[English] 日本語
Yorodumi
- PDB-4ol8: Ty3 reverse transcriptase bound to DNA/RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ol8
TitleTy3 reverse transcriptase bound to DNA/RNA
Components
  • 5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3'
  • 5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G)-3'
  • Reverse transcriptase/ribonuclease H
KeywordsTRANSFERASE / HYDROLASE/RNA/DNA / Protein-DNA/RNA / reverse transcription / DNA/RNA binding / HYDROLASE-RNA-DNA complex
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / RNA-directed DNA polymerase / telomerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / RNA-directed DNA polymerase / telomerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / proteolysis / DNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Peptidase A2B, Ty3 transposon peptidase / Ty3 transposon peptidase / Tf2-1-like, SH3 domain / Ty3 transposon capsid-like protein / Ty3 transposon capsid-like protein / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase ...Peptidase A2B, Ty3 transposon peptidase / Ty3 transposon peptidase / Tf2-1-like, SH3 domain / Ty3 transposon capsid-like protein / Ty3 transposon capsid-like protein / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Transposon Ty3-G Gag-Pol polyprotein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsNowak, E. / Miller, J.T. / Bona, M.K. / Studnicka, J. / Szczepanowski, R.H. / Jurkowski, J. / Le Grice, S.F.J. / Nowotny, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry.
Authors: Nowak, E. / Miller, J.T. / Bona, M.K. / Studnicka, J. / Szczepanowski, R.H. / Jurkowski, J. / Le Grice, S.F. / Nowotny, M.
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Structure summary
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Apr 16, 2014Group: Database references
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H
B: Reverse transcriptase/ribonuclease H
C: 5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G)-3'
D: 5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3'
G: 5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G)-3'
H: 5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3'
F: Reverse transcriptase/ribonuclease H
E: Reverse transcriptase/ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,72910
Polymers241,5378
Non-polymers1922
Water181
1
A: Reverse transcriptase/ribonuclease H
B: Reverse transcriptase/ribonuclease H
C: 5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G)-3'
D: 5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9616
Polymers120,7694
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-53 kcal/mol
Surface area43600 Å2
MethodPISA
2
G: 5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G)-3'
H: 5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3'
F: Reverse transcriptase/ribonuclease H
E: Reverse transcriptase/ribonuclease H


Theoretical massNumber of molelcules
Total (without water)120,7694
Polymers120,7694
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-33 kcal/mol
Surface area43990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)320.700, 75.062, 108.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Reverse transcriptase/ribonuclease H / Ty3 reverse transcriptase / RT / RT-RH / p55


Mass: 55059.449 Da / Num. of mol.: 4 / Fragment: UNP residues 536-1101 / Mutation: D426N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TY3B-G, YGRWTy3-1 POL, YGR109W-B, G5984 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99315, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: RNA chain 5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G)-3'


