-0.5261-0.062-0.0291-0.40680.52020.3974-0.16810.12250.013-0.08150.22-0.05420.236244.736174.989244.2651
277.37570.58162.093617.7048-6.9699.4762-0.0066-0.100400.48030.0346-0.158-0.27710.2244-0.0280.1406-0.0278-0.10650.232-0.07110.196148.29883.810448.9938
288.6985-1.48235.08896.5828-3.458917.2530.17640.0309-0.27840.21390.0356-0.07810.42490.4009-0.2120.089-0.04220.01960.1238-0.01070.231626.962490.788734.9721
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A401 - 440
2X-RAY DIFFRACTION2A441 - 445
3X-RAY DIFFRACTION3A446 - 473
4X-RAY DIFFRACTION4A474 - 533
5X-RAY DIFFRACTION5A534 - 553
6X-RAY DIFFRACTION6A554 - 579
7X-RAY DIFFRACTION7A580 - 622
8X-RAY DIFFRACTION8A623 - 627
9X-RAY DIFFRACTION9A628 - 665
10X-RAY DIFFRACTION10A666 - 672
11X-RAY DIFFRACTION11A673 - 694
12X-RAY DIFFRACTION12A695 - 704
13X-RAY DIFFRACTION13A705 - 731
14X-RAY DIFFRACTION14B379 - 388
15X-RAY DIFFRACTION15C402 - 411
16X-RAY DIFFRACTION16C412 - 425
17X-RAY DIFFRACTION17C426 - 439
18X-RAY DIFFRACTION18C440 - 458
19X-RAY DIFFRACTION19C459 - 464
20X-RAY DIFFRACTION20C465 - 470
21X-RAY DIFFRACTION21C471 - 526
22X-RAY DIFFRACTION22C527 - 559
23X-RAY DIFFRACTION23C560 - 581
24X-RAY DIFFRACTION24C582 - 622
25X-RAY DIFFRACTION25C623 - 661
26X-RAY DIFFRACTION26C662 - 706
27X-RAY DIFFRACTION27C707 - 731
28X-RAY DIFFRACTION28D379 - 389

+
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