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- PDB-6uis: HIV-1 M184V reverse transcriptase-DNA complex with dCTP -

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Basic information

Entry
Database: PDB / ID: 6uis
TitleHIV-1 M184V reverse transcriptase-DNA complex with dCTP
Components
  • Primer DNA
  • Template DNA
  • p51 Reverse transcriptase/RNaseH
  • p66 Reverse transcriptase/RNaseH
KeywordsVIRAL PROTEIN / HIV-1 reverse transcriptase NRTI polymerase 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / 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: 2.74833813248 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 1, 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)132,7239
Polymers132,0154
Non-polymers7085
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint-89 kcal/mol
Surface area46400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.554, 169.109, 103.3
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
Components on special symmetry positions
IDModelComponents
11A-786-

HOH

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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: 65855.258 Da / Num. of mol.: 1 / Mutation: M771V,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: 51350.922 Da / Num. of mol.: 1 / Mutation: M771V,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, 150 molecules

#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
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: 0.99999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.748→50 Å / Num. obs: 37257 / % possible obs: 99.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 35.2056855708 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.2
Reflection shellResolution: 2.748→2.8 Å / Rmerge(I) obs: 0.483 / Num. unique obs: 2922

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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: 2.74833813248→47.4556800366 Å / SU ML: 0.351251158725 / Cross valid method: THROUGHOUT / σ(F): 1.33538889328 / Phase error: 26.1493650712
RfactorNum. reflection% reflection
Rfree0.258600867878 2002 5.37810611148 %
Rwork0.18756999817 --
obs0.191309865102 37225 50.3891708968 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.6119077064 Å2
Refinement stepCycle: LAST / Resolution: 2.74833813248→47.4556800366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7728 820 40 145 8733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009772731844838886
X-RAY DIFFRACTIONf_angle_d1.1621346949912238
X-RAY DIFFRACTIONf_chiral_restr0.04801036916371338
X-RAY DIFFRACTIONf_plane_restr0.005774072707921394
X-RAY DIFFRACTIONf_dihedral_angle_d19.00149825423410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.81710.3386818128471120.2360259751581871X-RAY DIFFRACTION37.2045028143
2.8171-2.89320.3443699234521290.2328412204032305X-RAY DIFFRACTION46.4326592903
2.8932-2.97830.3287353307951420.2378503921262476X-RAY DIFFRACTION49.5364238411
2.9783-3.07450.3400998025541430.2323638563242535X-RAY DIFFRACTION51.0192417603
3.0745-3.18430.2982943984651480.2196391018822581X-RAY DIFFRACTION51.6562559152
3.1843-3.31180.2616390456371470.2061183407522587X-RAY DIFFRACTION51.7313150426
3.3118-3.46250.2710654182931450.1975406045032576X-RAY DIFFRACTION51.5927189989
3.4625-3.64490.2660789229911440.1955076596342589X-RAY DIFFRACTION51.8104265403
3.6449-3.87320.2619165547671490.1851404761112579X-RAY DIFFRACTION51.8138651472
3.8732-4.17210.2254478044781480.1630146623132593X-RAY DIFFRACTION51.9128787879
4.1721-4.59170.2030780328271450.1526469106612604X-RAY DIFFRACTION52.0939927989
4.5917-5.25530.2156883628071460.1564976594572594X-RAY DIFFRACTION52.1011599163
5.2553-6.61830.2339995817461500.1868376886772640X-RAY DIFFRACTION52.6117292099
6.6183-47.450.2532867993561540.1721093904422693X-RAY DIFFRACTION54.0946228387

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