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- PDB-5w0n: Structure of human TUT7 catalytic module (CM) in complex with UMP... -

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Basic information

Entry
Database: PDB / ID: 5w0n
TitleStructure of human TUT7 catalytic module (CM) in complex with UMPNPP and U2 RNA
ComponentsTerminal uridylyltransferase 7
KeywordsTRANSFERASE / terminal uridyltransferase / TUTase
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / RNA 3'-end processing / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA ...polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / RNA 3'-end processing / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA / pre-miRNA processing / oocyte maturation / miRNA binding / Zygotic genome activation (ZGA) / RNA binding / zinc ion binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 type domain signature. / Nucleotidyltransferase superfamily / zinc finger ...Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 type domain signature. / Nucleotidyltransferase superfamily / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Chem-2KH / IODIDE ION / Chem-UPU / Terminal uridylyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsFaehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis.
Authors: Faehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
History
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminal uridylyltransferase 7
B: Terminal uridylyltransferase 7
C: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,75818
Polymers139,9773
Non-polymers3,78115
Water3,927218
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A: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0057
Polymers46,6591
Non-polymers1,3466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9096
Polymers46,6591
Non-polymers1,2505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8445
Polymers46,6591
Non-polymers1,1854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.972, 135.972, 181.574
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 987 and (name N or name...
21(chain B and (resseq 987:995 or resseq 997 or resseq...
31(chain C and (resseq 987:995 or resseq 997 or resseq...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU(chain A and ((resid 987 and (name N or name...AA98725
12ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
13ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
14ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
15ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
16ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
17ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
18ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
19ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
110ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
111ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
112ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
113ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
114ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
115ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
116ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
117ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
118ILEILEARGARG(chain A and ((resid 987 and (name N or name...AA985 - 136323 - 401
21LEULEUPROPRO(chain B and (resseq 987:995 or resseq 997 or resseq...BB987 - 99525 - 33
22PHEPHEPHEPHE(chain B and (resseq 987:995 or resseq 997 or resseq...BB99735
23ASNASNILEILE(chain B and (resseq 987:995 or resseq 997 or resseq...BB999 - 100637 - 44
24CYSCYSGLUGLU(chain B and (resseq 987:995 or resseq 997 or resseq...BB1008 - 102346 - 61
25ILEILEGLNGLN(chain B and (resseq 987:995 or resseq 997 or resseq...BB1025 - 102763 - 65
26LEULEUTHRTHR(chain B and (resseq 987:995 or resseq 997 or resseq...BB1029 - 104067 - 78
27LEULEUASNASN(chain B and (resseq 987:995 or resseq 997 or resseq...BB1042 - 106680 - 104
28GLYGLYGLYGLY(chain B and (resseq 987:995 or resseq 997 or resseq...BB1067105
29LEULEUMETMET(chain B and (resseq 987:995 or resseq 997 or resseq...BB987 - 136225 - 400
210LEULEUMETMET(chain B and (resseq 987:995 or resseq 997 or resseq...BB987 - 136225 - 400
211LEULEUMETMET(chain B and (resseq 987:995 or resseq 997 or resseq...BB987 - 136225 - 400
212LEULEUMETMET(chain B and (resseq 987:995 or resseq 997 or resseq...BB987 - 136225 - 400
213LEULEUMETMET(chain B and (resseq 987:995 or resseq 997 or resseq...BB987 - 136225 - 400
31LEULEUPROPRO(chain C and (resseq 987:995 or resseq 997 or resseq...CC987 - 99525 - 33
32PHEPHEPHEPHE(chain C and (resseq 987:995 or resseq 997 or resseq...CC99735
33ASNASNILEILE(chain C and (resseq 987:995 or resseq 997 or resseq...CC999 - 100637 - 44
34CYSCYSGLUGLU(chain C and (resseq 987:995 or resseq 997 or resseq...CC1008 - 102346 - 61
35ILEILEGLNGLN(chain C and (resseq 987:995 or resseq 997 or resseq...CC1025 - 102763 - 65
36LEULEUTHRTHR(chain C and (resseq 987:995 or resseq 997 or resseq...CC1029 - 104067 - 78
37LEULEUASNASN(chain C and (resseq 987:995 or resseq 997 or resseq...CC1042 - 106680 - 104
38GLYGLYGLYGLY(chain C and (resseq 987:995 or resseq 997 or resseq...CC1067105
39LEULEUASPASP(chain C and (resseq 987:995 or resseq 997 or resseq...CC987 - 134425 - 382
310LEULEUASPASP(chain C and (resseq 987:995 or resseq 997 or resseq...CC987 - 134425 - 382
311LEULEUASPASP(chain C and (resseq 987:995 or resseq 997 or resseq...CC987 - 134425 - 382
312LEULEUASPASP(chain C and (resseq 987:995 or resseq 997 or resseq...CC987 - 134425 - 382
313LEULEUASPASP(chain C and (resseq 987:995 or resseq 997 or resseq...CC987 - 134425 - 382

