[English] 日本語
Yorodumi
- PDB-5w0m: Structure of human TUT7 catalytic module (CM) in complex with U5 RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w0m
TitleStructure of human TUT7 catalytic module (CM) in complex with U5 RNA
Components
  • Terminal uridylyltransferase 7
  • U5 single-stranded RNA
KeywordsTRANSFERASE/RNA / terminal uridyltransferase / TUTase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / uridylyltransferase activity / transposable element silencing by mRNA destabilization / : / RNA uridylyltransferase / RNA 3'-end processing / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA ...polyuridylation-dependent mRNA catabolic process / uridylyltransferase activity / transposable element silencing by mRNA destabilization / : / RNA uridylyltransferase / RNA 3'-end processing / 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 / cytosol / cytoplasm
Similarity search - Function
Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Nucleotidyltransferase superfamily ...Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Nucleotidyltransferase superfamily / Zinc finger C2H2 type domain signature. / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
IODIDE ION / RNA / Terminal uridylyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Terminal uridylyltransferase 7
B: Terminal uridylyltransferase 7
C: Terminal uridylyltransferase 7
H: U5 single-stranded RNA
I: U5 single-stranded RNA
J: U5 single-stranded RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,64616
Polymers138,6236
Non-polymers1,02310
Water3,693205
1
A: Terminal uridylyltransferase 7
H: U5 single-stranded RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5926
Polymers46,2082
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-46 kcal/mol
Surface area18400 Å2
MethodPISA
2
B: Terminal uridylyltransferase 7
I: U5 single-stranded RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4314
Polymers46,2082
Non-polymers2232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-40 kcal/mol
Surface area16890 Å2
MethodPISA
3
C: Terminal uridylyltransferase 7
J: U5 single-stranded RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6236
Polymers46,2082
Non-polymers4154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-42 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.472, 135.472, 179.268
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 988 and (name N or name...
21(chain C and (resseq 988:992 or resseq 994:997 or resseq...
12chain H
22chain I
32chain J

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
111GLUGLUGLUGLU(chain A and ((resid 988 and (name N or name...AA98812
121LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
131LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
141LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
151LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
161LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
171LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
181LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
191LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
1101LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
1111LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
1121LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
1131LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
1141LEULEUARGARG(chain A and ((resid 988 and (name N or name...AA987 - 136311 - 387
211GLUGLUPROPRO(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 99212 - 16
221THRTHRPHEPHE(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC994 - 99718 - 21
231ASNASNGLUGLU(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC999 - 102323 - 47
241ILEILEGLNGLN(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC1025 - 103549 - 59
251ASPASPASPASP(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC103660
261GLUGLUMETMET(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 136212 - 386
271GLUGLUMETMET(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 136212 - 386
281GLUGLUMETMET(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 136212 - 386
291GLUGLUMETMET(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 136212 - 386
2101GLUGLUMETMET(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 136212 - 386
2111GLUGLUMETMET(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 136212 - 386
2121GLUGLUMETMET(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 136212 - 386
2131GLUGLUMETMET(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 136212 - 386
2141GLUGLUMETMET(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 136212 - 386
2151GLUGLUMETMET(chain C and (resseq 988:992 or resseq 994:997 or resseq...CC988 - 136212 - 386
112UUUUchain HHD1 - 41 - 4
212UUUUchain IIE1 - 41 - 4
312UUUUchain JJF1 - 41 - 4

NCS ensembles :
ID
1
2

-
Components

-
Protein / RNA chain , 2 types, 6 molecules ABCHIJ

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


Mass: 44721.812 Da / Num. of mol.: 3
Fragment: nucleotidyltransferase domain (UNP residues 983-1365)
Mutation: D1160A
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
#2: RNA chain U5 single-stranded RNA


Mass: 1485.872 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 215 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.42 Å3/Da / Density % sol: 64.06 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.298→179 Å / Num. obs: 82731 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 43.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.7
Reflection shellResolution: 2.298→2.31 Å / Rmerge(I) obs: 0.556 / CC1/2: 0.784

