[English] 日本語
Yorodumi
- PDB-6o9e: Structure of HIV-1 Reverse Transcriptase in complex with DNA and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o9e
TitleStructure of HIV-1 Reverse Transcriptase in complex with DNA and INDOPY-1
Components
  • (Reverse transcriptase ...) x 2
  • DNA (38-MER)
KeywordsTRANSFERASE/DNA / Human immunodeficiency virus 1 / Protein/DNA / nucleotide-competing reverse transcriptase inhibitor / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain 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
sucrose / Chem-IY1 / AMMONIUM ION / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRuiz, F.X. / Hoang, A. / Das, K. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)MERIT Award R37 AI027690 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structural Basis of HIV-1 Inhibition by Nucleotide-Competing Reverse Transcriptase Inhibitor INDOPY-1.
Authors: Ruiz, F.X. / Hoang, A. / Das, K. / Arnold, E.
History
DepositionMar 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reverse transcriptase p66
B: Reverse transcriptase p51
C: Reverse transcriptase p66
D: Reverse transcriptase p51
F: DNA (38-MER)
E: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,10524
Polymers251,4366
Non-polymers2,66818
Water2,000111
1
A: Reverse transcriptase p66
B: Reverse transcriptase p51
E: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,39815
Polymers125,7183
Non-polymers1,68012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-92 kcal/mol
Surface area46290 Å2
MethodPISA
2
C: Reverse transcriptase p66
D: Reverse transcriptase p51
F: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7079
Polymers125,7183
Non-polymers9896
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12790 Å2
ΔGint-64 kcal/mol
Surface area47350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.762, 127.663, 131.610
Angle α, β, γ (deg.)90.00, 101.50, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Reverse transcriptase ... , 2 types, 4 molecules ACBD

#1: Protein Reverse transcriptase p66


Mass: 63874.133 Da / Num. of mol.: 2 / Mutation: C280S, D498N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein Reverse transcriptase p51


Mass: 50096.539 Da / Num. of mol.: 2 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, HIV-1 retropepsin

-
DNA chain / Sugars , 2 types, 4 molecules FE

#3: DNA chain DNA (38-MER)


Mass: 11747.539 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 7 types, 127 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-IY1 / 5-methyl-1-(4-nitrophenyl)-2-oxo-2,5-dihydro-1H-pyrido[3,2-b]indole-3-carbonitrile / Indopy-1


Mass: 344.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H12N4O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 10-12% PEG 8000, 50 MM BISTRIS-PROPANE PH 7.2, 50 MM AMMONIUM SULFATE, 5% GLYCEROL, 5% SUCROSE

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 113545 / % possible obs: 100 % / Redundancy: 19 % / Biso Wilson estimate: 73.6 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.055 / Rrim(I) all: 0.171 / Net I/σ(I): 11.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 19.5 % / Rmerge(I) obs: 6.118 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5622 / CC1/2: 0.311 / Rpim(I) all: 2.035 / Rrim(I) all: 6.45 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3G

