[English] 日本語
Yorodumi
- PDB-2be2: Crystal structure of HIV-1 reverse transcriptase (RT) in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2be2
TitleCrystal structure of HIV-1 reverse transcriptase (RT) in complex with R221239
Components(REVERSE TRANSCRIPTASE ...) x 2
KeywordsTRANSFERASE / AIDS / HIV / DRUG DESIGN / REVERSE TRANSCRIPTASE / RT / PROTEIN-INHIBITOR COMPLEX / DRUG RESISTANCE
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / 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 / viral translational frameshifting / 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. / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / 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
sucrose / : / Chem-R22 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsHimmel, D.M. / Das, K. / Clark Jr., A.D. / Hughes, S.H. / Benjahad, A. / Oumouch, S. / Guillemont, J. / Coupa, S. / Poncelet, A. / Csoka, I. ...Himmel, D.M. / Das, K. / Clark Jr., A.D. / Hughes, S.H. / Benjahad, A. / Oumouch, S. / Guillemont, J. / Coupa, S. / Poncelet, A. / Csoka, I. / Meyer, C. / Andries, K. / Nguyen, C.H. / Grierson, D.S. / Arnold, E.
Citation
Journal: J.Med.Chem. / Year: 2005
Title: Crystal Structures for HIV-1 Reverse Transcriptase in Complexes with Three Pyridinone Derivatives: A New Class of Non-Nucleoside Inhibitors Effective against a Broad Range of Drug-Resistant Strains.
Authors: Himmel, D.M. / Das, K. / Clark Jr., A.D. / Hughes, S.H. / Benjahad, A. / Oumouch, S. / Guillemont, J. / Coupa, S. / Poncelet, A. / Csoka, I. / Meyer, C. / Andries, K. / Nguyen, C.H. / Grierson, D.S. / Arnold, E.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: 3-iodo-4-phenoxypyridinones (IOPY's), a New Family of Highly Potent Non-nucleoside Inhibitors of HIV-1 Reverse Transcriptase
Authors: Benjahad, A. / Guillemont, J. / Andries, K. / Nguyen, C.H. / Grierson, D.S.
#2: Journal: J.Med.Chem. / Year: 2005
Title: 4-Benzyl and 4-Benzoyl-3-Dimethylaminopyridin-2(1H)-Ones: In Vitro Evaluation of New C-3-Amino-Substituted and C-5,6-Alkyl-Substituted Analogues Against Clinically Important HIV Mutant Strains
Authors: Benjahad, A. / Croisy, M. / Monneret, C. / Bisagni, E. / Mabire, D. / Coupa, S. / Poncelet, A. / Csoka, I. / Guillemont, J. / Meyer, C. / Andries, K. / Pauwels, R. / De Bethune, M.P. / ...Authors: Benjahad, A. / Croisy, M. / Monneret, C. / Bisagni, E. / Mabire, D. / Coupa, S. / Poncelet, A. / Csoka, I. / Guillemont, J. / Meyer, C. / Andries, K. / Pauwels, R. / De Bethune, M.P. / Himmel, D.M. / Das, K. / Arnold, E. / Nguyen, C.H. / Grierson, D.S.
#3: Journal: J.Med.Chem. / Year: 2004
Title: Roles of Conformational and Positional Adaptability in Structure-Based Design of Tmc125-R165335 (Etravirine) and Related Non-Nucleoside Reverse Transcriptase Inhibitors that are Highly Potent ...Title: Roles of Conformational and Positional Adaptability in Structure-Based Design of Tmc125-R165335 (Etravirine) and Related Non-Nucleoside Reverse Transcriptase Inhibitors that are Highly Potent and Effective Against Wild-Type and Drug-Resistant HIV-1 Variants
Authors: Das, K. / Clark Jr., A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M.H. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. ...Authors: Das, K. / Clark Jr., A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M.H. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, H. / Lichtenstein, M.A. / Andries, K. / Pauwels, R. / De Bethune, M.-P. / Boyer, P.L. / Clark, P. / Hughes, S.H. / Janssen, P.A.J. / Arnold, E.
#4: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal Structures of 8-Cl and 9-Cl TIBO Complexed with Wild-Type HIV-1 RT and 8-Cl TIBO Complexed with the Tyr181Cys HIV-1 RT Drug-Resistant Mutant.
Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Jr., A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Jr., R.H. / Kroeger Smith, M.B. / ...Authors: Das, K. / Ding, J. / Hsiou, Y. / Clark Jr., A.D. / Moereels, H. / Koymans, L. / Andries, K. / Pauwels, R. / Janssen, P.A. / Boyer, P.L. / Clark, P. / Smith Jr., R.H. / Kroeger Smith, M.B. / Michejda, C.J. / Hughes, S.H. / Arnold, E.
#5: Journal: J.Mol.Biol. / Year: 1998
Title: Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA Template-Primer and an Antibody Fab Fragment at 2.8 A Resolution.
Authors: Ding, J. / Das, K. / Hsiou, Y. / Sarafianos, S.G. / Clark Jr., A.D. / Jacobo-Molina, A. / Tantillo, C. / Hughes, S.H. / Arnold, E.
#6: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors.
Authors: Ding, J. / Das, K. / Moereels, H. / Koymans, L. / Andries, K. / Janssen, P.A.J. / Hughes, S.H. / Arnold, E.
History
DepositionOct 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.type / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: REVERSE TRANSCRIPTASE P66 SUBUNIT
B: REVERSE TRANSCRIPTASE P51 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1888
Polymers114,7832
Non-polymers1,4056
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-23 kcal/mol
Surface area48040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.853, 68.798, 104.430
Angle α, β, γ (deg.)90.00, 107.22, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
REVERSE TRANSCRIPTASE ... , 2 types, 2 molecules AB