-
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

5w0b


Resolution: 2.298→98.168 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.33
RfactorNum. reflection% reflection
Rfree0.2287 4139 5.01 %
Rwork0.1883 --
obs0.1904 82655 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 204.5 Å2 / Biso mean: 65.9348 Å2 / Biso min: 20.33 Å2
Refinement stepCycle: final / Resolution: 2.298→98.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8863 231 26 205 9325
Biso mean--61.54 52.3 -
Num. residues----1105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059355
X-RAY DIFFRACTIONf_angle_d0.68312680
X-RAY DIFFRACTIONf_chiral_restr0.0441405
X-RAY DIFFRACTIONf_plane_restr0.0041573
X-RAY DIFFRACTIONf_dihedral_angle_d11.3025593
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4430X-RAY DIFFRACTION7.128TORSIONAL
12C4430X-RAY DIFFRACTION7.128TORSIONAL
21H147X-RAY DIFFRACTION7.128TORSIONAL
22I147X-RAY DIFFRACTION7.128TORSIONAL
23J147X-RAY DIFFRACTION7.128TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2976-2.32370.30961380.259625892727100
2.3237-2.35110.29471320.254126232755100
2.3511-2.37970.29621310.234526362767100
2.3797-2.40990.2831230.232626162739100
2.4099-2.44160.27951270.230726372764100
2.4416-2.4750.27641380.227325952733100
2.475-2.51040.2721280.236626272755100
2.5104-2.54790.3161410.230325962737100
2.5479-2.58770.28631490.230126212770100
2.5877-2.63010.31451530.230325982751100
2.6301-2.67540.30871440.223626152759100
2.6754-2.72410.27671500.21825932743100
2.7241-2.77650.24781410.2226192760100
2.7765-2.83320.29891520.20725862738100
2.8332-2.89480.26641310.210626512782100
2.8948-2.96210.28761130.216826182731100
2.9621-3.03620.27811450.224326462791100
3.0362-3.11830.2751280.231526012729100
3.1183-3.21010.29381440.224226352779100
3.2101-3.31370.28841410.213126212762100
3.3137-3.43210.23631360.20225612697100
3.4321-3.56960.25441420.191626692811100
3.5696-3.7320.22481450.186126012746100
3.732-3.92880.19781490.165626092758100
3.9288-4.17490.18591410.15222604274599
4.1749-4.49730.15911230.142326242747100
4.4973-4.94980.15341320.140926162748100
4.9498-5.6660.191390.16092623276299
5.666-7.13830.20171310.186726512782100
7.1383-98.25760.17921520.16612635278799
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)
16.7295-0.75466.63581.61840.25487.8342-0.00820.6078-0.11810.2141-0.1075-0.48250.01271.42080.14340.2685-0.0193-0.0680.44430.03120.39635.5344-53.215516.526
22.2464-5.41289.31753.658-2.32747.6182-0.08190.54350.0926-0.12940.20150.123-0.64250.06010.02870.3908-0.032-0.01330.48230.16350.4385-16.3144-43.4283-10.0278
39.0017-0.89874.76993.5645-1.93954.961-0.28540.27790.4436-0.22210.12070.4806-0.4668-0.22860.15080.3370.0571-0.05510.41630.08870.4169-22.4415-40.7737-0.8562
43.3408-1.8318-1.99935.79944.035.8553-0.02180.2960.1117-0.2868-0.09860.4879-0.0917-0.74810.08190.312-0.0092-0.05770.45390.1720.4237-27.5438-50.3638-3.8334
54.0139-0.06220.4194.22020.41812.9882-0.1118-0.37350.5980.3797-0.01310.2868-0.599-0.27410.12450.37180.031-0.00370.3532-0.03380.3198-11.7606-40.948419.6372
63.7577-1.07030.97183.29130.83697.8306-0.1119-0.702-0.59510.41070.1632-0.22620.84520.55170.06020.45340.0001-0.07250.30470.07250.3247-2.0666-61.756122.3437
72.66333.30933.87792.8455-0.40865.3040.3818-0.5809-0.46060.07030.08530.29030.3156-0.7464-0.43970.44820.07570.0290.42260.04130.3739-18.323-64.56412.5442
82.2996-0.4512-1.88034.22820.54982.68550.19730.59310.2975-0.2751-0.3499-0.87-0.07990.82910.10510.31420.04730.04180.72960.09370.456218.8157-66.9682-3.6409
92.15716.52572.62745.92921.28171.30650.5188-0.62070.33570.5696-0.40150.21240.1002-0.19020.00120.30850.02740.01590.34870.01750.3409-15.7706-68.7285.3469
105.63851.7209-0.79971.8457-0.12344.21660.01620.0495-0.3028-0.1198-0.04180.0080.4947-0.1364-0.00140.32090.034-0.0280.2290.01090.2807-13.8081-79.58694.0313
114.9609-3.09411.056410.0105-3.52715.96650.16380.5959-0.8298-0.75080.27210.68181.1514-0.5633-0.42060.4685-0.0989-0.08480.4702-0.06270.3561-21.1232-80.0254-6.9855
123.45430.1466-0.24531.1019-1.18932.3584-0.16010.0721-0.1507-0.09480.0127-0.11220.31710.23420.16560.34330.06380.04040.3059-0.02940.2605-1.5921-75.96850.581
132.08210.7341-0.55512.1396-1.1262.5717-0.0028-0.174-0.33320.0223-0.3151-0.41610.57360.84390.30380.43470.24650.07180.54130.07090.448810.8536-83.78145.7469