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Terminal uridylyltransferase 7 / TUT7 / TUTase 7 / Zinc finger CCHC domain-containing protein 6


Mass: 46659.129 Da / Num. of mol.: 3
Fragment: nucleotidyltransferase domain (UNP residues 963-1365)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZCCHC6, HS2, KIAA1711, TUT7 / Plasmid: Multi-Bac, pFL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q5VYS8, RNA uridylyltransferase

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Non-polymers , 7 types, 233 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-2KH / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#4: Chemical ChemComp-UPU / [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-4-HYDROXY-2-(HYDROXYMETHYL)TETRAHYDROFURAN-3-YL HYDROGEN (S)-PHOSPHATE


Mass: 550.367 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H23N4O14P
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.8-1.0 M lithium sulfate, 0.075-0.2 M potassium iodide, 0.05-0.2 M trisodium citrate, pH 5-6
PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.497→98.798 Å / Num. obs: 65579 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 48.74 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.5
Reflection shellResolution: 2.497→2.51 Å / CC1/2: 0.872

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5W0B
Resolution: 2.497→58.878 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.26
RfactorNum. reflection% reflection
Rfree0.2151 3249 4.96 %
Rwork0.1867 --
obs0.1881 65534 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.46 Å2 / Biso mean: 69.0815 Å2 / Biso min: 27.29 Å2
Refinement stepCycle: final / Resolution: 2.497→58.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8936 0 313 218 9467
Biso mean--56.72 51.01 -
Num. residues----1101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059393
X-RAY DIFFRACTIONf_angle_d0.58512699
X-RAY DIFFRACTIONf_chiral_restr0.0411394
X-RAY DIFFRACTIONf_plane_restr0.0031585
X-RAY DIFFRACTIONf_dihedral_angle_d11.3235524
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6319X-RAY DIFFRACTION5.759TORSIONAL
12B6319X-RAY DIFFRACTION5.759TORSIONAL
13C6319X-RAY DIFFRACTION5.759TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4972-2.53450.31380.260527502888100
2.5345-2.57410.3141500.257726992849100
2.5741-2.61630.27261660.25226942860100
2.6163-2.66140.28561660.248226782844100
2.6614-2.70980.23691360.23527092845100
2.7098-2.76190.26861290.225127112840100
2.7619-2.81830.25291470.224727022849100
2.8183-2.87960.24351220.2327222844100
2.8796-2.94660.26931410.230827282869100
2.9466-3.02020.26931230.243127412864100
3.0202-3.10190.27281540.232426932847100
3.1019-3.19320.24651500.225226742824100
3.1932-3.29620.26421390.213927342873100
3.2962-3.4140.24951330.217827032836100
3.414-3.55070.24861270.206827152842100
3.5507-3.71230.24341580.19612693285199
3.7123-3.9080.21551310.175827212852100
3.908-4.15270.16381150.1512712282799
4.1527-4.47330.1611530.14882687284099
4.4733-4.92320.16531380.14042709284799
4.9232-5.63510.18221130.15322745285899
5.6351-7.09780.19391820.17892663284599
7.0978-58.89390.17771380.15432702284098
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)
14.52951.49735.60312.18670.62978.27690.0367-0.46440.031-0.2409-0.20.34560.1807-1.30460.24560.32170.0434-0.04590.3969-0.06020.4475-72.704564.1601-17.9972