5d3g


Resolution: 2.4→50 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.68
RfactorNum. reflection% reflection
Rfree0.2416 1998 1.76 %
Rwork0.203 --
obs0.2037 113316 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15836 1441 175 111 17563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218076
X-RAY DIFFRACTIONf_angle_d0.48924857
X-RAY DIFFRACTIONf_dihedral_angle_d17.4916945
X-RAY DIFFRACTIONf_chiral_restr0.0392692
X-RAY DIFFRACTIONf_plane_restr0.0032923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.43251410.40047836X-RAY DIFFRACTION99
2.46-2.52660.38151430.3657928X-RAY DIFFRACTION100
2.5266-2.60090.3691430.34217879X-RAY DIFFRACTION100
2.6009-2.68490.35251400.32247933X-RAY DIFFRACTION100
2.6849-2.78080.29861420.30517925X-RAY DIFFRACTION100
2.7808-2.89220.31461430.26637940X-RAY DIFFRACTION100
2.8922-3.02380.29521420.2477915X-RAY DIFFRACTION100
3.0238-3.18320.26241430.23867972X-RAY DIFFRACTION100
3.1832-3.38270.27861420.23497944X-RAY DIFFRACTION100
3.3827-3.64390.25611430.2067957X-RAY DIFFRACTION100
3.6439-4.01060.23531440.18627983X-RAY DIFFRACTION100
4.0106-4.59090.17491430.16667987X-RAY DIFFRACTION100
4.5909-5.78390.22441430.17898003X-RAY DIFFRACTION100
5.7839-500.22961460.17588116X-RAY DIFFRACTION100
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)
16.8496-2.9707-2.41857.41892.83832.23740.1974-0.57151.54180.73920.4467-1.3777-0.96860.3469-0.64611.7730.0133-0.1031.1531-0.15991.0776-22.527682.5125-15.3778
22.7881-1.2625-2.01932.58911.68314.61420.5054-0.10620.87760.1099-0.0068-0.2782-1.247-0.2807-0.35920.90230.10790.08830.54840.11180.9235-27.09376.7132-45.2128
38.1486-1.2954-1.48734.78251.13294.2554-0.03560.2597-0.28390.24840.2573-0.57950.06440.5768-0.20690.361-0.0716-0.02920.66430.0150.70885.961351.0731-68.1268
42.3225-0.1866-0.88225.48791.03533.0329-0.2315-0.3251-0.59160.97740.13760.48430.6126-0.40410.01410.80730.04010.18750.73190.24470.8538-35.553746.3831-33.7602
54.29821.5624-3.88921.6163-1.26615.5185-0.58990.5302-1.02260.13430.0570.22990.9612-0.46370.58930.8498-0.12830.10580.6056-0.05711.2394-18.843127.9944-55.2033
64.3978-1.24030.56844.1938-1.26894.945-0.26870.2655-0.25010.1695-0.062-0.11280.3110.1860.33320.4512-0.04190.03880.48640.12530.8018-20.761241.505-53.0647
71.73880.05510.70011.93362.352.4330.3362-1.316-0.39611.52860.3484-0.42560.98310.0456-0.64952.789-0.5776-0.3752.1860.27661.0388-16.3549-6.072122.6327
82.41881.24961.21425.2787-2.24822.93050.6321-1.0381-0.33470.7789-0.5612-1.09170.34070.2325-0.06011.9204-0.4478-0.091.68840.10750.8471-16.00925.80628.7052
92.05161.6061-0.00752.1797-0.232.39440.8484-1.31880.36821.7942-0.5166-0.0005-0.12250.1131-0.24372.4403-0.7162-0.03191.8915-0.1470.8176-18.506311.23569.577
107.5418-1.98920.43767.3940.35474.61730.38780.05390.56061.0811-0.2543-1.4348-0.6241.0656-0.12721.2259-0.385-0.15981.14590.05970.8097-2.020314.1425-14.0158
114.88520.6843-2.72743.60173.11418.34360.2374-0.25710.26040.5724-0.15220.0639-0.46510.1158-0.08180.7256-0.073-0.01080.42770.14740.5862-17.219913.4256-26.1193
122.971-1.4372-1.02042.69840.74534.68640.050.3417-0.17820.0750.0892-0.32210.23170.6872-0.17550.313-0.0224-0.06520.75420.06330.7027-2.8682-8.4066-47.8648
130.7885-0.825-0.40335.2477-0.89897.4563-0.05430.0795-0.05910.2988-0.0148-0.263-0.05680.79820.0610.32350.0018-0.05570.66310.12870.6464-4.0046-4.3036-42.9806
