[English] 日本語
Yorodumi
- PDB-6p1x: Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p1x
TitleStructure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and L-ddCTP
Components
  • DNA Primer 20-mer
  • DNA template 27-mer
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE/DNA / Reverse Transcriptase / ternary complex / L-ddCTP / chain terminator / stereochemistry / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / zinc ion binding / identical protein 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / 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
Chem-NQ4 / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.553 Å
AuthorsBertoletti, N. / Anderson, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049551 United States
CitationJournal: Protein Sci. / Year: 2019
Title: Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active ...Title: Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine.
Authors: Bertoletti, N. / Chan, A.H. / Schinazi, R.F. / Yin, Y.W. / Anderson, K.S.
History
DepositionMay 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 28, 2019Group: Data collection / 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 1.4Oct 11, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H
B: p51 RT
P: DNA Primer 20-mer
T: DNA template 27-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,92710
Polymers132,1394
Non-polymers7886
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-101 kcal/mol
Surface area47020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.213, 171.502, 107.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Reverse transcriptase/ribonuclease H


Mass: 64521.895 Da / Num. of mol.: 1 / Mutation: C280S, Q258C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 RT


Mass: 52748.418 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04585

-
DNA chain , 2 types, 2 molecules PT

#3: DNA chain DNA Primer 20-mer


Mass: 6460.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA template 27-mer


Mass: 8408.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 39 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NQ4 / [[(2~{R},5~{S})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 451.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O12P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 6-10% (w/v) PEG 8000, 15 mM magnesium sulfate, and 50 mM MES adjusted at pH 6.0
PH range: 5.5-6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 97351 / % possible obs: 99.4 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rsym value: 0.115 / Net I/σ(I): 12.13
Reflection shellResolution: 2.55→2.71 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 15225 / CC1/2: 0.837 / Rsym value: 0.715 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OR7