Mass: 5938.644 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3'


Mass: 4711.053 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.2 M ammonium sulfate, 17% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.999→48.898 Å / Num. all: 53285 / Num. obs: 53285 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.9
Reflection shellResolution: 2.999→3.29 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 2.1 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
XDSdata scaling
AutoSolphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.1→48.898 Å / SU ML: 0.51 / σ(F): 1.3 / Phase error: 30.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2956 2425 5 %RANDOM
Rwork0.227 ---
obs0.2305 48418 99.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12734 1360 10 1 14105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01614634
X-RAY DIFFRACTIONf_angle_d1.06920104
X-RAY DIFFRACTIONf_dihedral_angle_d15.7825398
X-RAY DIFFRACTIONf_chiral_restr0.0662325
X-RAY DIFFRACTIONf_plane_restr0.0052352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13520.39191580.34822914X-RAY DIFFRACTION100
3.1352-3.17210.37051490.33052820X-RAY DIFFRACTION99
3.1721-3.21080.36941560.32322929X-RAY DIFFRACTION100
3.2108-3.25140.37681510.30072900X-RAY DIFFRACTION100
3.2514-3.29420.35891550.29282901X-RAY DIFFRACTION100
3.2942-3.33930.36461520.28582826X-RAY DIFFRACTION100
3.3393-3.3870.34441580.28152948X-RAY DIFFRACTION99
3.387-3.43750.32831520.28382855X-RAY DIFFRACTION99
3.4375-3.49120.351490.26362872X-RAY DIFFRACTION99
3.4912-3.54850.33781560.25492895X-RAY DIFFRACTION99
3.5485-3.60960.34131490.25282874X-RAY DIFFRACTION99
3.6096-3.67530.29651480.23332852X-RAY DIFFRACTION99
3.6753-3.74590.29791550.22922909X-RAY DIFFRACTION99
3.7459-3.82240.30691510.222834X-RAY DIFFRACTION99
3.8224-3.90540.26991510.21722892X-RAY DIFFRACTION98
3.9054-3.99620.32481530.2252881X-RAY DIFFRACTION99
3.9962-4.09610.29231470.21982853X-RAY DIFFRACTION99
4.0961-4.20680.27931520.21112914X-RAY DIFFRACTION99
4.2068-4.33050.29981500.20692873X-RAY DIFFRACTION99
4.3305-4.47020.29321430.20362860X-RAY DIFFRACTION99
4.4702-4.62990.25281510.19432886X-RAY DIFFRACTION99
4.6299-4.81510.30531530.19032854X-RAY DIFFRACTION99
4.8151-5.0340.21491500.17992904X-RAY DIFFRACTION99
5.034-5.29910.28711500.20222888X-RAY DIFFRACTION99
5.2991-5.63070.29571460.2012850X-RAY DIFFRACTION99
5.6307-6.06470.30331490.21292879X-RAY DIFFRACTION99
6.0647-6.67370.29111450.20672874X-RAY DIFFRACTION98
6.6737-7.63620.25431510.20632860X-RAY DIFFRACTION99
7.6362-9.60880.23951590.2092867X-RAY DIFFRACTION99
9.6088-48.9040.30451510.2492828X-RAY DIFFRACTION98
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)
11.61471.246-0.80861.0236-0.20471.3254-0.1442-1.5577-0.23591.27750.2929-0.0652-0.0439-0.3731-0.13991.57940.4804-0.17321.88640.03060.7656-69.0606-2.378960.1986
22.80761.7024-1.05964.02091.17771.52660.6009-1.535-0.45621.1104-0.3043-0.3411-0.4635-1.6431-0.21841.56860.2776-0.11372.49570.40390.8422-60.8877-12.541168.1716
33.2663-0.69770.50884.1688-0.00921.7179-0.3817-1.4141-0.06070.83790.1803-0.21720.01180.20790.191.10870.3090.00111.75440.04560.6195-64.8311-1.05354.9873
47.18260.16240.06538.53741.49795.8633-0.9428-1.59731.35920.10470.9728-0.4075-0.9659-0.64220.0510.99440.1819-0.23631.3745-0.37020.8212-68.281517.392151.9957