146.69992.60221.92427.4412-2.58615.43340.22550.3067-1.0897-0.7583-0.36820.49280.92750.4770.11320.5150.06470.06950.8184-0.01670.733-8.2886-13.5418-52.0089
154.53180.1101-0.18455.4494-0.38444.12550.3949-0.61580.15481.3419-0.26450.44340.3697-0.8464-0.21851.5107-0.4460.35451.3814-0.04980.7614-38.9799-1.7862-7.9883
161.76590.75081.84231.5903-0.05331.79590.6535-0.891-0.05551.1574-0.52090.80470.4303-1.3721-0.15411.5259-0.56070.50242.0462-0.12911.1518-47.6436-9.8252-11.3994
173.8237-1.63814.98476.587-1.70598.0344-0.119-0.21570.64040.2119-0.44030.8668-0.7416-1.35090.67611.0109-0.02490.32952.0523-0.15341.4713-58.4641-5.9171-25.2465
182.58360.6761-1.33031.92182.36736.30690.10450.0052-0.47790.3388-0.40170.0720.408-0.3770.3110.44040.02320.00830.67020.13950.7181-29.153-14.868-48.2375
198.01313.98352.80445.96351.31725.21990.27760.0496-0.3630.4553-0.3667-0.33470.0966-0.23740.11090.7463-0.09290.11090.69940.08840.6375-32.579-5.0636-28.9361
203.93870.238-0.79592.35920.50430.22760.5358-0.6387-0.41611.5794-0.5737-0.92770.7026-0.1358-0.03281.7689-0.1873-0.28691.18390.30691.0167-11.5925-6.2729-12.5123
217.0154-4.4942-0.79633.47073.19879.84150.3887-0.3713-1.15641.5646-1.04050.0021.046-1.10030.57171.3184-0.14780.19240.99220.12181.1196-10.9227-12.7494-23.9456
224.34430.648-2.72877.12567.2322.02250.8919-1.725-0.93132.2324-0.8852-0.82260.05850.9437-0.44312.3002-0.6499-0.49991.77520.15430.9333-8.03714.3441-1.7657
238.41461.4848-4.06316.8678-4.22067.12030.0243-0.88750.93281.12530.4003-0.715-0.77841.2678-0.45650.98490.0236-0.13110.9182-0.24741.1762-14.745574.0502-37.9446
243.55064.4093-1.38029.15963.21717.9246-0.3381-0.8088-0.69952.49180.6265-0.48730.68650.4168-0.29281.4130.4709-0.15881.61520.08121.05291.281852.0605-45.9961
253.6119-5.4302-2.82898.30591.74935.2693-0.2913-0.61151.26252.39480.2164-0.9026-0.12021.5481-0.05810.95950.0499-0.02751.0944-0.17611.1346-13.182671.0015-41.4946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 421 )
3X-RAY DIFFRACTION3chain 'A' and (resid 422 through 553 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 174 )
5X-RAY DIFFRACTION5chain 'B' and (resid 175 through 325 )
6X-RAY DIFFRACTION6chain 'B' and (resid 326 through 428 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 59 )
8X-RAY DIFFRACTION8chain 'C' and (resid 60 through 114 )
9X-RAY DIFFRACTION9chain 'C' and (resid 115 through 269 )
10X-RAY DIFFRACTION10chain 'C' and (resid 270 through 325 )
11X-RAY DIFFRACTION11chain 'C' and (resid 326 through 421 )
12X-RAY DIFFRACTION12chain 'C' and (resid 422 through 473 )
13X-RAY DIFFRACTION13chain 'C' and (resid 474 through 527 )
14X-RAY DIFFRACTION14chain 'C' and (resid 528 through 553 )
15X-RAY DIFFRACTION15chain 'D' and (resid 6 through 83 )
16X-RAY DIFFRACTION16chain 'D' and (resid 84 through 174 )
17X-RAY DIFFRACTION17chain 'D' and (resid 175 through 238 )
18X-RAY DIFFRACTION18chain 'D' and (resid 239 through 363 )
19X-RAY DIFFRACTION19chain 'D' and (resid 364 through 427 )
20X-RAY DIFFRACTION20chain 'F' and (resid 0 through 16 )
21X-RAY DIFFRACTION21chain 'F' and (resid 17 through 26 )
22X-RAY DIFFRACTION22chain 'F' and (resid 27 through 33 )
23X-RAY DIFFRACTION23chain 'E' and (resid -1 through 10 )
24X-RAY DIFFRACTION24chain 'E' and (resid 11 through 20 )
25X-RAY DIFFRACTION25chain 'E' and (resid 21 through 33 )

+
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://pdbjlvh1.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