6or7


Resolution: 2.553→29.749 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.69
RfactorNum. reflection% reflection
Rfree0.2304 4853 4.99 %
Rwork0.1879 --
obs0.19 97318 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.553→29.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7673 868 44 33 8618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078893
X-RAY DIFFRACTIONf_angle_d0.95112297
X-RAY DIFFRACTIONf_dihedral_angle_d17.7935155
X-RAY DIFFRACTIONf_chiral_restr0.0521355
X-RAY DIFFRACTIONf_plane_restr0.0061412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5533-2.58230.37631360.34392590X-RAY DIFFRACTION85
2.5823-2.61270.29961600.27543123X-RAY DIFFRACTION100
2.6127-2.64450.3321550.27563115X-RAY DIFFRACTION100
2.6445-2.6780.3451600.26833123X-RAY DIFFRACTION100
2.678-2.71320.34011620.263016X-RAY DIFFRACTION100
2.7132-2.75030.25311650.27843147X-RAY DIFFRACTION100
2.7503-2.78960.33231620.27393071X-RAY DIFFRACTION100
2.7896-2.83120.30811670.27423146X-RAY DIFFRACTION100
2.8312-2.87540.32561570.26243054X-RAY DIFFRACTION100
2.8754-2.92250.33551670.25083119X-RAY DIFFRACTION100
2.9225-2.97280.3031610.26013051X-RAY DIFFRACTION100
2.9728-3.02680.31821610.24713088X-RAY DIFFRACTION100
3.0268-3.0850.33831650.24913135X-RAY DIFFRACTION100
3.085-3.14790.31651640.24263091X-RAY DIFFRACTION100
3.1479-3.21630.2591580.22273092X-RAY DIFFRACTION100
3.2163-3.2910.20851630.20973106X-RAY DIFFRACTION100
3.291-3.37320.23571640.20753135X-RAY DIFFRACTION100
3.3732-3.46430.27781600.21283080X-RAY DIFFRACTION100
3.4643-3.5660.25611660.21223112X-RAY DIFFRACTION100
3.566-3.68090.23221640.19393086X-RAY DIFFRACTION100
3.6809-3.81230.25051620.18443086X-RAY DIFFRACTION100
3.8123-3.96460.2091670.16153098X-RAY DIFFRACTION100
3.9646-4.14450.16361630.15523134X-RAY DIFFRACTION100
4.1445-4.36240.21351640.14513069X-RAY DIFFRACTION100
4.3624-4.63480.1881620.13723135X-RAY DIFFRACTION100
4.6348-4.99110.17081650.13663067X-RAY DIFFRACTION100
4.9911-5.49050.19881620.14213104X-RAY DIFFRACTION100
5.4905-6.27850.1971660.16933109X-RAY DIFFRACTION100
6.2785-7.88580.19611620.15593088X-RAY DIFFRACTION100
7.8858-29.7510.15481630.14153095X-RAY DIFFRACTION99
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)
12.7231-0.2123-0.13022.17460.19892.0682-0.02850.4190.5171-0.3771-0.0923-0.2818-0.49340.22450.12740.5448-0.090.0990.44570.06240.4983-31.32138.9879-28.7363
21.9435-1.45310.62126.3998-0.14776.0083-0.10380.7386-0.0566-0.9465-0.09770.0346-0.1382-0.02930.13280.56070.01820.03480.44910.11930.3818-39.10762.0929-34.6998
32.5154-0.2567-0.14741.96140.35981.1685-0.15070.19570.3035-0.0970.101-0.2803-0.19660.09310.0680.3038-0.0015-0.04580.27870.0010.2676-39.3444-6.3061-19.9766
46.54920.70290.4413.20753.76024.5315-0.53271.28390.751-0.3864-0.3305-0.1389-1.64520.14760.86510.7503-0.16830.08130.65390.1750.7473-29.093214.2629-35.06
50.87170.15450.32182.40310.54250.2828-0.00880.14450.0485-0.09680.04070.0586-0.1885-0.0029-0.01880.34630.0211-0.00140.31870.02470.2693-49.4016-9.6188-22.9413
60.2831-0.00740.40032.03890.45530.8401-0.05320.2711-0.0964-0.1603-0.07960.111-0.0573-0.06660.13540.3071-0.0005-0.04180.4224-0.01990.317-47.6335-32.5447-33.0257
71.5432-0.8503-1.00381.66130.67941.4498-0.0664-0.1079-0.2121-0.0038-0.04660.32150.0686-0.03520.10860.2968-0.0516-0.05070.3214-0.0440.3812-38.0443-54.0067-29.88
82.0424-0.0514-0.26392.2949-0.08331.9137-0.01090.2101-0.0529-0.40770.0247-0.08090.08110.003-0.00950.3501-0.01170.00840.2869-0.06240.3404-24.5971-59.3218-44.8892
92.16570.7480.77116.5898-4.7484.2354-0.32170.62540.83250.4336-0.4834-1.3253-0.43661.18930.8290.4583-0.0789-0.10270.79080.08870.9515-10.3547-15.6055-7.5104
104.0865-1.05510.45033.08510.06962.0727-0.0676-0.199-0.31520.36250.0322-0.07570.0336-0.04150.04620.3297-0.0013-0.03120.28020.00980.2668-30.8201-22.5093-6.8446
