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- PDB-6ujz: HIV-1 wild-type reverse transcriptase-DNA complex with (+)-FTC-TP -

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Basic information

Entry
Database: PDB / ID: 6ujz
TitleHIV-1 wild-type reverse transcriptase-DNA complex with (+)-FTC-TP
Components
  • p51 Reverse transcriptase/RNaseH
  • p66 Reverse transcriptase/RNaseH
  • primer DNA
  • template DNA
KeywordsViral Protein/DNA / HIV-1 reverse transcriptase NRTI polymerase DNA complex / VIRAL PROTEIN / Viral Protein-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 / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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-N8G / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5564255195 Å
AuthorsLansdon, E.B.
CitationJournal: Commun Biol / Year: 2019
Title: Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance.
Authors: Hung, M. / Tokarsky, E.J. / Lagpacan, L. / Zhang, L. / Suo, Z. / Lansdon, E.B.
History
DepositionOct 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: p66 Reverse transcriptase/RNaseH
B: p51 Reverse transcriptase/RNaseH
P: primer DNA
T: template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7828
Polymers132,0794
Non-polymers7044
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-75 kcal/mol
Surface area47050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.277, 168.829, 102.548
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein p66 Reverse transcriptase/RNaseH / Exoribonuclease H / p66 RT


Mass: 65887.328 Da / Num. of mol.: 1 / Mutation: Q845C,C867S
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 (E. coli)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 Reverse transcriptase/RNaseH / Exoribonuclease H / p51 RT


Mass: 51382.984 Da / Num. of mol.: 1 / Mutation: C867S
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 (E. coli)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H

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DNA chain , 2 types, 2 molecules PT

#3: DNA chain primer DNA


Mass: 6360.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: DNA chain template DNA


Mass: 8448.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

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Non-polymers , 4 types, 51 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-N8G / [[(2~{S},5~{R})-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 487.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13FN3O12P3S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2% PEG 4000, 100mM MES pH 6.0, 10mM magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 47323 / % possible obs: 99.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 60.077967744 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.2
Reflection shellResolution: 2.55→2.71 Å / Rmerge(I) obs: 0.886 / Num. unique obs: 4516

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KK1

3kk1


Resolution: 2.5564255195→47.3428641098 Å / SU ML: 0.36764792705 / Cross valid method: THROUGHOUT / σ(F): 1.33937601348 / Phase error: 26.3274335792
RfactorNum. reflection% reflection
Rfree0.236264879966 3803 4.24110627858 %
Rwork0.184750582552 85867 -
obs0.186949198587 47318 98.1813403992 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.4463326859 Å2
Refinement stepCycle: LAST / Resolution: 2.5564255195→47.3428641098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7795 862 39 47 8743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009758573135689012
X-RAY DIFFRACTIONf_angle_d1.167003805412418
X-RAY DIFFRACTIONf_chiral_restr0.04495251208581348
X-RAY DIFFRACTIONf_plane_restr0.005982657182581410
X-RAY DIFFRACTIONf_dihedral_angle_d19.04974598533459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5564255195-2.58880.3154354439221330.2948249981552761X-RAY DIFFRACTION84.8182883939
2.5888-2.62280.3204528326671280.2738538134053141X-RAY DIFFRACTION97.147102526
2.6228-2.65880.3105089096371360.2829377962253146X-RAY DIFFRACTION97.0431697221
2.6588-2.69680.3284868015641390.2649204196413159X-RAY DIFFRACTION97.4298375185
2.6968-2.7370.336559158511350.2785997890033107X-RAY DIFFRACTION97.0658682635
2.737-2.77980.3147023367841400.2632847751913173X-RAY DIFFRACTION97.1839249047
2.7798-2.82530.3381310146151430.2742827907213190X-RAY DIFFRACTION97.6560210958
2.8253-2.8740.290544136711290.2602482337893089X-RAY DIFFRACTION97.2205438066
2.874-2.92630.3106347918171460.2658440674433201X-RAY DIFFRACTION98.0949589683
2.9263-2.98260.3499843507421440.2611631451953182X-RAY DIFFRACTION98.4023668639
2.9826-3.04340.3673134107281420.2770003778713195X-RAY DIFFRACTION98.6694263749
3.0434-3.10960.3141456056551440.263028093863216X-RAY DIFFRACTION99.2614475628
3.1096-3.18190.3504307048881390.2423389065793225X-RAY DIFFRACTION99.556081681
3.1819-3.26150.2903318923941340.2301762167793197X-RAY DIFFRACTION99.0484686292
3.2615-3.34960.2464143187461510.2173688036863225X-RAY DIFFRACTION98.6845951476
3.3496-3.44820.2928071914081320.1965603948213146X-RAY DIFFRACTION97.9970104634
3.4482-3.55940.2354270858571430.205980135093219X-RAY DIFFRACTION99.438036084
3.5594-3.68660.2507812000111390.1893423183623246X-RAY DIFFRACTION99.6467471298
3.6866-3.83420.2305880369831450.180146418353255X-RAY DIFFRACTION99.7359929598
3.8342-4.00860.2065691738641470.1618338065073212X-RAY DIFFRACTION99.7327790974
4.0086-4.21980.1941379819381420.1572752704993218X-RAY DIFFRACTION99.5260663507
4.2198-4.4840.2289196317271460.1449358762773246X-RAY DIFFRACTION99.3847055377
4.484-4.82990.2034457147511460.1375463576163191X-RAY DIFFRACTION99.4042299672
4.8299-5.31530.1970245548251390.1378881098063231X-RAY DIFFRACTION99.7336490086
5.3153-6.08310.1808861599491520.1543799994883227X-RAY DIFFRACTION99.616745283
6.0831-7.65880.1902631552661410.1501102081423235X-RAY DIFFRACTION99.7930830624
7.6588-47.34286410.1708181106421480.1444570962913234X-RAY DIFFRACTION99.7345915659

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