26.9724-0.5033.21682.2262-0.67733.90970.0661-1.05030.84570.0708-0.0508-0.1609-0.5127-0.2076-0.01380.4613-0.03870.01680.5652-0.10330.4388-51.936674.26769.9546
36.31951.78673.1353.36612.45893.8-0.1142-0.15460.48980.07550.0371-0.2231-0.49440.17210.08460.4493-0.0795-0.00760.4454-0.06080.4212-45.759376.99710.8254
43.75391.5631-1.45844.8207-2.45345.16920.0263-0.1637-0.24380.0765-0.0552-0.4820.08740.67660.04370.353-0.0087-0.04920.5466-0.11450.4448-40.763867.3553.7257
53.05940.12950.36832.49650.01132.7407-0.06850.34910.5158-0.2912-0.0162-0.1033-0.58370.18460.07510.4618-0.0475-0.0230.43270.03650.3862-56.274377.6061-19.5935
60.4751-1.0311.35324.0772-0.36897.16260.10630.1086-0.0326-0.22210.09740.26980.688-0.5387-0.13820.4684-0.0238-0.08390.4147-0.06870.3801-65.731856.1919-22.63
78.1167-1.66690.28683.01641.50152.9921-0.5043-0.2121-0.17080.13590.5711-0.38570.17410.5527-0.13060.43960.0378-0.0060.4173-0.01530.3331-49.686553.2937-12.9041
82.2697-1.17281.14232.9424-1.83753.3608-0.034-0.1532-0.1523-0.0124-0.04420.00770.1108-0.04520.0960.2804-0.02240.03680.4205-0.01660.3742-65.184260.28723.3129
92.2868-0.1198-0.19652.1753-1.09974.974-0.0643-0.20980.02870.33160.06860.2413-0.3742-0.643-0.01730.35490.1010.0060.4761-0.04190.4074-80.222474.494828.0521
107.0559-1.09991.12187.39920.48027.04990.19590.76630.223-0.6789-0.24620.0023-1.035-0.02720.08330.47820.04880.01480.44350.09560.4441-70.749585.046110.079
113.8915-3.04514.94886.5572-2.57766.75020.24770.56080.20360.0113-0.1159-0.6561-0.05840.55560.09020.5437-0.1217-0.05550.713-0.0010.6399-51.605178.428325.4607
125.8075-0.7305-0.97862.08520.28711.52050.13370.25050.70610.0098-0.07080.242-0.0472-0.4147-0.04490.3145-0.0127-0.01420.4217-0.07770.2898-72.169149.4018-0.3285
139.132-2.8117-1.07782.3716-0.53332.9550.14060.2972-0.126-0.1201-0.0832-0.15830.46290.1121-0.04870.442-0.03460.02160.4325-0.05250.3615-54.298638.1118-4.5825
145.01760.121.60397.66792.18155.9017-0.0696-0.3074-0.39520.34630.1848-0.45020.78350.5789-0.1250.47850.07960.00580.50220.04730.3708-49.698639.86795.1851
152.9355-0.7585-0.8981.98660.79682.707-0.2544-0.1058-0.38240.2289-0.16220.37270.6605-0.51170.37290.5112-0.21180.14350.5588-0.05860.5271-78.05333.75170.2975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 985 through 1015 )A985 - 1015
2X-RAY DIFFRACTION2chain 'A' and (resid 1016 through 1035 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1036 through 1075 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1076 through 1124 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1125 through 1293 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1294 through 1324 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1325 through 1363 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 987 through 1124 )B987 - 1124
9X-RAY DIFFRACTION9chain 'B' and (resid 1125 through 1293 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1294 through 1335 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1336 through 1362 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 987 through 1035 )C987 - 1035
13X-RAY DIFFRACTION13chain 'C' and (resid 1036 through 1075 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 1076 through 1124 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 1125 through 1344 )C0

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