115.3942-1.0544-1.23765.96754.05652.83711.0232-0.01890.0790.4767-0.2578-0.8220.65571.2677-0.66430.6187-0.0719-0.00790.8819-0.03351.0928-11.0341-22.3897-10.6097
121.2024-1.16660.6321.1792-0.72680.7750.0029-0.33030.23140.1205-0.0521-0.1998-0.06060.09250.03520.4263-0.0222-0.0850.4414-0.03750.4323-23.0856-23.7476-2.6836
131.99570.9281-0.58224.3193-0.94692.05170.1367-0.47810.20860.7244-0.33380.0614-0.0679-0.06850.22050.5043-0.0879-0.07510.52280.010.3873-13.5904-36.201210.3776
143.7363-1.3682-0.66623.4994.81377.87510.1074-0.31140.05340.48090.07980.93110.5394-0.1806-0.25630.8832-0.19980.16860.6834-0.02660.727-19.183-41.59418.9455
152.39642.53761.93163.8971.72471.96340.3956-0.1686-0.21860.2612-0.1777-0.5240.17420.227-0.23490.3507-0.0185-0.00680.4632-0.02710.5105-10.8194-66.0075-23.9669
164.23270.0230.54253.4390.5362.5445-0.03960.163-0.0812-0.06370.04610.0803-0.0089-0.09370.00130.3565-0.0136-0.00660.36580.01910.376-22.9473-45.4068-14.5853
173.1133.65912.03494.54373.16616.0327-0.39880.71230.429-0.32540.617-0.0789-0.07660.6285-0.22310.50090.01260.00020.51890.15320.9493-8.8068-41.6247-43.2494
184.99550.4249-0.35924.6197-1.26321.4704-0.32190.1590.57940.72040.15060.32510.0553-0.25250.14450.6360.03490.02340.5768-0.0360.6794-23.3028-39.2647-37.1001
192.01511.33010.9419.64913.44134.00330.22380.5581.09490.9368-0.840.3574-1.20480.44930.54530.91030.0067-0.06120.5202-0.00670.846-26.6822-23.3279-34.6161
204.8697-1.0090.20156.34872.05836.95870.72060.4610.1047-0.7927-0.0133-0.42050.0198-0.168-0.58960.530.1181-0.00120.5253-0.02470.3884-43.1299-15.0392-35.6549
217.66232.0437-3.04593.0736-4.13516.11280.47710.6651-0.0994-1.4967-0.59920.246-0.1990.46390.10550.77060.04070.09290.5599-0.02910.4884-34.926-5.0392-34.3993
220.3283-0.16040.20024.10342.29763.3225-0.08840.4455-0.1339-0.7901-0.4172-0.258-0.2151-0.35720.47030.5050.02030.10840.4676-0.02390.3904-38.1512-19.9922-29.8038
234.8132-3.9413-0.96056.8693-0.96222.60950.06710.88390.48670.54-0.5074-1.3105-0.0870.22490.4010.58410.0499-0.0860.6566-0.06330.7125-21.4799-33.5123-37.7778
249.2273-6.3977-1.98867.40624.57083.9385-1.04491.6019-0.11440.80520.81271.13570.7924-0.39040.26580.4607-0.04190.04870.75610.04210.7187-5.7733-50.9849-43.6587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:62 )A1 - 62
2X-RAY DIFFRACTION2( CHAIN A AND RESID 63:79 )A63 - 79
3X-RAY DIFFRACTION3( CHAIN A AND RESID 80:125 )A80 - 125
4X-RAY DIFFRACTION4( CHAIN A AND RESID 126:142 )A126 - 142
5X-RAY DIFFRACTION5( CHAIN A AND RESID 143:277 )A143 - 277
6X-RAY DIFFRACTION6( CHAIN A AND RESID 278:387 )A278 - 387
7X-RAY DIFFRACTION7( CHAIN A AND RESID 388:448 )A388 - 448
8X-RAY DIFFRACTION8( CHAIN A AND RESID 449:555 )A449 - 555
9X-RAY DIFFRACTION9( CHAIN B AND RESID 6:16 )B6 - 16
10X-RAY DIFFRACTION10( CHAIN B AND RESID 17:82 )B17 - 82
11X-RAY DIFFRACTION11( CHAIN B AND RESID 83:87 )B83 - 87
12X-RAY DIFFRACTION12( CHAIN B AND RESID 96:153 )B96 - 153
13X-RAY DIFFRACTION13( CHAIN B AND RESID 154:204 )B154 - 204
14X-RAY DIFFRACTION14( CHAIN B AND RESID 205:240 )B205 - 240
15X-RAY DIFFRACTION15( CHAIN B AND RESID 241:324 )B241 - 324
16X-RAY DIFFRACTION16( CHAIN B AND RESID 325:429 )B325 - 429
17X-RAY DIFFRACTION17( CHAIN P AND RESID 805:808 )P805 - 808
18X-RAY DIFFRACTION18( CHAIN P AND RESID 809:812 )P809 - 812
19X-RAY DIFFRACTION19( CHAIN P AND RESID 813:816 )P813 - 816
20X-RAY DIFFRACTION20( CHAIN P AND RESID 818:821 )P818 - 821
21X-RAY DIFFRACTION21( CHAIN T AND RESID 704:707 )T704 - 707
22X-RAY DIFFRACTION22( CHAIN T AND RESID 708:711 )T708 - 711
23X-RAY DIFFRACTION23( CHAIN T AND RESID 712:721 )T712 - 721
24X-RAY DIFFRACTION24( CHAIN T AND RESID 722:725 )T722 - 725

+
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