144.66-0.5557-2.23861.63521.84086.72830.33770.2656-0.828-0.6302-0.1929-0.69951.64980.933-0.10250.92190.4630.19730.68010.04820.756113.3856-95.2636-1.4959
155.22290.10571.26.517-2.95861.6793-0.25110.9349-1.0528-0.95720.0954-0.62031.63210.18730.29510.76150.1290.17870.4949-0.11050.56454.1677-93.6189-5.3285
166.69966.63254.6858.24222.41615.9315-0.24630.7627-0.5214-1.0043-0.0034-0.7810.47980.58950.27690.67430.26870.23160.8978-0.010.498614.8246-80.8103-15.8902
176.52174.32390.85445.4812-0.00353.975-0.19180.5934-0.1944-0.8369-0.1265-0.51020.32940.57870.32720.51490.23040.13390.75050.13850.487311.0665-72.5959-17.5735
184.92785.93112.56749.92714.51954.19930.4387-0.62090.0130.8395-0.3099-0.5452-0.1180.4657-0.14250.3381-0.1157-0.07560.6242-0.00530.387712.1027-40.6094-6.0675
198.17563.93528.35915.68465.58638.90060.3426-0.1366-0.42220.4121-0.13580.01370.9187-0.0408-0.25050.38090.01750.10780.28180.04940.3431-3.2385-68.3107-21.9902
204.74261.97895.02023.68684.81928.32810.07590.5147-0.32840.04270.1004-0.26590.36150.2531-0.14480.27990.01150.07770.3461-0.01370.3016-2.1075-61.2352-30.6631
215.19330.6296-1.46954.7993-0.86535.4949-0.09210.4362-0.1318-0.0280.12540.49260.0168-0.6338-0.02230.24610.03330.01380.3874-0.0410.3236-12.9581-59.7163-28.5351
221.4950.0578-1.20742.89941.43786.7187-0.0535-0.0208-0.1862-0.18520.0841-0.45150.02070.9562-0.03770.2178-0.0125-0.00170.39390.03510.331512.3309-47.6245-27.2126
235.05660.03410.21382.79372.05396.60930.01490.13830.5954-0.5084-0.0553-0.5357-1.06421.06220.03560.4958-0.21950.06640.51340.04950.452315.2086-35.3676-25.8196
248.1571.1613-4.7212.58912.37886.86570.39270.80430.6461-1.6642-0.25220.6124-1.6343-0.3437-0.18160.62990.0207-0.09390.43160.07350.35622.4523-37.7167-35.0366
252.31891.79038.72124.54751.38412.2826-0.2091-0.24480.6992-0.096-0.10430.1206-1.2461-0.27780.50570.5058-0.0182-0.00370.4905-0.0230.45531.0473-29.5764-16.9673
268.75310.3928-1.16196.2835-4.41536.31610.116-1.5467-0.01811.3276-0.1547-0.1744-1.30330.11630.0660.5686-0.13370.01190.6397-0.0970.37833.5477-35.8065-1.383
276.03525.86416.05119.49246.05212.5036-0.1664-0.57410.6203-0.3983-0.38781.3332-0.4246-1.03270.51440.55520.1175-0.06110.630.03460.5229-16.5489-39.0471-25.0875
286.42741.96335.26554.5934.86858.8333-0.4912-0.54610.30240.93310.29860.05260.0754-0.60740.25860.38560.1131-0.00250.49740.11530.5839-24.5533-50.002410.7494
293.1304-3.91674.84794.8788-6.03147.4542-0.2271.561-1.2436-1.26110.2947-0.49080.42061.406-0.07170.5141-0.08860.11460.7255-0.13890.4923-5.7538-85.3499-7.2865
307.21713.1216-3.41837.25174.6237.9544-0.3587-0.16861.3055-0.46450.31370.663-1.1108-0.13780.17370.43030.0534-0.10.3802-0.07290.5025-5.4817-46.9094-30.3304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 987 through 1015 )A987 - 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 988 through 1015 )B988 - 1015
9X-RAY DIFFRACTION9chain 'B' and (resid 1016 through 1035 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1036 through 1075 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1076 through 1105 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1106 through 1157 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 1158 through 1247 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 1248 through 1269 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 1270 through 1293 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 1294 through 1312 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 1313 through 1347 )B0
18X-RAY DIFFRACTION18chain 'C' and (resid 988 through 1015 )C988 - 1015
19X-RAY DIFFRACTION19chain 'C' and (resid 1016 through 1035 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 1036 through 1075 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 1076 through 1124 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 1125 through 1223 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 1224 through 1269 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 1270 through 1293 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 1294 through 1312 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 1313 through 1335 )C0
27X-RAY DIFFRACTION27chain 'C' and (resid 1336 through 1362 )C0
28X-RAY DIFFRACTION28chain 'H' and (resid 1 through 4 )H1 - 4
29X-RAY DIFFRACTION29chain 'I' and (resid 1 through 4 )I1 - 4
30X-RAY DIFFRACTION30chain 'J' and (resid 1 through 4 )J1 - 4

+
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