53.5142-0.67940.54126.45572.62294.6427-0.8914-1.0550.52710.52150.7403-0.4997-1.6261-0.33530.0451.3280.48-0.17421.6158-0.50160.7205-73.37817.446660.7714
61.57840.6081-2.60793.4703-0.92164.5221-0.4221-1.69340.9210.538-0.1965-1.54590.12220.99480.42511.27350.1105-0.57841.9259-0.37321.2405-45.612915.453252.6672
70.62380.5149-1.21362.7411-0.48632.4662-0.5241-0.86870.34021.0908-0.4444-1.6389-0.5522.0430.15840.8061-0.4752-0.37311.663-0.40211.3234-37.938418.814543.7955
80.13450.38810.72655.40380.42964.4217-0.7629-0.16431.5611.0305-0.0418-0.072-0.86830.69570.38431.5435-0.3325-0.42771.3323-0.56051.6518-47.866630.557235.6794
98.0972-2.0572-0.22313.6792-1.97671.3353-0.1691-0.53870.46030.52610.0447-1.7727-0.24820.93260.01491.0073-0.1933-0.20850.9689-0.18431.3188-44.700119.254429.6381
103.1722-2.3506-3.08871.75471.98089.21210.194-0.11690.3185-0.081-0.0118-0.1152-0.53340.3336-0.16981.012-0.2414-0.09041.01-0.06471.2442-53.246723.856325.9657
113.6856-2.50422.1873.69751.90567.0296-0.7552-0.92240.82670.2277-0.1199-0.1277-0.2394-1.44350.82220.76490.02610.00540.8717-0.05230.7501-96.55067.328119.9422
127.37040.0271-0.65725.5097-0.27575.37150.2111-0.68460.26410.4509-0.2878-0.1362-0.40720.12540.10390.68650.0638-0.1050.7996-0.03740.5174-71.69226.902231.1673
137.4605-1.01511.7062.5448-0.72095.28020.07910.5786-0.3453-0.3285-0.06660.35550.6257-0.2699-0.00320.6983-0.0176-0.02350.535-0.06560.5435-88.46971.299513.5678
148.6844.0041-2.90324.1877-2.34222.4698-0.34960.8683-0.4773-0.931-0.1433-0.62170.3091-0.03960.45961.18580.18980.10721.14320.07610.7575-66.908113.824-9.9511
155.70631.8153-1.42925.3609-2.73429.2084-0.16551.26290.064-0.8530.1925-0.21160.39030.3574-0.02410.81930.05390.09580.84740.07090.5954-62.82619.4664-7.4232
167.10751.31870.29022.9767-0.0167.43770.0439-0.1337-0.0114-0.167-0.1487-0.3576-0.3822-0.01530.13390.78840.09440.09510.47120.12590.6156-63.26897.7719.8186
179.40583.2914-0.63933.86313.00464.1174-0.5438-0.7305-0.1211-0.0024-0.4853-1.1126-0.28442.08851.22911.15410.1109-0.13521.81050.08090.7715-56.4571-0.718147.5888
187.36851.96934.07927.61596.72887.6252-0.68180.1306-1.8105-0.39141.442-0.99710.94073.5442-0.48031.43670.08910.28421.98090.04771.4798-44.5813-1.995325.0996
196.8529-0.38461.13236.42534.42393.2767-0.0298-0.27060.24590.07370.934-1.98390.64242.4315-1.12691.15060.15220.08912.12420.08921.5535-47.59330.328434.1717
208.48354.3240.73344.41684.00536.0309-0.78992.37162.63180.19140.00190.696-1.32350.38780.92051.02660.2869-0.08751.29370.56691.9186-32.9745-21.2151-33.3704
215.8461.4692-3.77062.20311.02344.5427-0.2609-1.58552.73390.76710.2059-1.14160.6130.9650.02441.43060.5391-0.0641.6746-0.07032.1329-39.1215-8.6863-11.3069
226.5923-5.4726-4.74954.53483.92393.76981.3216-0.26492.68510.6684-2.17112.0691-3.83740.44320.66111.9505-0.0540.28351.4941-0.48512.1493-36.105-6.2517-1.2544
235.52494.5394-7.05866.8896-4.73379.3850.36071.10331.8841-0.75792.0408-0.22640.9552-0.8533-2.28891.17510.3664-0.01441.61260.38281.8485-41.717-14.5278-17.4571
240.61280.01070.23620.1446-0.02330.0993-0.75410.03220.9408-0.26-0.2601-1.11940.10370.89470.74341.24210.52520.13861.49450.95672.0813-32.0195-10.1453-34.1456
253.47523.8958-0.47656.8171-2.77797.47490.31420.5436-0.0332-0.2527-0.3031-0.52020.33410.72710.012.0841.09-0.6273.330.60992.596-24.9496-20.6296-40.4019
263.7774-2.03121.74423.8759-2.32414.4799-0.06-0.545-0.40680.02830.3560.12651.03830.1079-0.29881.17980.2096-0.17680.62940.05361.1885-22.4222-45.7553-3.1673