#1: Protein REVERSE TRANSCRIPTASE P66 SUBUNIT / HIV-1 RT


Mass: 64500.965 Da / Num. of mol.: 1 / Fragment: residues 599-1158 / Mutation: C447S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: isolate BH10 / Description: HIV-1 CLONE 12 / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein REVERSE TRANSCRIPTASE P51 SUBUNIT / HIV-1 RT


Mass: 50281.762 Da / Num. of mol.: 1 / Fragment: residues 599-1028 / Mutation: C447S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: isolate BH10 / Description: HIV-1 CLONE 12 / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase

-
Sugars , 1 types, 2 molecules

#3: 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 , 4 types, 158 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-R22 / 4-(3,5-DIMETHYLPHENOXY)-5-(FURAN-2-YLMETHYLSULFANYLMETHYL)-3-IODO-6-METHYLPYRIDIN-2(1H)-ONE


Mass: 481.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20INO3S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.3 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 277 K / pH: 6.8
Details: 50mM bisTris Propane, 100mM Ammonium Sulfate, 12% PEG 8000, 10% Glycerol, pH 6.8, temperature 277K, VAPOR DIFFUSION, HANGING DROP, pH 6.80

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.95043
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95043 Å / Relative weight: 1
ReflectionResolution: 2.4→23 Å / Num. obs: 54672 / % possible obs: 91.7 % / Observed criterion σ(I): -1 / Redundancy: 2.8 % / Biso Wilson estimate: 55.7 Å2 / Rsym value: 0.056 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.9 % / Rsym value: 0.517 / % possible all: 54.9

-
Phasing

Phasing dm shellResolution: 2.43→23 Å / Delta phi final: 0.111 / FOM : 0.112 / Reflection: 50774

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S6P

1s6p


Resolution: 2.43→22.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 426382.844 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2483 4.9 %RANDOM
Rwork0.235 ---
obs0.235 50774 88.4 %-
all-57447 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.36 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 63.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å20 Å25.48 Å2
2--1.3 Å20 Å2
3----5.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.43→22.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8023 0 85 154 8262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.11
X-RAY DIFFRACTIONc_mcangle_it7.72
X-RAY DIFFRACTIONc_scbond_it6.79
X-RAY DIFFRACTIONc_scangle_it9.2
LS refinement shellResolution: 2.43→2.58 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 348 5 %
Rwork0.408 6580 -
obs--73.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.TOPPROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.TOPION.PARAM
X-RAY DIFFRACTION3WATER.TOPWATER.PARAM
X-RAY DIFFRACTION4221.TOP221.PAR
X-RAY DIFFRACTION5SUC.TOPSUC.PAR

+
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