270.44650.28170.05270.27380.06180.35920.23950.06120.193-0.1862-0.8873-0.0105-0.8892-0.31610.63492.01660.5292-0.38111.2902-0.24131.154-25.5262-23.74229.9851
282.77210.5850.26213.7538-1.75678.4426-0.1907-1.05091.12961.10340.51340.0136-1.0551-0.6352-0.29191.25180.4111-0.22721.0741-0.43041.3539-27.716-26.05079.3097
292.0614-0.40421.09081.14940.30641.03611.37011.9568-0.8548-0.7151-0.7431-0.23870.65650.8083-0.64661.45690.6758-0.01612.18760.27651.5814-29.4924-34.5493-45.5405
302.6018-1.73992.04531.1118-1.37586.89521.27611.74190.1959-1.1818-0.4686-0.23050.6912-0.5773-0.94851.55650.6964-0.07361.94760.30181.3578-38.9174-28.6214-47.0044
310.8756-0.7567-1.09991.727-0.252.31340.8571.80520.9616-1.04-0.8345-0.41360.17690.23860.0281.58280.97210.16522.09760.46871.5664-18.9687-28.7539-40.6979
328.3096-0.94190.8787.53982.2543.89241.06882.06740.8547-1.3296-0.65911.4-0.662-0.7934-0.41481.24120.17930.0841.5120.49451.9719-25.053-2.1809-38.6265
333.0098-2.1262-1.19812.98552.23052.53410.10370.20810.2244-0.42990.2410.176-1.1797-0.7157-0.11111.76470.3097-0.38730.49820.80872.4526-23.69273.56-29.1355
340.5427-1.68070.48035.6928-0.16836.22510.10520.43642.0808-1.17420.9754-0.3611-2.12460.87890.05491.6167-0.18230.21590.87570.30071.9996-12.0481-2.5679-28.6185
355.92051.1174-4.12651.18240.60835.40891.18910.47240.24090.3407-0.8852-0.5253-1.21010.0201-0.23031.20120.0612-0.04950.83450.14592.1919-15.7775-6.3843-11.9507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 201 )
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 221 )
5X-RAY DIFFRACTION5chain 'A' and (resid 222 through 248 )
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 305 )
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 352 )
8X-RAY DIFFRACTION8chain 'A' and (resid 353 through 378 )
9X-RAY DIFFRACTION9chain 'A' and (resid 379 through 411 )
10X-RAY DIFFRACTION10chain 'A' and (resid 412 through 459 )
11X-RAY DIFFRACTION11chain 'B' and (resid 15 through 53 )
12X-RAY DIFFRACTION12chain 'B' and (resid 54 through 123 )
13X-RAY DIFFRACTION13chain 'B' and (resid 124 through 262 )
14X-RAY DIFFRACTION14chain 'B' and (resid 263 through 299 )
15X-RAY DIFFRACTION15chain 'B' and (resid 300 through 411 )
16X-RAY DIFFRACTION16chain 'B' and (resid 412 through 476 )
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 6 )
18X-RAY DIFFRACTION18chain 'C' and (resid 7 through 18 )
19X-RAY DIFFRACTION19chain 'D' and (resid 33 through 47 )
20X-RAY DIFFRACTION20chain 'G' and (resid 2 through 6 )
21X-RAY DIFFRACTION21chain 'G' and (resid 7 through 18 )
22X-RAY DIFFRACTION22chain 'H' and (resid 32 through 36 )
23X-RAY DIFFRACTION23chain 'H' and (resid 37 through 41 )
24X-RAY DIFFRACTION24chain 'H' and (resid 42 through 46 )
25X-RAY DIFFRACTION25chain 'H' and (resid 47 through 47 )
26X-RAY DIFFRACTION26chain 'F' and (resid 15 through 263 )
27X-RAY DIFFRACTION27chain 'F' and (resid 264 through 339 )
28X-RAY DIFFRACTION28chain 'F' and (resid 340 through 473 )
29X-RAY DIFFRACTION29chain 'E' and (resid 22 through 70 )
30X-RAY DIFFRACTION30chain 'E' and (resid 71 through 133 )
31X-RAY DIFFRACTION31chain 'E' and (resid 134 through 262 )
32X-RAY DIFFRACTION32chain 'E' and (resid 263 through 297 )
33X-RAY DIFFRACTION33chain 'E' and (resid 298 through 330 )
34X-RAY DIFFRACTION34chain 'E' and (resid 331 through 358 )
35X-RAY DIFFRACTION35chain 'E' and (resid 359 through 458 )

+
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